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)