RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor
RpoD [Candidatus Liberibacter asiaticus str. psy62]
(682 letters)
>gnl|CDD|180186 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 931 bits (2410), Expect = 0.0
Identities = 345/667 (51%), Positives = 435/667 (65%), Gaps = 53/667 (7%)
Query: 19 DDSLVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVV 78
DS + D KK+IK ++RGY+T ELN LP D V SEQ+ED +AML++MGI VV
Sbjct: 1 GDSPMLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVV 60
Query: 79 ----DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELL 134
D DDL E D+ + ++ L + R TDDPVRMYLREMG++ELL
Sbjct: 61 EEAPDADDLLLAENEADAQTDEDAEEEAAAALSSVESEIGR-TDDPVRMYLREMGTVELL 119
Query: 135 SREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDLEACIGPE 194
+REGEI IAKRIEAG +M+A+LCESPLT A++ W D L +G LRE+ID P
Sbjct: 120 TREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRELIDGFV--DPN 177
Query: 195 SKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAEND 254
++ H + + + D
Sbjct: 178 AEEDPAHVGS----------------------------------------ELEELDDDED 197
Query: 255 ERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKC 314
E +E+ED++ +L+A E +L KV+ +A+ Y++LR Q+ V G+ K
Sbjct: 198 E---EEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVEGR--LAQHKKY 252
Query: 315 KVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGELLRLAQSYGIKRDVFLERH 374
L+EKL + + SL L +ID LVEQL DI+KR+ E ELLRL + + R FL+
Sbjct: 253 AKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLRLVERLKMPRKDFLKLF 312
Query: 375 QGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEFRHIVSMV 434
QG ELD W+ W F+ D I K++ E+++I ETG++I E + I +
Sbjct: 313 QGNELDITWLEKE-IASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQI 371
Query: 435 RKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGY 494
KGE +A AKKEMVEANLRLVIS+AKKYTNRGLQFLDLIQEGNIGLMKA +KF++ GY
Sbjct: 372 SKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 431
Query: 495 KFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAK 554
KFSTYA WW++QAITRSIADQ+ TIRIPVHM + I+K+ R +R+M +I REPTPEE+A+
Sbjct: 432 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAE 491
Query: 555 KLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTT 614
+L MP + VRKVLKI KEPISLETPIGD++ SHLGDFIEDKNA P+D+AIQ +LRE TT
Sbjct: 492 RLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATT 551
Query: 615 RVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSK 674
VLASLTPRE +VLRMRFGI MNTDHTLEEVGKQF VTRERIRQIEAKA+RKL+HPSRS+
Sbjct: 552 DVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSR 611
Query: 675 KLRSFLD 681
KLRSFLD
Sbjct: 612 KLRSFLD 618
>gnl|CDD|162836 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal
domain. This model represents the well-conserved
C-terminal region of the major, essential sigma factor
of most bacteria. Members of this clade show
considerable variability in domain architecture and
molecular weight, as well as in nomenclature: RpoD in E.
coli and other Proteobacteria, SigA in Bacillus subtilis
and many other Gram-positive bacteria, HrdB in
Streptomyces, MysA in Mycobacterium smegmatis, etc.
Length = 238
Score = 388 bits (998), Expect = e-108
Identities = 157/238 (65%), Positives = 197/238 (82%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
AKK++VE+NLRLV+S+AKKYTNRGL FLDLIQEGNIGLMKA EKFD+ GYKFSTYA WW
Sbjct: 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWW 60
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
++QAITR+IADQ+ TIRIPVHM + I+K+++ R+++ ++ REPT EE+A+++ MP E V
Sbjct: 61 IRQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKV 120
Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
R++ KI +EPISLETPIG+E+ S LGDFIED + SP D A + LRE VL +LT R
Sbjct: 121 REIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTER 180
Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
E +VLRMR+G+ HTLEEVGK+F VTRERIRQIE+KA+RKL+HPSRSKKL+SFLD
Sbjct: 181 ERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD 238
>gnl|CDD|181701 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated.
Length = 367
Score = 372 bits (956), Expect = e-103
Identities = 153/238 (64%), Positives = 193/238 (81%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
AK+ + EANLRLV+S+AK+Y RG+ FLDLIQEGN+GLMKA EKFD+ G+KFSTYA WW
Sbjct: 130 AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 189
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
++QAITR+IADQ+ TIRIPVHM + I+K++R R++ ++ REPTPEEIA+++ MP E V
Sbjct: 190 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKV 249
Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
R++LKI +EP+SLETPIG+ED SHLGDFIED++A SP D A L+E VL +LT R
Sbjct: 250 REILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDR 309
Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
EE VLR+RFG+ TLEEVGK F VTRERIRQIEAKA+RKL+HPSRSK+L+ FL+
Sbjct: 310 EENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
Score = 82.0 bits (203), Expect = 5e-16
Identities = 43/123 (34%), Positives = 66/123 (53%), Gaps = 17/123 (13%)
Query: 32 KKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDD-----LEDE 86
K++I+ ++RG +T +E+ L P E+ S+Q++D L + GI++VD + E
Sbjct: 16 KELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVE 75
Query: 87 EGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRI 146
E E+ LD S +DPVRMYL+E+G + LL+ E EI +AKRI
Sbjct: 76 EEEEEELDNDLSVPPGV------------KINDPVRMYLKEIGRVPLLTAEEEIELAKRI 123
Query: 147 EAG 149
E G
Sbjct: 124 EEG 126
>gnl|CDD|180310 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 359 bits (923), Expect = 2e-99
Identities = 138/238 (57%), Positives = 180/238 (75%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
AK ++EANLRLV+S+AK+YTNRGL FLDLIQEGN+GL+KA EKFD+ GYKFSTYA WW
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 331
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
++QAITR++ADQ+ TIRIPVHM + I+K+ R R + ++ REPTPEE+AK++ E V
Sbjct: 332 IRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKV 391
Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
R++ K +EPISL+ IG E S GDFIED AVSP+D+ L++ VL +L+ R
Sbjct: 392 REIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSER 451
Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
E V+RMRFG+ TL+E+G+ + VTRERIRQIE+K +RKL+HPSRS+ LR FLD
Sbjct: 452 EAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509
Score = 63.1 bits (154), Expect = 2e-10
Identities = 26/71 (36%), Positives = 42/71 (59%)
Query: 79 DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
+ + ++ E D D +S Q RKD+ +T DPV+ YL+++G ++LL+ E
Sbjct: 171 EKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKLTATADPVKAYLKQIGKVKLLNAEE 230
Query: 139 EIAIAKRIEAG 149
E+ +AKRIEAG
Sbjct: 231 EVELAKRIEAG 241
>gnl|CDD|163097 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor,
cyanobacterial RpoD-like family. This family includes a
number of closely related sigma-70 (TIGR02937) factors
in the cyanobacteria. All appear most closely related to
the essential sigma-70 factor RpoD, and some score above
trusted to the RpoD C-terminal domain model (TIGR02393).
Length = 298
Score = 302 bits (776), Expect = 2e-82
Identities = 121/248 (48%), Positives = 180/248 (72%), Gaps = 8/248 (3%)
Query: 421 GISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIG 480
G+S +E R + ++ AK++M++ANLRLV+SVAKKY NRGL+ LDLIQEG++G
Sbjct: 59 GLSEAELRQRLRQGQR-------AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLG 111
Query: 481 LMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMS 540
L +A EKFD GYKFSTYA WW++Q ITR+IA+QS TIR+P+H+ +K++K+ + R +S
Sbjct: 112 LERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELS 171
Query: 541 NKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSP 600
K+ R P+ EIA+ L + E VR++L+ ++P+SL+ P+GDE+ + LGD +ED + SP
Sbjct: 172 QKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESP 230
Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIE 660
+ + +LR+ +LA LTPRE +VLR+RFG+ TL E+G++ ++RER+RQIE
Sbjct: 231 EEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIE 290
Query: 661 AKAIRKLK 668
AKA+RKL+
Sbjct: 291 AKALRKLR 298
Score = 35.7 bits (83), Expect = 0.036
Identities = 15/36 (41%), Positives = 26/36 (72%), Gaps = 3/36 (8%)
Query: 119 DPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMM 154
D VR+YL+E+G + LL+ E EI +A+++ + MM+
Sbjct: 1 DLVRLYLQEIGRVPLLTPEEEIELARQV---QQMMV 33
>gnl|CDD|180964 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated.
Length = 373
Score = 293 bits (751), Expect = 1e-79
Identities = 136/262 (51%), Positives = 188/262 (71%), Gaps = 8/262 (3%)
Query: 419 ETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGN 478
+ + +FR + + R+ AK++MV++NLRLV+S+AKKY NRGL F DLIQEG+
Sbjct: 119 LVDMPLPKFRRRLMLGRR-------AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGS 171
Query: 479 IGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARR 538
+GL++AAEKFD GYKFSTYA WW++QAITR+IADQS TIR+PVH+ + I ++ +T +
Sbjct: 172 LGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKV 231
Query: 539 MSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAV 598
+S + R+PT EEIA+ + M +E +R + K + PISLETPIG E+ S LGDFIE
Sbjct: 232 LSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGE- 290
Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
+P D + LRE VLA+L+PRE VLR+R+G+ TLEE+G+ F VTRERIRQ
Sbjct: 291 TPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQ 350
Query: 659 IEAKAIRKLKHPSRSKKLRSFL 680
IEAKA+RKL+HP+R+ L+ ++
Sbjct: 351 IEAKALRKLRHPNRNSVLKEYI 372
Score = 44.4 bits (105), Expect = 1e-04
Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 79 DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADR-STDDPVRMYLREMGSIELLSRE 137
D D EDEE S ++ D S + L + K + T+D +R+YL+E+G I LL +
Sbjct: 22 DLDSDEDEESSSENADELSEKEAKAKALARIKIGPKKVYTEDSIRVYLQEIGRIRLLRPD 81
Query: 138 GEIAIAKRI 146
EI +A++I
Sbjct: 82 EEIELARKI 90
>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed.
Length = 324
Score = 271 bits (696), Expect = 3e-73
Identities = 111/240 (46%), Positives = 175/240 (72%)
Query: 440 EASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTY 499
+ A++ ++EANLRLV+S+AK+YT RG+ LDLIQEGN+GL++A EKFD+ G+KFSTY
Sbjct: 83 DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTY 142
Query: 500 AMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMP 559
A WW++QAITR +ADQS TIR+PVH+ ++++K+ R R + ++ RE T EE+A++ +P
Sbjct: 143 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIP 202
Query: 560 VEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLAS 619
E + +L+ +++P+SL+ P+G ++ + LGDFIED A S ++ I L VLA+
Sbjct: 203 EEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLAT 262
Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSF 679
L RE++V+R+RFG+ TL+++GK F ++RER+RQIE + + KL++ R+ +LRS+
Sbjct: 263 LDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
Score = 36.6 bits (85), Expect = 0.019
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 96 ASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
A + + ++ A D VR+YL +G LL+ E+ +AKRIEAG
Sbjct: 3 ADATARATTSRVDSDLDAQSPAADLVRVYLNGIGKTALLTAADEVELAKRIEAG 56
>gnl|CDD|181056 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated.
Length = 415
Score = 251 bits (642), Expect = 5e-67
Identities = 113/238 (47%), Positives = 169/238 (71%), Gaps = 1/238 (0%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
AK+ M++ANLRLV+SVAKKY NRGL+ LDL+QEG +GL +A EKFD GY+FSTYA WW
Sbjct: 176 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWW 235
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
++Q ITR+IA QS TIR+PVH+ +K++K+ + R++S + R PT E+IA++L M V
Sbjct: 236 IRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQV 295
Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
R+VL +SLET +G + + LGD +E + +SP + ++ +L+ +LA LT R
Sbjct: 296 REVLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPEEMLMRESLQRDLQHLLADLTSR 354
Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFLD 681
E V+RMRFG+ ++L E+G+ ++RER+RQIE+KA++KL+ P R ++R +L+
Sbjct: 355 ERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412
Score = 42.9 bits (101), Expect = 3e-04
Identities = 24/102 (23%), Positives = 47/102 (46%), Gaps = 2/102 (1%)
Query: 76 NVVDGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLS 135
+ D E+ +DSLD ++ + +R + D VR+YL+E+G + LL
Sbjct: 17 SRQALDPDILEDDPDDSLDDVQELEIAAADEAVETAARNRRSTDLVRLYLQEIGRVRLLG 76
Query: 136 REGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDG 177
R+ E++ A++++ R M + L + +I L +
Sbjct: 77 RDEEVSEAQKVQ--RYMKLIVLANAAKEGDEVIKPYLRLIEV 116
>gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS. A sigma
factor is a DNA-binding protein protein that binds to
the DNA-directed RNA polymerase core to produce the
holoenzyme capable of initiating transcription at
specific sites. Different sigma factors act in
vegetative growth, heat shock, extracytoplasmic
functions (ECF), etc. This model represents the clade of
sigma factors called RpoS (also called sigma-38, KatF,
etc.), found only in Proteobacteria. This sigma factor
is induced in stationary phase (in response to the
stress of nutrient limitation) and becomes the second
prinicipal sigma factor at that time. RpoS is a member
of the larger Sigma-70 subfamily (TIGR02937) and most
closely related to RpoD (TIGR02393).
Length = 285
Score = 246 bits (629), Expect = 2e-65
Identities = 107/262 (40%), Positives = 160/262 (61%), Gaps = 3/262 (1%)
Query: 416 ISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQ 475
I + ++ E G+ EA +K M+E+NLRLV+S+AK Y NRGL LDLI+
Sbjct: 22 IGFKPLLTAEEEIAYARRALAGDFEA---RKVMIESNLRLVVSIAKHYVNRGLPLLDLIE 78
Query: 476 EGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRT 535
EGN+GLM A EKFD G++FSTYA WW++Q I R+I +Q+ TIR+PVH+ +++ +R
Sbjct: 79 EGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRA 138
Query: 536 ARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDK 595
AR++ K+ REP+ EEIA+ L PVE V +VL + + SL+ P+ D+ + L D I D+
Sbjct: 139 ARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADE 198
Query: 596 NAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRER 655
++ P +L++ LA L R+ VL RFG+ TLEEV + +TRER
Sbjct: 199 QSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRER 258
Query: 656 IRQIEAKAIRKLKHPSRSKKLR 677
+RQI+ +A++KL+ +
Sbjct: 259 VRQIQVEALKKLRRILERDGVD 280
Score = 32.8 bits (75), Expect = 0.34
Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAG 149
K+ ++ R D ++YLRE+G LL+ E EIA A+R AG
Sbjct: 2 FKKAETETRVAD-VTQLYLREIGFKPLLTAEEEIAYARRALAG 43
>gnl|CDD|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated.
Length = 327
Score = 228 bits (582), Expect = 4e-60
Identities = 105/237 (44%), Positives = 162/237 (68%), Gaps = 3/237 (1%)
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+ +T R +S K+ R TP EIAK+L + +
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQI 211
Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
R+ L + ++PISL+ +GD + L + +ED SP Q LR+ +LA LTP+
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELSELLED-EGPSPDQYITQELLRQDLNNLLAELTPQ 270
Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRSKKLRSFL 680
+ VL +RFG+ + +L +VG++ ++RER+RQ+E +A+ L+ R ++ +L
Sbjct: 271 QREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVKEYL 325
Score = 35.2 bits (81), Expect = 0.050
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 107 QKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASL 157
K + D VR YL E+G + LL+ E EI K+++ MM+ L
Sbjct: 6 TNTKTKQPTFSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQ----MMSLL 52
>gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated.
Length = 317
Score = 223 bits (571), Expect = 9e-59
Identities = 108/249 (43%), Positives = 171/249 (68%), Gaps = 8/249 (3%)
Query: 420 TGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNI 479
+S E R S + +GE AK++MVEANLRLV+SVAKKY R + LDLIQEG I
Sbjct: 65 AKLSEEELR---SAIAEGE----AAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTI 117
Query: 480 GLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRM 539
G+ + EKFD GY+FSTYA WW++QAITR+IA++S TIR+P+H+ +K++K+ + R++
Sbjct: 118 GMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQL 177
Query: 540 SNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVS 599
S ++ R T E+A++L + + VR+ L+ ++P+SL+ +GD + LG+ +ED A S
Sbjct: 178 SQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGA-S 236
Query: 600 PLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQI 659
P D A Q++L+ R++ LTP+++ V+ +RFG+ TL ++G++ ++RER+RQI
Sbjct: 237 PEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQI 296
Query: 660 EAKAIRKLK 668
E +A+ KL+
Sbjct: 297 EREALSKLR 305
Score = 40.5 bits (95), Expect = 0.001
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 115 RSTDDPVRMYLREMGSIELLSREGEIAIAKRIE 147
+++ D VR YLRE+G + LL+ E EI K+++
Sbjct: 4 KTSTDLVRTYLREIGRVPLLTHEEEILYGKQVQ 36
>gnl|CDD|180185 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated.
Length = 325
Score = 220 bits (564), Expect = 6e-58
Identities = 96/251 (38%), Positives = 158/251 (62%), Gaps = 5/251 (1%)
Query: 429 HIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKF 488
+ +G+ A ++ M+E+NLRLV+ +AK+Y NRGL LDLI+EGN+GL++A EKF
Sbjct: 75 YFARRALRGDFAA---RQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKF 131
Query: 489 DWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPT 548
D G++FSTYA WW++Q I R+I +Q+ TIR+PVH+ +++ +R AR + +K+ EP+
Sbjct: 132 DPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPS 191
Query: 549 PEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQAN 608
EEIA+ L PV+ V ++L + + SL+TP+G + L D + D+ P + Q +
Sbjct: 192 AEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGP-EDTTQDD 250
Query: 609 LRETTTRV-LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
+ + L L ++ VL RFG+ TLE+V ++ +TRER+RQI+ +A+R+L
Sbjct: 251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRL 310
Query: 668 KHPSRSKKLRS 678
+ +++ L
Sbjct: 311 REILQTQGLSI 321
Score = 31.5 bits (72), Expect = 0.69
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 4/71 (5%)
Query: 79 DGDDLEDEEGSEDSLDLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREG 138
+G ++ DE+ + + + + + + R D ++YL E+G LL+ E
Sbjct: 17 NGVEVFDEKALVEEEPSDNDLAEEELL---SQGATQRVLD-ATQLYLNEIGYSPLLTAEE 72
Query: 139 EIAIAKRIEAG 149
E+ A+R G
Sbjct: 73 EVYFARRALRG 83
>gnl|CDD|162835 TIGR02392, rpoH_proteo, alternative sigma factor RpoH. A sigma
factor is a DNA-binding protein protein that binds to
the DNA-directed RNA polymerase core to produce the
holoenzyme capable of initiating transcription at
specific sites. Different sigma factors act in
vegetative growth, heat shock, extracytoplasmic
functions (ECF), etc. This model represents the clade of
sigma factors called RpoH and further restricted to the
Proteobacteria. This protein may be called sigma-32,
sigma factor H, heat shock sigma factor, and alternative
sigma factor RpoH. Note that in some species the single
locus rpoH may be replaced by two or more differentially
regulated stress response sigma factors.
Length = 270
Score = 127 bits (321), Expect = 1e-29
Identities = 76/246 (30%), Positives = 127/246 (51%), Gaps = 37/246 (15%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
A K++V ++LR V+ +A+ Y GL DLIQEGNIGLMKA ++FD G + ++A+ W
Sbjct: 36 AAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHW 95
Query: 504 VKQAITRSIADQSCTIRIPVHMRD-KIHKVVRTA---------RRMSNKIKREPTPEE-- 551
+K I I +R+ ++ KV T R+M +++ PEE
Sbjct: 96 IKAEIHEYI------------LRNWRLVKVATTKAQRKLFFNLRKMKKRLQGWLNPEEVE 143
Query: 552 -IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSHLG--DFIEDKNAVSPLDSAIQA 607
IA++L + VR++ +++ + +SL I D++ ++ DK + P D+ +
Sbjct: 144 AIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKTS-DPEDTLEEE 202
Query: 608 NLRETTT----RVLASLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAK 662
E L SL R R++ R+ ++ D TL+E+ ++ V+ ERIRQIE
Sbjct: 203 QWEELQRQALANALGSLDARSRRIIEARW---LDDDKLTLQELAAEYGVSAERIRQIEKN 259
Query: 663 AIRKLK 668
A++KLK
Sbjct: 260 AMKKLK 265
>gnl|CDD|180635 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed.
Length = 284
Score = 122 bits (310), Expect = 2e-28
Identities = 78/246 (31%), Positives = 131/246 (53%), Gaps = 38/246 (15%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
A K++V ++LR V+ +A+ Y GL DLIQEGNIGLMKA ++FD +G + ++A+ W
Sbjct: 49 AAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHW 108
Query: 504 VKQAITRSIADQSCTIRIPVHMRD-KIHKVVRTA---------RRMSNKIKREPTPEE-- 551
+K I I +R+ +I KV T R+ ++ PEE
Sbjct: 109 IKAEIHEYI------------LRNWRIVKVATTKAQRKLFFNLRKAKKRLGWL-NPEEVE 155
Query: 552 -IAKKLAMPVEGVRKV-LKITKEPISLETPIGDEDTSH--LGDFIEDKNAVSPLDSAIQA 607
+A++L + E VR++ +++ + SL+ PI D+D D++EDK++ P D +
Sbjct: 156 MVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSS-DPADVLEED 214
Query: 608 NLRETTTRVLA----SLTPREERVLRMRFGIGMNTDH-TLEEVGKQFCVTRERIRQIEAK 662
N + +LA L R ++ R+ ++ D TL+E+ ++ V+ ER+RQIE
Sbjct: 215 NWEDQRRALLADALEGLDERSRDIIEARW---LDDDKSTLQELAAEYGVSAERVRQIEKN 271
Query: 663 AIRKLK 668
A++KLK
Sbjct: 272 AMKKLK 277
>gnl|CDD|163094 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G
subfamily. This group of similar sigma-70 factors
includes clades found in Bacilli (including the
sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as
well as SigB:TIGR02941), and the high GC gram positive
bacteria (Actinobacteria) where a variable number of
them are found depending on the lineage.
Length = 227
Score = 121 bits (305), Expect = 7e-28
Identities = 74/231 (32%), Positives = 122/231 (52%), Gaps = 17/231 (7%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
A++++VE NL LV S+A+++ NRG DL+Q G IGL+KA ++FD G KFST+A+
Sbjct: 4 AREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPT 63
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
+ I R D + +R+P +++ K+ + ++ ++ R PT EIA++L + E V
Sbjct: 64 IMGEIKRFFRDDTWAVRVPRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEV 123
Query: 564 RKVLKITK--EPISLETPIG--DEDTSHLGDFIEDKNAVSPLDSAI-QANLRETTTRVLA 618
+ L+ +SL+ PI D D L D + D+ D A+ R +LA
Sbjct: 124 VEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDE------DDALETVEDRLALKPLLA 177
Query: 619 SLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLK 668
+L RE R+L +RF E +G Q V+R + +A++KL+
Sbjct: 178 ALPERERRILLLRFFEDKTQSEIAERLGISQMHVSR-----LLRRALKKLR 223
>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed.
Length = 258
Score = 116 bits (292), Expect = 2e-26
Identities = 81/252 (32%), Positives = 135/252 (53%), Gaps = 21/252 (8%)
Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
+ E R + ++ G+ EA +++++ NLRLV+SV +++ NRG DL Q G IGL
Sbjct: 19 LKNEEMRELFERMQNGDKEA---REKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGL 75
Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
MKA + FD KFSTYA+ + I R + D + IR+ +RD +K ++ ++ N
Sbjct: 76 MKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLIN 134
Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE--DTSHLGDFIED-KNAV 598
+ +EPT EEIAK+L +P E V L ++P+SL PI + D ++ D I D KN
Sbjct: 135 ENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-- 192
Query: 599 SPLDSAIQAN--LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERI 656
D L+E + L RE+ +L +RF G T EV ++ +++ ++
Sbjct: 193 --KDENWLEEIALKEA----MKKLNDREKLILNLRFFQG----KTQMEVAEEIGISQAQV 242
Query: 657 RQIEAKAIRKLK 668
++E A++ ++
Sbjct: 243 SRLEKAALKHMR 254
>gnl|CDD|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor. Members of
this family comprise the Firmicutes lineage endospore
formation-specific sigma factor SigG. It is also
desginated stage III sporulation protein G (SpoIIIG).
This protein is rather closely related to sigma-F
(SpoIIAC), another sporulation sigma factor.
Length = 254
Score = 113 bits (283), Expect = 2e-25
Identities = 74/245 (30%), Positives = 130/245 (53%), Gaps = 13/245 (5%)
Query: 425 SEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKA 484
E R + ++ G+ A +++++ NLRLV+SV +++ NRG DL Q G IGLMK+
Sbjct: 19 QEMRELFIRMQSGDTTA---REKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKS 75
Query: 485 AEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIK 544
+ FD KFSTYA+ + I R + D + IR+ +RD +K ++ ++ ++
Sbjct: 76 IDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKLISENS 134
Query: 545 REPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSA 604
+EPT EIAK+L +P E V L ++P+SL PI ++ GD I + +S +
Sbjct: 135 KEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDG----GDPIYVMDQISDEKNK 190
Query: 605 IQANLRETTTR-VLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKA 663
L + + L RE+ +L MRF G T EV ++ +++ ++ ++E A
Sbjct: 191 DSQWLEGIALKEAMKRLNEREKMILNMRFFEG----KTQMEVAEEIGISQAQVSRLEKAA 246
Query: 664 IRKLK 668
++ ++
Sbjct: 247 LKHMR 251
>gnl|CDD|162877 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA/WhiG
family. Most members of this family are the flagellar
operon sigma factor FliA, controlling transcription of
bacterial flagellar genes by RNA polymerase. An
exception is the sigma factor WhiG in the genus
Streptomyces, involved in the production of sporulating
aerial mycelium.
Length = 224
Score = 107 bits (270), Expect = 9e-24
Identities = 65/203 (32%), Positives = 106/203 (52%), Gaps = 16/203 (7%)
Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI---TRSIADQSCTIRIPVHMRDK 528
DLIQ G GL+ A E++D G KF TYA+ ++ A+ R + +P +R K
Sbjct: 28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD------WVPRSLRQK 81
Query: 529 IHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLETPIGDEDTS 586
K+ R R + ++ REPT EEIA++L M ++ R+ L +SL+ + D
Sbjct: 82 ARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDG 141
Query: 587 -HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEV 645
L D IED + P + + LRE + SL+ RE+ VL + + +N L+E+
Sbjct: 142 GSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQLVLSLYYYEELN----LKEI 197
Query: 646 GKQFCVTRERIRQIEAKAIRKLK 668
G+ +T R+ QI ++A++KL+
Sbjct: 198 GEVLGLTESRVSQIHSQALKKLR 220
>gnl|CDD|181003 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed.
Length = 289
Score = 104 bits (262), Expect = 7e-23
Identities = 79/268 (29%), Positives = 127/268 (47%), Gaps = 51/268 (19%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
A ++ A++RLVIS+A K+ GL DLIQEG +GL++AA +F+ +FSTYA WW
Sbjct: 41 ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWW 100
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA------------RRMSNKIKREPTP-- 549
++ +I I +R+ +VR RR+ ++ +
Sbjct: 101 IRASIQDYI------------LRN--WSIVRGGTSSAQKALFFNLRRLRARLAQADEELT 146
Query: 550 -----EEIAKKLAMPVEGVRKV-LKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPL 601
EIA L + + V + +++ SL P DE S DF+ D SPL
Sbjct: 147 KQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDD---SPL 203
Query: 602 DSAIQANLRETTTR------VLASLTPREERVLRMRFGIGMNTD-HTLEEVGKQFCVTRE 654
+ + R L +L RE R++R R + D TLE +G++ +++E
Sbjct: 204 PDEQVESSIDGERRRRWLTQALQTLNERELRIIRER---RLREDGATLEALGEELGISKE 260
Query: 655 RIRQIEAKAIRKLKHP--SRSKKLRSFL 680
R+RQIEA+A+ KL+ S+S ++ F
Sbjct: 261 RVRQIEARALEKLRRALLSQSPEVAYFA 288
>gnl|CDD|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor. Members of
this protein family are the RNA polymerase sigma factor
F. Sigma-F is specifically and universally a component
of the Firmicutes lineage endospore formation program,
and is expressed in the forespore to turn on expression
of dozens of genes. It is closely homologous to sigma-G,
which is also expressed in the forespore.
Length = 231
Score = 96.3 bits (240), Expect = 2e-20
Identities = 71/241 (29%), Positives = 125/241 (51%), Gaps = 15/241 (6%)
Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
++ + + G+ EA + +++E NLRLV S+ K++ NRG + DL Q G IGL+KA +KFD
Sbjct: 1 LIKLAQNGDKEA---RDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFD 57
Query: 490 WCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTP 549
KFSTYA+ + I R + D I++ +++ K+ +S ++ REPT
Sbjct: 58 LSYDVKFSTYAVPMIMGEIKRFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTI 116
Query: 550 EEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFIEDKNAVSPLDSAIQA 607
E+A+ L + E + L+ + P SL + D D +L D I DK + DS
Sbjct: 117 NELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKGSE---DSDWLE 173
Query: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667
+ ++ L RE +++ +R+ D T EV +++ ++ ++E K ++K+
Sbjct: 174 KI--ALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKM 227
Query: 668 K 668
K
Sbjct: 228 K 228
>gnl|CDD|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated.
Length = 252
Score = 92.7 bits (231), Expect = 3e-19
Identities = 75/259 (28%), Positives = 136/259 (52%), Gaps = 17/259 (6%)
Query: 412 EIKSISVETGISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFL 471
E+K+ + + E + ++ + G+ EA + +VE NLRLV SV +++ NRG +
Sbjct: 4 EVKNKKKKPQLKDEENKELIKKSQDGDQEA---RDTLVEKNLRLVWSVVQRFLNRGYEPD 60
Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
DL Q G IGL+KA +KFD KFSTYA+ + I R + D T+++ +++ +K
Sbjct: 61 DLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANK 119
Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPI--GDEDTSHLG 589
+ + +S ++ REPT EE+A+ L + E V + ++ P S+ + D D L
Sbjct: 120 IRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLL 179
Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
D I D++ D + L+E + L RE ++ +R+ D T EV K+
Sbjct: 180 DQIADQSEEDWFD---KIALKE----AIRELDERERLIVYLRY----FKDKTQSEVAKRL 228
Query: 650 CVTRERIRQIEAKAIRKLK 668
+++ ++ ++E K ++++K
Sbjct: 229 GISQVQVSRLEKKILKQMK 247
>gnl|CDD|180512 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed.
Length = 268
Score = 90.1 bits (224), Expect = 2e-18
Identities = 65/208 (31%), Positives = 103/208 (49%), Gaps = 18/208 (8%)
Query: 469 QFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI---TRSIADQSCTIRIPVHM 525
+F DL+ G GL+ A EKFD KF TYA+ ++ AI RSI IP +
Sbjct: 60 EFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID------WIPRSV 113
Query: 526 RDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLK--ITKEPISLET--PIG 581
R K ++ R + ++ R P+ EEIA +L + +E +L +SL G
Sbjct: 114 RQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGG 173
Query: 582 DE-DTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
DE D L D +E A++P + A + ++ + +L RE++VL + + +
Sbjct: 174 DEGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYYEDL---- 229
Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
TL+E+GK VT RI Q+ KA+ +L+
Sbjct: 230 TLKEIGKVLGVTESRISQLHTKAVLQLR 257
>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated.
Length = 251
Score = 84.7 bits (210), Expect = 7e-17
Identities = 56/201 (27%), Positives = 94/201 (46%), Gaps = 10/201 (4%)
Query: 472 DLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHK 531
DL G +GL A EKFD KF TYA + ++ AI + + +P MR+K K
Sbjct: 54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED---WLPRSMREKTKK 110
Query: 532 VVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKIT--KEPISL-ETPIGDEDTSHL 588
V ++ + R TP+E+A +L M E V + +S+ E +D ++
Sbjct: 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENV 170
Query: 589 GDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQ 648
I D +P + ++ L E + L+ +E+ V+ + + + TL E+G+
Sbjct: 171 SVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQV 226
Query: 649 FCVTRERIRQIEAKAIRKLKH 669
++ RI QI +KA+ KLK
Sbjct: 227 LNLSTSRISQIHSKALFKLKK 247
>gnl|CDD|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed.
Length = 264
Score = 82.5 bits (204), Expect = 3e-16
Identities = 65/257 (25%), Positives = 120/257 (46%), Gaps = 21/257 (8%)
Query: 423 SISEFRHIVSMVRK------GECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQE 476
S E+ + M R+ G E + +V L L +A+++ RG DL+Q
Sbjct: 14 STDEYADVPEMFRELAGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQV 73
Query: 477 GNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTA 536
+GL+ A +FD G F ++A+ + + R D S ++++P +++ ++ R
Sbjct: 74 ARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRLGRAT 133
Query: 537 RRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIG--DEDTSHLGDFI 592
+S ++ R PT E+A +L M E V + L +S+++ G D+D + D +
Sbjct: 134 AELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTL 193
Query: 593 EDKNAVSPLDSAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCV 651
D +D+ + Q RE +LA+L RE VL +RF M E VG +
Sbjct: 194 GD------VDAGLDQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVG----I 243
Query: 652 TRERIRQIEAKAIRKLK 668
++ + ++ AK + +L+
Sbjct: 244 SQMHVSRLLAKTLARLR 260
>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed.
Length = 233
Score = 78.1 bits (193), Expect = 7e-15
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 FD G K +TYA
Sbjct: 50 ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA--- 106
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
AR + N+I L +
Sbjct: 107 --------------------------------ARCIENEI------------LMH----L 118
Query: 564 RKVLKITKEPISLETPIG-DEDTSH--LGDFIEDKNAVSPLDSAIQANLR-ETTTRVLAS 619
R + K KE +SL+ PIG D++ + L D + + + ++ + E + +
Sbjct: 119 RNLKKTKKE-VSLQDPIGVDKEGNEISLIDILGSEE--DDVIEQVELKMEVEKLYKKIDI 175
Query: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKH 669
L RE+ V+ MR+G+G + T E+ K ++R + +IE +A++KL
Sbjct: 176 LDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225
>gnl|CDD|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed.
Length = 256
Score = 76.5 bits (189), Expect = 2e-14
Identities = 46/153 (30%), Positives = 94/153 (61%), Gaps = 5/153 (3%)
Query: 447 EMVEANLRLVISVAKKYTNRGLQ-FLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVK 505
++VE NL LV A +++N+ + + DL+Q G++GL++A E+FD G+ FS++A+ +++
Sbjct: 29 QLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIR 88
Query: 506 QAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR- 564
I + D+S T+RIP ++ + + + + ++ R+PT +EIA+ L + +E +
Sbjct: 89 GEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE 148
Query: 565 -KVLKITKEPISLETPI--GDEDTSHLGDFIED 594
K+ + P+SL+ P+ ++ ++ LGD + D
Sbjct: 149 IKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD 181
>gnl|CDD|180784 PRK06986, fliA, flagellar biosynthesis sigma factor; Validated.
Length = 236
Score = 74.5 bits (184), Expect = 9e-14
Identities = 68/208 (32%), Positives = 105/208 (50%), Gaps = 21/208 (10%)
Query: 468 LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR----IPV 523
+ DLIQ G IGL++AA ++D G F TYA Q I ++ D+ +R +P
Sbjct: 36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYA----GQRIRGAMLDE---LRSLDWVPR 88
Query: 524 HMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDE 583
+R +V + R++ ++ REPT E+A+KL + +E R++L T IS I DE
Sbjct: 89 SVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTN--ISQLFSI-DE 145
Query: 584 DTSHLGDFI---EDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDH 640
GD I ED PL LRE + SL RE+ VL + + +N
Sbjct: 146 LRGEHGDSILVTEDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEELN--- 202
Query: 641 TLEEVGKQFCVTRERIRQIEAKAIRKLK 668
L+E+G V+ R+ QI ++AI++L+
Sbjct: 203 -LKEIGAVLGVSESRVSQIHSQAIKRLR 229
>gnl|CDD|163078 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70
family. Several PFAM models hit segments of these
sequences including Sigma-70 region 2 (pfam04542) and
Sigma-70, region 4 (pfam04545), but not always above
their respective trusted cutoffs.
Length = 158
Score = 73.5 bits (181), Expect = 2e-13
Identities = 38/225 (16%), Positives = 73/225 (32%), Gaps = 71/225 (31%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
A +E+ E L L+ A++Y DL+QE + L++A ++FD F +
Sbjct: 2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRI 59
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
R+ I +R RR+ ++ +
Sbjct: 60 ---------------------ARNLILDYLRRKRRLRRELDLLEELLD------------ 86
Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPR 623
+ SP + Q RE L L R
Sbjct: 87 --------------------------------SDPSPEEELEQEEEREALREALEKLPER 114
Query: 624 EERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
E VL +R+ G+ + +E+ + ++ +++ +A +KL+
Sbjct: 115 EREVLVLRYLEGL----SYKEIAEILGISVGTVKRRLKRARKKLR 155
>gnl|CDD|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor. The
sporulation-specific transcription factor sigma-K (also
called sigma-27) is expressed in the mother cell
compartment of endospore-forming bacteria such as
Bacillus subtilis. Like its close homolog sigma-E
(sigma-29) (see TIGR02835), also specific to the mother
cell compartment, it must be activated by a proteolytic
cleavage. Note that in Bacillus subtilis (and apparently
also Clostridium tetani), but not in other endospore
forming species such as Bacillus anthracis, the sigK
gene is generated by a non-germline (mother cell only)
chromosomal rearrangement that recombines coding regions
for the N-terminal and C-terminal regions of sigma-K.
Length = 227
Score = 72.8 bits (179), Expect = 3e-13
Identities = 66/252 (26%), Positives = 105/252 (41%), Gaps = 61/252 (24%)
Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
+S E + + +++G+ EA + ++E NLRLV + KK++N G DLI G IGL
Sbjct: 30 LSEEEEKKYLDRLKEGDEEA---RNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGL 86
Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
+KA + FD G + +TYA R I ++ I +H+R
Sbjct: 87 IKAIDSFDPDKGTRLATYA--------ARCIENE-----ILMHLRA-------------- 119
Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH---LGDFIEDKNAV 598
LK TK +SL+ PIG + + L D +
Sbjct: 120 -------------------------LKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDS 154
Query: 599 SPLDSAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIR 657
++ NL L+ L RE V+ MR+G+G T E+ K ++R +
Sbjct: 155 VI--EQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVS 212
Query: 658 QIEAKAIRKLKH 669
+IE +A+ KL
Sbjct: 213 RIEKRALMKLYK 224
>gnl|CDD|131987 TIGR02941, Sigma_B, RNA polymerase sigma-B factor. This sigma
factor is restricted to certain lineages of the order
Bacillales including Staphylococcus, Listeria and
Bacillus.
Length = 255
Score = 66.5 bits (162), Expect = 2e-11
Identities = 55/235 (23%), Positives = 116/235 (49%), Gaps = 24/235 (10%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
A++++V+ LV S+A KY+ G DL+Q G +GL+ A ++D+ +G F +A+
Sbjct: 30 AQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPT 89
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
+ I R + D++ ++ +P +++ K+ + +++ ++R P EIA L + E V
Sbjct: 90 IIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEV 149
Query: 564 RKVLKITKEPISLETPIGDEDTSHLGDFIE---DKNAVSPLDSAIQAN-------LRETT 613
+++++ + + D IE D + V+ LDS + R
Sbjct: 150 LEIMEMGQ----------SYRALSVDDVIEADSDGSTVARLDSVGEVEDGYDQTERRMVL 199
Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
++L L+ RE+ ++ F ++ T E +G +++ + +++ +AI KLK
Sbjct: 200 EKILPILSEREKSIIHCTFEENLSQKETGERLG----ISQMHVSRLQRQAISKLK 250
>gnl|CDD|131882 TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor. Members of
this family comprise the Firmicutes lineage endospore
formation-specific sigma factor SigE, also called
SpoIIGB and sigma-29. As characterized in Bacillus
subtilis, this protein is synthesized as a precursor,
specifically in the mother cell compartment, and must
cleaved by the SpoIIGA protein to be made active.
Length = 234
Score = 64.8 bits (158), Expect = 7e-11
Identities = 58/247 (23%), Positives = 115/247 (46%), Gaps = 53/247 (21%)
Query: 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGL 481
++ E ++ + +G+ A K ++E NLRLV+ +A+K+ N G+ DL+ G IGL
Sbjct: 34 LTGEEEEALLQKLTQGDESA---KSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGL 90
Query: 482 MKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSN 541
+KA F+ K +TYA +R I ++ I +++ R +N
Sbjct: 91 IKAVNTFNPSKKIKLATYA--------SRCIENE-----ILMYL------------RRNN 125
Query: 542 KIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSHLGDFIEDKNAVSPL 601
K + E + +E L + +G +L + + D+ + ++E++
Sbjct: 126 KTRSEVSFDE---PLNVDWDGNELLL----------SDVLGTDSDIVYKYLEEEVD---- 168
Query: 602 DSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661
RE + LA L RE++++ +RFG+ T+ T +EV +++ I ++E
Sbjct: 169 --------RELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEK 220
Query: 662 KAIRKLK 668
+ +++LK
Sbjct: 221 RILKRLK 227
>gnl|CDD|181489 PRK08583, PRK08583, RNA polymerase sigma factor SigB; Validated.
Length = 257
Score = 60.9 bits (148), Expect = 1e-09
Identities = 58/236 (24%), Positives = 116/236 (49%), Gaps = 26/236 (11%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503
A++++V+ LV S+A KY+ DL+Q G +GL+ A ++D G F +A+
Sbjct: 30 AQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPT 89
Query: 504 VKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGV 563
+ I R + D++ ++ +P +++ K+ + ++ +++R P EIA +L + E V
Sbjct: 90 IIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEV 149
Query: 564 RKVLKITK--EPISLETPI-GDEDTSHLGDFIEDKNAVSPLDSAIQ-------ANLRETT 613
+ +++ K + +S++ I D D S V+ LD Q R
Sbjct: 150 LEAMEMGKSYQALSVDHSIEADSDGS----------TVTLLDIVGQQEDGYELTEQRMIL 199
Query: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-KQFCVTRERIRQIEAKAIRKLK 668
++L L+ RE+ +++ F ++ T E +G Q V+R ++ +AI+KL+
Sbjct: 200 EKILPVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSR-----LQRQAIKKLR 250
>gnl|CDD|135656 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed.
Length = 257
Score = 52.7 bits (126), Expect = 3e-07
Identities = 64/242 (26%), Positives = 106/242 (43%), Gaps = 40/242 (16%)
Query: 448 MVEANLRLVISVAKKYTN---RGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWV 504
++E L LV +VA + + ++ DL G GL++A E+FD +F YA++ +
Sbjct: 28 LIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLI 87
Query: 505 KQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVE--- 561
K AI + Q +P + K +K+ + + +EPT E+ + L + +
Sbjct: 88 KAAIIDDLRKQDW---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELS 144
Query: 562 ----GVRKVLKIT-----------KEPISLETPIGDEDTSHLGDFIEDKNAVSPLDSAIQ 606
R L ++ + ++LE I DE D ++ K S L AI
Sbjct: 145 GWFSSARPALILSLNEEFPCQSDDEAGLALEERIADERAETGYDVVDKKEFSSILAEAIL 204
Query: 607 ANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666
A L E +V+A L EE VL+ E+GK V+ R+ QI +KA+ K
Sbjct: 205 A-LEEKERKVMA-LYYYEELVLK--------------EIGKILGVSESRVSQIHSKALLK 248
Query: 667 LK 668
L+
Sbjct: 249 LR 250
>gnl|CDD|181367 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed.
Length = 234
Score = 50.6 bits (122), Expect = 1e-06
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYA 500
+ ++E NLRLV+ +A+K+ N G+ DLI G IGL+KA F+ K +TYA
Sbjct: 53 VRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109
Score = 31.8 bits (73), Expect = 0.61
Identities = 16/59 (27%), Positives = 35/59 (59%)
Query: 610 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
R+ + L L+ RE++++ +RFG+ + T +EV +++ I ++E + I++LK
Sbjct: 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227
>gnl|CDD|183523 PRK12427, PRK12427, flagellar biosynthesis sigma factor;
Provisional.
Length = 231
Score = 38.3 bits (89), Expect = 0.007
Identities = 35/154 (22%), Positives = 64/154 (41%), Gaps = 25/154 (16%)
Query: 522 PVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581
P +R K HK R ++ ++ EP EEI+ +L + E ++ L +
Sbjct: 93 PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLE----------N 142
Query: 582 DEDTSHLGDFIEDKNAVSPLDS-------AIQANLRETTTRVLASLTPREERVLRMRFGI 634
L + + + L S I+ NL++ L+ L RE+ +L + +
Sbjct: 143 AGTLESLDELLALEAHNDILQSRDLEENIIIEDNLKQA----LSQLDEREQLILHLYYQH 198
Query: 635 GMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
M+ L+E+ +T RI Q+ K +K+K
Sbjct: 199 EMS----LKEIALVLDLTEARICQLNKKIAQKIK 228
>gnl|CDD|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated.
Length = 208
Score = 35.3 bits (82), Expect = 0.059
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
+V + R G+ A + ++E V + A+ Y G D++QEG IGL KA +D
Sbjct: 14 LVELARSGD---KEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYD 70
>gnl|CDD|131997 TIGR02952, Sig70_famx2, RNA polymerase sigma-70 factor, TIGR02952
family. This group of sigma factors are members of the
sigma-70 family (TIGR02937). They and appear by
homology, tree building, bidirectional best hits and
one-to-a-genome distribution, to represent a conserved
family. This family is found in a limited number of
Gram-positive bacterial lineages.
Length = 170
Score = 34.0 bits (78), Expect = 0.14
Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 599 SPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQ 658
+P ++ ++ E + L LTP+++ V+ +RFG + +GK T ++
Sbjct: 102 NPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGK----TEGAVKI 157
Query: 659 IEAKAIRKLK 668
++ +AI+KL
Sbjct: 158 LQFRAIKKLA 167
>gnl|CDD|178762 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 33.8 bits (77), Expect = 0.14
Identities = 28/99 (28%), Positives = 43/99 (43%), Gaps = 22/99 (22%)
Query: 226 TEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALD 285
T +I+ AA + D +V P+ DED+D+ L DQL+ +L+
Sbjct: 1545 TADEIDQAAHMLMD---QVGQVPD---------DEDDDEDGDVLEKEVDQLQQ----SLE 1588
Query: 286 EIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKL 324
+AEV REL Q + GQK + +L +L
Sbjct: 1589 RLAEVQRELAEGQVKVIEGQKQMAER------QSRLSQL 1621
>gnl|CDD|182011 PRK09639, PRK09639, RNA polymerase sigma factor SigX; Provisional.
Length = 166
Score = 29.9 bits (68), Expect = 2.4
Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 590 DFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQF 649
+ E N SP + I+ VLA +T R+ VL +RF + ++ +E+ +
Sbjct: 83 QWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEAL 137
Query: 650 CVTRERIRQIEAKAIRKLK 668
+ + A+A +K +
Sbjct: 138 GIKESSVGTTLARAKKKFR 156
>gnl|CDD|131906 TIGR02859, spore_sigH, RNA polymerase sigma-H factor. Members of
this protein family are RNA polymerase sigma-H factor
for sporulation in endospore-forming bacteria. This
protein is also called Sigma-30 and SigH. Although
rather close homologs are detected in Listeria, Listeria
does not form spores and the role of the related sigma
factor in that genus is in doubt.
Length = 198
Score = 29.8 bits (67), Expect = 2.5
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 430 IVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFD 489
IV + R+G + A + ++ V + A+ Y G D+IQEG IGL KA F
Sbjct: 9 IVELARQGN---THALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFR 65
>gnl|CDD|177950 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 29.5 bits (66), Expect = 2.7
Identities = 17/68 (25%), Positives = 24/68 (35%), Gaps = 2/68 (2%)
Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVS--KDDRSKVDSPPENAEND 254
GF T S QKR + + D T SA + + + +VD +
Sbjct: 12 RGFAPRTTVESSQKRIQQNNGDKEDSSTSTSSLSVSAVEKTSNAKEEIQVDFQHNSESAV 71
Query: 255 ERNLDEDE 262
E EDE
Sbjct: 72 EEVEAEDE 79
>gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent.
Length = 1164
Score = 29.3 bits (66), Expect = 3.4
Identities = 33/170 (19%), Positives = 62/170 (36%), Gaps = 22/170 (12%)
Query: 197 GGFFHGTEGHSYQKREDSSQEKERDDVQETEGD----------IESAAKVSKDDRSKVDS 246
GG G + + E + ++ R+ ++ + + IE+ + S
Sbjct: 657 GGSRAPRGGILFSRSEPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASR 716
Query: 247 PPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQK 306
E + L+++E+ L +E+ L EI V EL+ + +
Sbjct: 717 KIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLE----QEIENVKSELK-----ELEARI 767
Query: 307 DEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISKRIMHNEGEL 356
+E K L+E L L LS SRI + +L + + + E L
Sbjct: 768 EELEEDLHK-LEEALNDLEARLS--HSRIPEIQAELSKLEEEVSRIEARL 814
>gnl|CDD|151510 pfam11065, DUF2866, Protein of unknown function (DUF2866). This
bacterial family of proteins have no known function.
Length = 65
Score = 29.3 bits (66), Expect = 3.5
Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 12/59 (20%)
Query: 515 QSCTIRIPVH---------MRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVR 564
+SC + P+ + + +RR+ + E TP EIA+ + V G R
Sbjct: 4 RSCRVSEPIQRPWGRGYRLVEWTMDLDGPISRRV---VPAESTPAEIAEAVRRHVPGRR 59
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 28.9 bits (64), Expect = 4.4
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 217 EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTL 269
EK R + +E E +E + K D + D + E +E+ ++E DDS H +
Sbjct: 129 EKARQEREELEERMEWERREEKIDERE-DQEEQEREREEQTIEEQSDDSEHEI 180
>gnl|CDD|162931 TIGR02578, cas_TM1811_Csm1, CRISPR-associated protein, Csm1 family.
The family is designated Csm2, for CRISPR/Cas Subtype
Mtube Protein 2. A typical example is TM1811 from
Thermotoga maritima. CRISPR are Clustered Regularly
Interspaced Short Palindromic Repeats. This protein
family belongs to a conserved gene cluster regularly
found near CRISPR repeats.
Length = 648
Score = 28.5 bits (64), Expect = 5.6
Identities = 10/72 (13%), Positives = 22/72 (30%), Gaps = 4/72 (5%)
Query: 370 FLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISV----ETGISIS 425
L ++ D + K E ++ + + + + I + E +
Sbjct: 42 ALLEVLDKKADDLLKNLVKSHHEEDYLDDLIARAERLASGLEIIDRLEAGDDREEEELGN 101
Query: 426 EFRHIVSMVRKG 437
E +VS K
Sbjct: 102 EEEPLVSPFPKI 113
>gnl|CDD|181947 PRK09553, tauD, taurine dioxygenase; Reviewed.
Length = 277
Score = 28.5 bits (64), Expect = 6.1
Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 578 TPIGDEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTR--VL----ASLTPREERVLRMR 631
TP+G ++G I + PL L R VL +TP+++R L R
Sbjct: 6 TPLG----PYIGAQISGIDLTRPLSDNQFEQLYHALLRHQVLFFRDQPITPQQQRDLAAR 61
Query: 632 FG 633
FG
Sbjct: 62 FG 63
>gnl|CDD|181720 PRK09240, thiH, thiamine biosynthesis protein ThiH; Reviewed.
Length = 371
Score = 28.2 bits (64), Expect = 7.9
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 539 MSNKIKREP-TPEEIAKKL-AMPVEGVRKVLKITKE 572
MSNKIKR+ EEI +++ A+ G +L +T E
Sbjct: 95 MSNKIKRKTLDEEEIEREMAAIKKLGFEHILLLTGE 130
>gnl|CDD|182409 PRK10361, PRK10361, DNA recombination protein RmuC; Provisional.
Length = 475
Score = 28.0 bits (62), Expect = 8.2
Identities = 21/87 (24%), Positives = 45/87 (51%), Gaps = 15/87 (17%)
Query: 601 LDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEE-----VGKQFCVTRER 655
++++++A+LRE TTR+ A+ ++++ +M +N++ L E + F + R
Sbjct: 75 INTSLEADLREVTTRMEAAQQHADDKIRQM-----INSEQRLSEQFENLANRIFEHSNRR 129
Query: 656 IRQIEAKAIRKLKHPSRSKKLRSFLDG 682
+ + +++ L P LR LDG
Sbjct: 130 VDEQNRQSLNSLLSP-----LREQLDG 151
>gnl|CDD|131896 TIGR02849, spore_III_AD, stage III sporulation protein AD. Members
of this family are the uncharacterized protein SpoIIIAD,
part of the spoIIIA operon that acts at sporulation
stage III as part of a cascade of events leading to
endospore formation. Note that the start sites of
members of this family as annotated tend to be variable;
quite a few members have apparent homologous
protein-coding regions continuing upstream of the first
available start codon. The length of the alignment has
been set to try to detect all valid members of the
family, even if annotation of the start site begins too
far downstream.
Length = 101
Score = 28.0 bits (63), Expect = 8.6
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 124 YLREMGSIELLSREGEIAIAKRIE-AGRAMMM 154
Y+ E GS ++ GE AIA +IE AG+ +++
Sbjct: 53 YIAEFGS-QICKDAGEKAIASKIELAGKILIL 83
>gnl|CDD|180710 PRK06816, PRK06816, 3-oxoacyl-(acyl carrier protein) synthase
III; Reviewed.
Length = 378
Score = 28.0 bits (63), Expect = 8.7
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 44 VTIEELNAFLPPDEVSSEQMEDTVAMLSNM 73
V I AFLP + VS+++ME + +++
Sbjct: 3 VYITSTGAFLPGEPVSNDEMEAYLGLINGK 32
>gnl|CDD|165590 PHA03346, PHA03346, US22 family homolog; Provisional.
Length = 520
Score = 27.8 bits (62), Expect = 8.9
Identities = 9/48 (18%), Positives = 15/48 (31%)
Query: 217 EKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDD 264
E+ R D PP +D+ D+++DD
Sbjct: 391 ERRRPRGPPENEDEADGGGGLAPPPEPPRPPPPPFPDDDDEGDDEDDD 438
>gnl|CDD|178632 PLN03083, PLN03083, E3 UFM1-protein ligase 1 homolog; Provisional.
Length = 803
Score = 27.9 bits (62), Expect = 9.2
Identities = 23/115 (20%), Positives = 37/115 (32%), Gaps = 15/115 (13%)
Query: 175 NDGTTLLREIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQ---EKERDDVQETEGDIE 231
+ I D E + K K S+ +KE QE +I
Sbjct: 429 STKGGTAESIPDDEEDAPKKGKKN--QKKGRDKSSKVPSDSKAGGKKESVKSQEDNNNIP 486
Query: 232 SAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAHTLSAMEDQLRPKVMCALDE 286
V K ++ P+ E + +D L + D LRP ++ +L E
Sbjct: 487 PEEWVMK---KILEWVPDLEE-------DGTEDPGSILKHLADHLRPMLINSLKE 531
>gnl|CDD|119001 pfam10481, Cenp-F_N, Cenp-F N-terminal domain. Mitosin or
centromere-associated protein-F (Cenp-F) is found bound
across the centromere as one of the proteins of the
outer layer of the kinetochore. Most of the
kinetochore/centromere functions appear to depend upon
binding of the C-terminal par to f the molecule, whereas
the N-terminal part, here, may be a cytoplasmic player
in controlling the function of microtubules and dynein.
Length = 288
Score = 27.8 bits (61), Expect = 9.3
Identities = 16/75 (21%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 94 DLASSASNSSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKR-IEAGRAM 152
D+A ++SSVF +++ + R + + ++ LR S S E E+ ++ ++ G+
Sbjct: 206 DIARHQASSSVFSWQQEKTPSRLSSNALKTPLRRDFSASHFSGEQEVTPSRSTLQIGKGD 265
Query: 153 MMASLCESPLTFQAL 167
+S ++ + L
Sbjct: 266 ANSSFPDNSSSSHLL 280
>gnl|CDD|181072 PRK07661, PRK07661, acetyl-CoA acetyltransferase; Provisional.
Length = 391
Score = 27.8 bits (62), Expect = 9.9
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 636 MNTDHTLEEVGKQFCVTRE-------RIRQIEAKAIRKLK 668
M HT E+V ++ ++RE R Q AKA+ + K
Sbjct: 145 MGMGHTAEQVAVKYGISREDQDAFAVRSHQRAAKALAEGK 184
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.315 0.131 0.366
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 10,911,281
Number of extensions: 723130
Number of successful extensions: 1525
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1470
Number of HSP's successfully gapped: 97
Length of query: 682
Length of database: 5,994,473
Length adjustment: 100
Effective length of query: 582
Effective length of database: 3,833,673
Effective search space: 2231197686
Effective search space used: 2231197686
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 61 (27.2 bits)