Citrus Sinensis ID: 014852

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------
Protein Sequence
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHIHCG
Secondary Structure (PSIPRED)
ccccccHHcccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccHHHHHHHcccccccccccccccccccccHHHHccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHccccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHcccccccccHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHEEcccccHHHcccccccccccccccccccccccccccccccEEEEEcccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccEEcccccHHHHcHHHHccccccccccccccHHHHHHHHcccccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHcccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHcccEEccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHcccccEccccccccccccHHHHHHHHcc
Coil and Loop (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYIndlgsansqvgsTKNVVAAkkssnynpsfpssnrqtqpiKALKEhvdtnfastaepwaeppnsieeesseLDYSVEALLLLQKSMLEKQWNLSFertvltdspskkthkkvpvtcsgvsARQRRLNSKKKILSQNKSILQQNGSkqlrsmisPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIktglslddHKLRLkerlgcepSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIekfdsskgfkisTYVYWWIRQGVSRALvensrtlrlpnhlhERLGLIRNAKLrleekgvtpsvDRIAEYLNMSQKKVRNATEAIGKVFsldreafpslnglpgethhihcg
Flexible Loop (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnrqTQPIKALKEHVDTNFAstaepwaeppnSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERtvltdspskkthkkvpvtcsgvsarqrrlnskkkilsqnksilqqngskqlrsMISPELIQNRLKGYVKGVVSEELLTHAEVVRlskkiktglslddhKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGiekfdsskgfkisTYVYWWIRQGVSRALVENSrtlrlpnhlherlglirnaklrleekgvtpsvdrIAEYLNMSQKKVRNATEAIGKVFSLDREAFpslnglpgethhihcg
Low Complexity Region (SEG)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnRQTQPIKALKEHVDTNFASTAEPWAEPPNsieeesseLDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHIHCG
Disordered region (IsUnstruct)
*****AVIGLSAGKRLLSSSFYYSDISEKFSYINDL*********************************************************************YSVEALLLLQKSMLEKQWNLSFERTVL******************************************************ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGC**********LRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD********************
Disordered Region (DISOPRED)
***TAAV*GLSAGKRLLSSSFYYSDISEKFS****************************************************************************************************************************************************************RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLR***********EQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR*****VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS*NG*PGE*****C*
Disordered Region (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNY************PIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVL*****************GVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHIHCG
Disordered Region (DISPRO)
*MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNY******************************************SSELDYSVEALLLLQKSMLEKQWNLSFER*********************************************************ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHIHCG
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHIHCG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	417	2.2.26 [Sep-21-2011]
O24629	502	RNA polymerase sigma fact	yes	no	0.947	0.786	0.698	1e-165
Q31ME3	320	RNA polymerase sigma fact	yes	no	0.501	0.653	0.359	2e-34
Q03065	332	RNA polymerase sigma-B fa	no	no	0.462	0.581	0.355	2e-33
P26683	390	RNA polymerase sigma fact	no	no	0.467	0.5	0.382	7e-32
Q03066	416	RNA polymerase sigma-C fa	no	no	0.402	0.403	0.382	7e-32
Q59996	404	Probable RNA polymerase s	N/A	no	0.345	0.356	0.427	9e-32
Q31QG5	320	RNA polymerase sigma fact	no	no	0.491	0.640	0.362	1e-31
O22056	572	RNA polymerase sigma fact	no	no	0.508	0.370	0.359	2e-31
Q9LD95	547	RNA polymerase sigma fact	no	no	0.458	0.349	0.364	4e-31
P38023	399	RNA polymerase sigma fact	no	no	0.467	0.488	0.382	2e-30

>sp|O24629|SIGA_ARATH RNA polymerase sigma factor sigA OS=Arabidopsis thaliana GN=SIGA PE=1 SV=1

 Score =  582 bits (1500), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 296/424 (69%), Positives = 344/424 (81%), Gaps = 29/424 (6%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY+PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVDV--ASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHH 413
           ETHH
Sbjct: 404 ETHH 407

Essential protein. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Controls the transcription of the psaA gene and thus modulates photosystem stoichiometry. Thereby maintains an harmonious electron flow and photosynthetic efficiency.
Arabidopsis thaliana (taxid: 3702)

>sp|Q31ME3|RPOD2_SYNE7 RNA polymerase sigma factor rpoD2 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD2 PE=1 SV=1

 Score =  147 bits (371), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 77/214 (35%), Positives = 133/214 (62%), Gaps = 5/214 (2%)

Query: 185 SPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQL 244
           SP+L+    + Y++ +    LLT  E +   ++++  + L D +  L++RLG EPS E+ 
Sbjct: 9   SPDLV----RAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEW 64

Query: 245 AASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR 304
           AA++ ++  +L   + +   A+ K++ +N+RLV+SIA++Y     +  DL+Q G +GL R
Sbjct: 65  AAAVDLNLEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLER 124

Query: 305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK- 363
           G+EKFD SKG+K STY YWWIRQ ++RA+ + SRT+RLP H+ E+L  ++  +  L ++ 
Sbjct: 125 GVEKFDPSKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQL 184

Query: 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397
           G + +   +AE L +  ++VR   +   +  SLD
Sbjct: 185 GRSATASELAEVLELPLEQVREYIQMNRQPVSLD 218

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity). This sigma factor is a component of the biological clock pathway that affects the circadian expression of a subset of genes in this bacterium.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|Q03065|RPSB_NOSS1 RNA polymerase sigma-B factor OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=sigB PE=3 SV=1

 Score =  143 bits (361), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 69/194 (35%), Positives = 122/194 (62%), Gaps = 1/194 (0%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LL+H + +  +++++  + +   K  L E+L  EP++++ A  +++    L   L +  +
Sbjct: 37  LLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQLKEDVLLQQLSQGQI 96

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++K++ +N+RLV+SIA++Y     +  DL+Q G +GL RG+EKFD + G+K STY YWW
Sbjct: 97  AKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFDPTLGYKFSTYAYWW 156

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           IRQG++RA+ + SRT+RLP H+ ++L  I+  +  L +K G    V  IA+ LN+   ++
Sbjct: 157 IRQGITRAIAQQSRTIRLPIHMADKLNKIKCVQRELSQKLGYIAGVTEIAQALNLEPSQI 216

Query: 384 RNATEAIGKVFSLD 397
           R   + + +  SLD
Sbjct: 217 REYLQLVRQPVSLD 230

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|P26683|RPOD_NOSS1 RNA polymerase sigma factor RpoD OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rpoD PE=3 SV=1

 Score =  138 bits (348), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 75/196 (38%), Positives = 121/196 (61%), Gaps = 1/196 (0%)

Query: 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLR 249
           ++ ++ Y++ +    LL   E + L++KI   L L+  + RL E+L  +P   + A +++
Sbjct: 79  EDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQ 138

Query: 250 ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKF 309
           +  P  +  L     A++K+V SN+RLV+SIA++Y N G    DL+Q G +GL+R  EKF
Sbjct: 139 LPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKF 198

Query: 310 DSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLI-RNAKLRLEEKGVTPS 368
           D  KG+K STY  WWIRQ ++RA+ + SRT+RLP HL+E +  I +  KL  +E G  P+
Sbjct: 199 DHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPT 258

Query: 369 VDRIAEYLNMSQKKVR 384
            + IA  + M+ +K+R
Sbjct: 259 EEEIATRMEMTIEKLR 274

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|Q03066|RPSC_NOSS1 RNA polymerase sigma-C factor OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=sigC PE=3 SV=2

 Score =  138 bits (348), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 73/191 (38%), Positives = 118/191 (61%), Gaps = 23/191 (12%)

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECS----------------------LARE 267
           RL   LG  PS+E+ AA+  I+  +L+ IL E                         ++E
Sbjct: 120 RLASELGHRPSLERWAATAGINLCDLKPILSEGKRRWAEIAKMTVEELEKMQSQGLQSKE 179

Query: 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327
            ++ +N+RLV+S+A++Y N G ++ DLVQ G +GL R +EKFD +KG++ STY YWWIRQ
Sbjct: 180 HMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQ 239

Query: 328 GVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNA 386
           G++RA+  +SRT+RLP H+ E+L  I+ A+ ++ +EKG TP+++ +A  L+M+  +VR  
Sbjct: 240 GITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLEDLAIELDMTPTQVREV 299

Query: 387 TEAIGKVFSLD 397
              + +  SL+
Sbjct: 300 LLRVPRSVSLE 310

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|Q59996|RPSC_SYNY3 Probable RNA polymerase sigma-C factor OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=sigC PE=3 SV=1

 Score =  138 bits (347), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 62/145 (42%), Positives = 101/145 (69%), Gaps = 1/145 (0%)

Query: 254 ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSK 313
           EL++I  +   A+  ++ +N+RLV+S+A++Y N G ++ DL+Q G +GL R +EKFD +K
Sbjct: 154 ELENIEKQGITAKAHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTK 213

Query: 314 GFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRI 372
           G++ STY YWWIRQG++RA+   SR +RLP H+ E+L  I+ A+ ++ +EKG TP +D +
Sbjct: 214 GYRFSTYSYWWIRQGITRAIATQSRMIRLPVHITEKLNKIKRAQRKISQEKGHTPKIDEV 273

Query: 373 AEYLNMSQKKVRNATEAIGKVFSLD 397
           AE L M+ ++VR     + +  SL+
Sbjct: 274 AEELGMTPEQVREVLTQVPRSVSLE 298

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|Q31QG5|RPOD3_SYNE7 RNA polymerase sigma factor rpoD3 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD3 PE=3 SV=1

 Score =  138 bits (347), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 75/207 (36%), Positives = 128/207 (61%), Gaps = 2/207 (0%)

Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGC-EPSMEQLAASLRIS 251
           ++ Y++ +    LLTH E V L K+++  + L + +  L+   G  +PS  + AA+  +S
Sbjct: 12  VRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAAGLS 71

Query: 252 RPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDS 311
             EL+        A+ K++ +N+RLV+S+A++Y     D+ DL+Q G IG+ RG+EKFD 
Sbjct: 72  IEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEKFDP 131

Query: 312 SKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVD 370
           +KG++ STY YWWIRQ ++RA+ E +RT+RLP H+ E+L  I+  + +L ++ G T ++ 
Sbjct: 132 TKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKMQRQLSQQLGRTATLP 191

Query: 371 RIAEYLNMSQKKVRNATEAIGKVFSLD 397
            +A  L+++  +VR+  E      SLD
Sbjct: 192 ELAAALDLTPAQVRDYLEKARHPLSLD 218

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|O22056|SIGB_ARATH RNA polymerase sigma factor sigB OS=Arabidopsis thaliana GN=SIGB PE=2 SV=2

 Score =  137 bits (344), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 77/214 (35%), Positives = 127/214 (59%), Gaps = 2/214 (0%)

Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLR 230
           ++   S + + +++ E+  N    Y++   S  +LLT  E   LS  I+  L L+  +  
Sbjct: 238 VKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSAGIQDLLKLERLQTE 297

Query: 231 LKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGAD 290
           L ER G +P+  Q A++  + +  L+  +   +L ++K++ SN+RLV+SIA+ Y   G +
Sbjct: 298 LTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMN 357

Query: 291 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350
           + DLVQ G  GL+RG EKFD++KGFK STY +WWI+Q V ++L + SR +RLP H+ E  
Sbjct: 358 LQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEAT 417

Query: 351 GLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKV 383
             ++ A+ +L  E G  P  + IAE   +S K++
Sbjct: 418 YRVKEARKQLYSETGKHPKNEEIAEATGLSMKRL 451

Required for the transition of plastids into chloroplasts by coordinating nuclear and chloroplastic genomes under light conditions. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Promotes the biosynthesis of plastid-encoded tRNAs (e.g. trnE-UUC and trnV-UAC).

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis thaliana GN=SIGF PE=1 SV=1

 Score =  136 bits (342), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 70/192 (36%), Positives = 122/192 (63%), Gaps = 1/192 (0%)

Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISR 252
           L+ ++ G  +++LLT  E   L   I+  L L+  K +L+ + GCEP++ + A ++ IS 
Sbjct: 235 LQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISS 294

Query: 253 PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS 312
           P L+S +     +REKL+ +N+RLV+ IA++Y N G +  DL+Q G +GL++ +EKF   
Sbjct: 295 PVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQ 354

Query: 313 KGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNA-KLRLEEKGVTPSVDR 371
            G + +TY YWWIRQ + +++ +NSRT+RLP +++  LG +  A K  ++E    PS + 
Sbjct: 355 SGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEE 414

Query: 372 IAEYLNMSQKKV 383
           +A ++ +S +K+
Sbjct: 415 LAGHVGVSTEKL 426

Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Regulates transcription in chloroplast in a DG1-dependent manner. Involved in light-dependent chloroplast development. Required during early plant development and primary leaf formation.

Arabidopsis thaliana (taxid: 3702)

>sp|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD1 PE=3 SV=2

 Score =  133 bits (335), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 75/196 (38%), Positives = 120/196 (61%), Gaps = 1/196 (0%)

Query: 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLR 249
           ++ ++ Y++ +    LL   E + L+++I   L+L+  +  L E+L   PS  + AA++ 
Sbjct: 88  EDSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVD 147

Query: 250 ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKF 309
               E +  L     A++K+V SN+RLV+SIA++Y N G    DL+Q G +GL+R  EKF
Sbjct: 148 SPLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKF 207

Query: 310 DSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLI-RNAKLRLEEKGVTPS 368
           D  KG+K STY  WWIRQ ++RA+ + SRT+RLP HL+E +  I +  KL  +E G  P+
Sbjct: 208 DHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPT 267

Query: 369 VDRIAEYLNMSQKKVR 384
            + IA  + M+ +K+R
Sbjct: 268 EEEIATRMEMTIEKLR 283

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	417
255566078	508	RNA polymerase sigma factor rpoD, putati	0.988	0.811	0.801	0.0
224146103	509	predicted protein [Populus trichocarpa]	0.990	0.811	0.777	0.0
449468291	508	PREDICTED: RNA polymerase sigma factor s	0.988	0.811	0.753	1e-177
356543070	503	PREDICTED: RNA polymerase sigma factor r	0.971	0.805	0.739	1e-174
356531599	503	PREDICTED: RNA polymerase sigma factor r	0.971	0.805	0.734	1e-173
224124068	499	predicted protein [Populus trichocarpa]	0.966	0.807	0.748	1e-166
2565297	502	RNA polymerase sigma subunit 1 [Arabidop	0.947	0.786	0.700	1e-164
15217767	502	sigma factor A [Arabidopsis thaliana] gi	0.947	0.786	0.698	1e-163
334183639	498	sigma factor A [Arabidopsis thaliana] gi	0.947	0.793	0.698	1e-163
11762220	502	At1g64860 [Arabidopsis thaliana]	0.947	0.786	0.695	1e-163

>gi|255566078|ref|XP_002524027.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223536754|gb|EEF38395.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]

 Score =  668 bits (1724), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 331/413 (80%), Positives = 367/413 (88%), Gaps = 1/413 (0%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGLSAGKRLLSS+FYYSD++EK S  N+ G  + Q+ STK ++ AKKSSNY PS
Sbjct: 1   MATAAVIGLSAGKRLLSSTFYYSDLTEKLSSANEHGLTHYQITSTKTLIVAKKSSNYGPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFA-STAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLE 120
           FPSSNR TQ IKALKEHVDT  A STA    +  N +EEESS+LDYSVEALLLLQKSMLE
Sbjct: 61  FPSSNRNTQSIKALKEHVDTASAPSTAATQFKTFNDMEEESSDLDYSVEALLLLQKSMLE 120

Query: 121 KQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQL 180
           KQWNLSFERT  +DSPS+K+ KK+PVTCSGVSARQRR+N ++K LSQ+K  +Q N  KQL
Sbjct: 121 KQWNLSFERTDSSDSPSRKSQKKIPVTCSGVSARQRRINIRRKNLSQSKFTVQANVFKQL 180

Query: 181 RSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPS 240
           +S +SPEL+QNRLKGYVKGVVSEELL+HAEVVRLS+ IK GLSL+DHK RLKERLGC+PS
Sbjct: 181 KSAVSPELLQNRLKGYVKGVVSEELLSHAEVVRLSRIIKAGLSLEDHKSRLKERLGCDPS 240

Query: 241 MEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLI 300
            EQ+A SL+ISR ELQS  + CSLAREKL MSNVRLVMSIAQRYDNMGA+MADLVQGGLI
Sbjct: 241 DEQVATSLKISRAELQSKSIACSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLI 300

Query: 301 GLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 360
           GLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAK+RL
Sbjct: 301 GLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKIRL 360

Query: 361 EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH 413
           EEKGVTPS+DRIAE LN+SQKKVRNATEA+ KVFSLDREAFPSLNGLPGETHH
Sbjct: 361 EEKGVTPSIDRIAESLNISQKKVRNATEAVSKVFSLDREAFPSLNGLPGETHH 413

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146103|ref|XP_002325882.1| predicted protein [Populus trichocarpa] gi|222862757|gb|EEF00264.1| predicted protein [Populus trichocarpa]

 Score =  652 bits (1681), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 322/414 (77%), Positives = 361/414 (87%), Gaps = 1/414 (0%)

Query: 1   MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNP 60
           MMATAAVIGLS+GKRLLSSSFYYSD++EK S +ND G       +TKNV+ AKKSSNY P
Sbjct: 1   MMATAAVIGLSSGKRLLSSSFYYSDLTEKLSNVNDHGITYYPTATTKNVIVAKKSSNYGP 60

Query: 61  SFPSSNRQTQPIKALKEHVDTNFAST-AEPWAEPPNSIEEESSELDYSVEALLLLQKSML 119
           SFPSSNR +  IKALKEHVDT  AS+    W +  +  EEESS LDYSVEALLLLQKSML
Sbjct: 61  SFPSSNRNSHSIKALKEHVDTASASSNVATWFKTFDDFEEESSALDYSVEALLLLQKSML 120

Query: 120 EKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQ 179
           EKQWNLSFERT  +DS SKK +KK+PVTCSGVSARQRR+N+++K  +Q+K + Q +  K 
Sbjct: 121 EKQWNLSFERTNSSDSTSKKNNKKIPVTCSGVSARQRRVNNRRKNQNQSKFMSQSSDFKF 180

Query: 180 LRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP 239
           LRS+ SP+L+QNRLKGYVKGVVS+E+L H EVVRLS+ I+ GLS +DHK RLKERLGCEP
Sbjct: 181 LRSVSSPDLLQNRLKGYVKGVVSDEVLPHTEVVRLSRIIRAGLSFEDHKSRLKERLGCEP 240

Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
           S EQ+A SLRISR +LQS L++CSLAREKL MSNVRLVMSIAQ+YDNMGA+MADLVQGGL
Sbjct: 241 SDEQIADSLRISRADLQSKLIQCSLAREKLAMSNVRLVMSIAQKYDNMGAEMADLVQGGL 300

Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR 359
           IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALV+NSRTLRLPNHLHERLGLIRNAK+R
Sbjct: 301 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVDNSRTLRLPNHLHERLGLIRNAKIR 360

Query: 360 LEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH 413
           LEEKGVTPS+DRIAE LNMSQ+KVRNATEAI KVFSLDREAFPSLNGLPGETHH
Sbjct: 361 LEEKGVTPSIDRIAESLNMSQRKVRNATEAISKVFSLDREAFPSLNGLPGETHH 414

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468291|ref|XP_004151855.1| PREDICTED: RNA polymerase sigma factor sigA-like [Cucumis sativus] gi|449514942|ref|XP_004164521.1| PREDICTED: RNA polymerase sigma factor sigA-like [Cucumis sativus]

 Score =  627 bits (1616), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 312/414 (75%), Positives = 359/414 (86%), Gaps = 2/414 (0%)

Query: 1   MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNP 60
           MMATAA+IGL A KRLL+SS YYSD +EK  Y ND     +QV S+K+VV AK S+N++P
Sbjct: 1   MMATAAIIGLGAAKRLLNSSSYYSDFTEKILYANDYRLGQTQVSSSKSVVIAKSSANFSP 60

Query: 61  SFPSSNRQTQP-IKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSML 119
            +PSSNR +Q  IKA+KEHV+T  +  AEPW     S E+E +EL Y+VEALLLLQKSML
Sbjct: 61  RYPSSNRHSQQCIKAVKEHVETPSSPIAEPWHNT-TSWEDEETELKYTVEALLLLQKSML 119

Query: 120 EKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQ 179
           EKQW+LSFE+TV TD+P +KT KKVPVTCSGVSARQRR++SK+KI S++  + Q   SKQ
Sbjct: 120 EKQWSLSFEQTVSTDTPKEKTLKKVPVTCSGVSARQRRMSSKRKIQSKHVFMAQPKISKQ 179

Query: 180 LRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP 239
           LR  ISPEL+QNRLKGYVKG++SEELL+HAEVVRLSKKIK GL+L++ K RLK+RLGCEP
Sbjct: 180 LRPTISPELLQNRLKGYVKGLLSEELLSHAEVVRLSKKIKVGLTLEERKTRLKQRLGCEP 239

Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
           S +QLA SL+ISR EL+S +ME SLAREKL MSNVRLVMSIAQRYDNMGA+MADLVQGGL
Sbjct: 240 SEDQLAISLKISRAELRSRMMESSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGL 299

Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR 359
           IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP HLHERLGLIRNAK++
Sbjct: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPTHLHERLGLIRNAKVK 359

Query: 360 LEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH 413
           L+EKG+TPS+DRIAE LNMS+KKV+NATEAI KVFSLDREAFPSLNGLPGETHH
Sbjct: 360 LQEKGITPSLDRIAESLNMSKKKVQNATEAISKVFSLDREAFPSLNGLPGETHH 413

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543070|ref|XP_003539986.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  619 bits (1595), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 307/415 (73%), Positives = 359/415 (86%), Gaps = 10/415 (2%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGLS GKRLLSSS++YSDI EK SY +D GS + Q+  TK+++ AKKSSNY P+
Sbjct: 1   MATAAVIGLSGGKRLLSSSYHYSDIIEKLSYGSDFGSTHYQIVPTKSLIVAKKSSNYTPT 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNS--IEEESSELDYSVEALLLLQKSML 119
           FP+SN+Q Q IKALKEHVD +  + A+PW +  NS  +E ESSE+ YSVEALLLLQKSML
Sbjct: 61  FPASNQQNQSIKALKEHVD-DAPTIADPWFQSYNSNDLEVESSEMGYSVEALLLLQKSML 119

Query: 120 EKQWNLSFERTVLTDSPSK-KTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSK 178
           EKQWNLSFER VLT++ SK K  +KV VTCSGVSARQRR+N+K+K      + ++  G+ 
Sbjct: 120 EKQWNLSFEREVLTENSSKGKKCRKVAVTCSGVSARQRRMNTKRK------TAIKTCGAM 173

Query: 179 QLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCE 238
           QL+S ISPEL+Q+RLKGYVKG+VSEELL+HAEVV LS+KIK GLSL++HK RLKE+LGCE
Sbjct: 174 QLKSKISPELLQHRLKGYVKGLVSEELLSHAEVVNLSEKIKVGLSLEEHKSRLKEKLGCE 233

Query: 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 298
           PS +Q+A SL+ISR EL++ ++ECSLAREKL MSNVRLVMSIAQ+YDN+GA+M DLVQGG
Sbjct: 234 PSDDQMATSLKISRTELRARMIECSLAREKLAMSNVRLVMSIAQKYDNLGAEMGDLVQGG 293

Query: 299 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKL 358
           LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP HLHERL LIRNAK 
Sbjct: 294 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPAHLHERLSLIRNAKF 353

Query: 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH 413
           RLEE+G+TP++DRIA+YLNMSQKKVRNATEAI K+ SLDREAFPSLNGL GETHH
Sbjct: 354 RLEERGITPTIDRIAKYLNMSQKKVRNATEAISKIISLDREAFPSLNGLQGETHH 408

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531599|ref|XP_003534364.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  615 bits (1586), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 305/415 (73%), Positives = 357/415 (86%), Gaps = 10/415 (2%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGLS GKRLLSSS++YSD+ EK SY +D GS + Q+  TK+++AAKKSSNY P+
Sbjct: 1   MATAAVIGLSGGKRLLSSSYHYSDVIEKLSYGSDFGSTHYQIVPTKSLIAAKKSSNYTPT 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNS--IEEESSELDYSVEALLLLQKSML 119
           FP+SN+Q Q IKALKEHVD +  + A+ W +  NS  +E ESSE+ YSVEALLLLQKSML
Sbjct: 61  FPASNQQNQSIKALKEHVD-DAPTIADSWFQSCNSNDLEVESSEMGYSVEALLLLQKSML 119

Query: 120 EKQWNLSFERTVLTDSPSK-KTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSK 178
           EKQWNLSFER VLT+  SK K  KKV VTCSGVSARQRR+N+K+K      + ++  G+ 
Sbjct: 120 EKQWNLSFEREVLTEHSSKGKKCKKVAVTCSGVSARQRRMNTKRK------TAIKTCGAM 173

Query: 179 QLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCE 238
           QL+S ISPEL+Q+RLKGYVKG+VSEELL+HAEVV LS++IK GLSL++HK RLKERLGCE
Sbjct: 174 QLKSKISPELLQHRLKGYVKGIVSEELLSHAEVVNLSERIKVGLSLEEHKSRLKERLGCE 233

Query: 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 298
           PS +Q+A SL+ISR EL++ ++EC+LAREKL MSNVRLVMSIAQ+YDN+GA+M DLVQGG
Sbjct: 234 PSDDQMAISLKISRTELRARMIECTLAREKLAMSNVRLVMSIAQKYDNLGAEMGDLVQGG 293

Query: 299 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKL 358
           LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP HLHERL LIRNAK 
Sbjct: 294 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPAHLHERLSLIRNAKF 353

Query: 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH 413
           RLEE+G+TP++DRIA+YLNMSQKKVRNATEAI K  SLDREAFPSLNG+ GETHH
Sbjct: 354 RLEERGITPTIDRIAKYLNMSQKKVRNATEAISKTISLDREAFPSLNGIQGETHH 408

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124068|ref|XP_002319237.1| predicted protein [Populus trichocarpa] gi|222857613|gb|EEE95160.1| predicted protein [Populus trichocarpa]

 Score =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 310/414 (74%), Positives = 346/414 (83%), Gaps = 11/414 (2%)

Query: 1   MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNP 60
           MMATA+ IGL+ GKRLLSSSFY+SD++EK S +ND G A+ Q+ +TK+V+ AKKSS Y P
Sbjct: 1   MMATASFIGLTTGKRLLSSSFYFSDLTEKLSNVNDHGVAHYQITTTKSVIVAKKSSKYGP 60

Query: 61  SFPSSNRQTQPIKALKEHVDTNFAS-TAEPWAEPPNSIEEESSELDYSVEALLLLQKSML 119
           SFPSS R     KALKE +DT  AS T   W +  +  EEESS LDYSVEAL+LLQKSML
Sbjct: 61  SFPSSYRNPHSNKALKELIDTASASSTVATWFKTLDDFEEESSVLDYSVEALILLQKSML 120

Query: 120 EKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQ 179
           EKQWNLSFE    +DS  KK++KK+PVTCSGVSARQRRLN+K+K          QN SK 
Sbjct: 121 EKQWNLSFESINSSDSKIKKSNKKIPVTCSGVSARQRRLNNKRK---------NQNQSKF 171

Query: 180 LRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP 239
           + S ISP L+ NRLKGYVKGVVS+E+L H EVVRLS+ I+ GLSL+DHK  LKERLGCEP
Sbjct: 172 M-SDISPGLLLNRLKGYVKGVVSDEVLPHTEVVRLSRIIRAGLSLEDHKSSLKERLGCEP 230

Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
           S EQLA SLRISR +LQS L++CSLAREKL MSNVRLVMSIAQ+ DNMGA+MADLVQ GL
Sbjct: 231 SDEQLADSLRISRADLQSQLIQCSLAREKLAMSNVRLVMSIAQKNDNMGAEMADLVQAGL 290

Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR 359
           IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN RTLRLPNHLHERLGLIRNAK+R
Sbjct: 291 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENPRTLRLPNHLHERLGLIRNAKIR 350

Query: 360 LEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH 413
           LEEKGVTPS+DRIAE LNMSQ+KVRNATEAI KVFSLDREAFPSLNGLPGETHH
Sbjct: 351 LEEKGVTPSIDRIAESLNMSQRKVRNATEAISKVFSLDREAFPSLNGLPGETHH 404

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2565297|gb|AAB81958.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]

 Score =  583 bits (1503), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 297/424 (70%), Positives = 344/424 (81%), Gaps = 29/424 (6%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYRPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVDV--ASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+HAEVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHAEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHH 413
           ETHH
Sbjct: 404 ETHH 407

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15217767|ref|NP_176666.1| sigma factor A [Arabidopsis thaliana] gi|75098242|sp|O24629.1|SIGA_ARATH RecName: Full=RNA polymerase sigma factor sigA; Short=Sigma factor A; Short=Sigma-A; AltName: Full=RNA polymerase sigma factor sig1; Short=Atsig1; Short=Sigma factor 1; AltName: Full=RNA polymerase sigma factor sig2; Short=Atsig2; Short=Sigma factor 2; AltName: Full=RNA polymerase sigma factor sigB; Short=Sigma factor B; Short=Sigma-B; Flags: Precursor gi|5042421|gb|AAD38260.1|AC006193_16 RNA polymerase sigma subunit 1 [Arabidopsis thaliana] gi|2353171|gb|AAB69384.1| sigma factor 1 [Arabidopsis thaliana] gi|2443408|dbj|BAA22421.1| SigA [Arabidopsis thaliana] gi|2558514|emb|CAA74640.1| plastid RNA polymerase sigma factor [Arabidopsis thaliana] gi|5478439|dbj|BAA82448.1| sigma factor SigA [Arabidopsis thaliana] gi|17064900|gb|AAL32604.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana] gi|20259916|gb|AAM13305.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana] gi|222423019|dbj|BAH19492.1| AT1G64860 [Arabidopsis thaliana] gi|332196177|gb|AEE34298.1| sigma factor A [Arabidopsis thaliana]

 Score =  582 bits (1500), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 296/424 (69%), Positives = 344/424 (81%), Gaps = 29/424 (6%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY+PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVDV--ASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHH 413
           ETHH
Sbjct: 404 ETHH 407

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334183639|ref|NP_001185314.1| sigma factor A [Arabidopsis thaliana] gi|332196178|gb|AEE34299.1| sigma factor A [Arabidopsis thaliana]

 Score =  581 bits (1498), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 296/424 (69%), Positives = 344/424 (81%), Gaps = 29/424 (6%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY+PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVD--VASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHH 413
           ETHH
Sbjct: 404 ETHH 407

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|11762220|gb|AAG40388.1|AF325036_1 At1g64860 [Arabidopsis thaliana]

 Score =  580 bits (1494), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 295/424 (69%), Positives = 344/424 (81%), Gaps = 29/424 (6%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY+PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVDV--ASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRY+N+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYNNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHH 413
           ETHH
Sbjct: 404 ETHH 407

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	417
TAIR|locus:2010871	502	SIGA "AT1G64860" [Arabidopsis	0.952	0.790	0.670	6.5e-138
UNIPROTKB|O48655	519	rsigA "Plastid RNA polymerase	0.968	0.778	0.496	1.6e-93
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.613	0.447	0.343	1e-32
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.458	0.349	0.364	3.7e-31
TAIR|locus:2173249	419	SIG4 "AT5G13730" [Arabidopsis	0.491	0.489	0.379	4.2e-30
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.467	0.369	0.354	2.2e-29
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.453	0.585	0.364	4.7e-29
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.472	0.341	0.352	5.3e-29
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.652	0.475	0.285	6.7e-29
TIGR_CMR|BA_4515	373	BA_4515 "RNA polymerase sigma-	0.618	0.691	0.288	5.2e-28

TAIR|locus:2010871 SIGA "AT1G64860" [Arabidopsis thaliana (taxid:3702)]

 Score = 1350 (480.3 bits), Expect = 6.5e-138, P = 6.5e-138
 Identities = 283/422 (67%), Positives = 327/422 (77%)

Query:     2 MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKXXXXXXX 61
             MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK       
Sbjct:     1 MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query:    62 XXXXXRQTQPIKALKEHVDTNFASTAEPWA------EPPNXXXXXXXXLDYSVEALLLLQ 115
                  R TQ  KALKE VD   AST +PW       E           + +SVEA+LLLQ
Sbjct:    61 FPSSNRHTQSAKALKESVDV--ASTEKPWLPNGTDKELEEECYDDDDLISHSVEAILLLQ 118

Query:   116 KSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNKSI 171
             KSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K++
Sbjct:   119 KSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVKAV 178

Query:   172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
                +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK RL
Sbjct:   179 SDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKSRL 225

Query:   232 KERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 291
             K+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA+M
Sbjct:   226 KDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEM 285

Query:   292 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351
             +DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHERLG
Sbjct:   286 SDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLG 345

Query:   352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGET 411
             LIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPGET
Sbjct:   346 LIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPGET 405

Query:   412 HH 413
             HH
Sbjct:   406 HH 407

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS;IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0071482 "cellular response to light stimulus" evidence=IEP

GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP

GO:0071461 "cellular response to redox state" evidence=IDA

GO:0080005 "photosystem stoichiometry adjustment" evidence=IDA

GO:0006833 "water transport" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0009750 "response to fructose stimulus" evidence=RCA

GO:0016987 "sigma factor activity" evidence=ISS

UNIPROTKB|O48655 rsigA "Plastid RNA polymerase sigma factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 931 (332.8 bits), Expect = 1.6e-93, P = 1.6e-93
 Identities = 215/433 (49%), Positives = 278/433 (64%)

Query:     1 MMATAAVIGLSAGKRLLSSSFYYSDIS-EKFSYI---NDLGSANSQVGSTKNVVAAKKXX 56
             M AT AVIGLSAG RLLS+SF  +D+  +K S        G      G   +  AA    
Sbjct:     1 MTATPAVIGLSAGNRLLSASFGPTDLMPDKVSLGVGGGGGGGGGGGGGDAMSFAAAPATP 60

Query:    57 XXXXXXXXXXR-----QTQPIKALKEHVDTNFASTAEPWAEPPNX-----XXXXXXXLDY 106
                       +     + Q ++AL+ H     A    P   PP              L+ 
Sbjct:    61 KLTAVAAHRLKLSPHGRAQVMRALRHHSSAAAALAPPPPPPPPPTPSPASRAAHAHDLES 120

Query:   107 SVEALLLLQKSMLEKQWNLSFE------RTVLTDSPSKKTHKKVPVTCSGVSARQRRLNS 160
             S+EA++LLQ+SMLEKQW L F+         L +     +   V V  S VSARQRR++ 
Sbjct:   121 SLEAIVLLQRSMLEKQWELPFDDDNHAMAIGLAEDDDDTSKATVVVARSSVSARQRRMSG 180

Query:   161 KKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKT 220
             +++   + K     NG+      +SPELIQ+R + Y++G VS+ELLTH +VV LS KIK 
Sbjct:   181 RRR--GRTK-----NGAAHFA--VSPELIQSRNRIYLRGTVSKELLTHKQVVHLSHKIKD 231

Query:   221 GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280
             G+ L   + +LKE+LG EPS +QLA SL+IS PEL+S + E  LARE L MSN+RLV+SI
Sbjct:   232 GIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPELRSRMHESFLAREMLTMSNLRLVISI 291

Query:   281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340
             AQ+YDN+G ++ADL+QGGLIGLLRGIEKFD+S+GF+ISTYVYWWIRQGVSRAL ENS+T 
Sbjct:   292 AQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQGVSRALAENSKTF 351

Query:   341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREA 400
             RLP +LHERL  IR AK  LE++G+ P+++ IA  LN+S+KKV NATEA+ KV SLD++A
Sbjct:   352 RLPTYLHERLIAIRGAKYELEDQGIAPTIENIAGSLNISEKKVLNATEAVNKVLSLDQQA 411

Query:   401 FPSLNGLPGETHH 413
             FPSLNGLPGET H
Sbjct:   412 FPSLNGLPGETLH 424

GO:0009416 "response to light stimulus" evidence=IEP

TAIR|locus:2025650 SIG2 "AT1G08540" [Arabidopsis thaliana (taxid:3702)]

 Score = 361 (132.1 bits), Expect = 1.0e-32, P = 1.0e-32
 Identities = 89/259 (34%), Positives = 144/259 (55%)

Query:   154 RQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSE-ELLTHAEVV 212
             + RR    +K  S   S+   +  K+ R +++ E+  N    Y++   S  +LLT  E  
Sbjct:   221 KARRAKGLEKTASGIPSVKTGSSPKKKR-LVAQEVDHNDPLRYLRMTTSSSKLLTVREEH 279

Query:   213 RLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMS 272
              LS  I+  L L+  +  L ER G +P+  Q A++  + +  L+  +   +L ++K++ S
Sbjct:   280 ELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKS 339

Query:   273 NVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRA 332
             N+RLV+SIA+ Y   G ++ DLVQ G  GL+RG EKFD++KGFK STY +WWI+Q V ++
Sbjct:   340 NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKS 399

Query:   333 LVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391
             L + SR +RLP H+ E    ++ A+ +L  E G  P  + IAE   +S K++     +  
Sbjct:   400 LSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPK 459

Query:   392 KVFSLDREAFPSLNGLPGE 410
                SLD++   + N  P E
Sbjct:   460 PPRSLDQKIGMNQNLKPSE 478

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0071482 "cellular response to light stimulus" evidence=IEP;IMP

GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA;TAS

GO:0009658 "chloroplast organization" evidence=IMP

GO:0006399 "tRNA metabolic process" evidence=IMP

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP

GO:0009637 "response to blue light" evidence=IGI;RCA

GO:0010114 "response to red light" evidence=IEP;RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0016987 "sigma factor activity" evidence=ISS

TAIR|locus:2057996 SIGF "AT2G36990" [Arabidopsis thaliana (taxid:3702)]

 Score = 346 (126.9 bits), Expect = 3.7e-31, P = 3.7e-31
 Identities = 70/192 (36%), Positives = 122/192 (63%)

Query:   193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISR 252
             L+ ++ G  +++LLT  E   L   I+  L L+  K +L+ + GCEP++ + A ++ IS 
Sbjct:   235 LQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISS 294

Query:   253 PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS 312
             P L+S +     +REKL+ +N+RLV+ IA++Y N G +  DL+Q G +GL++ +EKF   
Sbjct:   295 PVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQ 354

Query:   313 KGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNA-KLRLEEKGVTPSVDR 371
              G + +TY YWWIRQ + +++ +NSRT+RLP +++  LG +  A K  ++E    PS + 
Sbjct:   355 SGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEE 414

Query:   372 IAEYLNMSQKKV 383
             +A ++ +S +K+
Sbjct:   415 LAGHVGVSTEKL 426

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0006352 "DNA-dependent transcription, initiation" evidence=TAS

GO:0009507 "chloroplast" evidence=IDA

GO:0009536 "plastid" evidence=IDA

GO:0016987 "sigma factor activity" evidence=ISS;IDA

GO:0071483 "cellular response to blue light" evidence=IEP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA;IMP

GO:0071482 "cellular response to light stimulus" evidence=IMP

GO:0090351 "seedling development" evidence=IMP

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

TAIR|locus:2173249 SIG4 "AT5G13730" [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 4.2e-30, Sum P(2) = 4.2e-30
 Identities = 80/211 (37%), Positives = 109/211 (51%)

Query:   197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQ 256
             V G      L+  E V+L   +K G  L++    ++E    E     LA+     +    
Sbjct:   114 VVGASRSGFLSRLEEVQLCLYLKEGAKLENLGTSVEEN---EMVSVLLASGRGKKKRSAN 170

Query:   257 SILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFK 316
              IL     AREK+     RLV+SIA  Y   G ++ DL+Q G IGLLRG E+FD  +G+K
Sbjct:   171 EILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYK 230

Query:   317 ISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEY 375
             +STYVYWWI+Q + RA+   SR ++LP  + E    +  A   L  K    PS + IAE+
Sbjct:   231 LSTYVYWWIKQAILRAIAHKSRLVKLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEH 290

Query:   376 LNMSQKKVRNATEAIGKVFSLDREAFPSLNG 406
             LN++   VR A E      SLDR A  S NG
Sbjct:   291 LNLNVSAVRLAVERSRSPVSLDRVA--SQNG 319

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0006352 "DNA-dependent transcription, initiation" evidence=TAS

GO:0016987 "sigma factor activity" evidence=ISS

GO:0071482 "cellular response to light stimulus" evidence=IEP

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP

GO:0000023 "maltose metabolic process" evidence=RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0016556 "mRNA modification" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

UNIPROTKB|P0A602 rpoD "RNA polymerase sigma factor RpoD" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 307 (113.1 bits), Expect = 2.2e-29, Sum P(2) = 2.2e-29
 Identities = 74/209 (35%), Positives = 124/209 (59%)

Query:   193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISR 252
             ++ Y+K +    LL   E V L+K+I+ GL        L ER G     E+L A+    R
Sbjct:   228 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSER-G-----EKLPAA---QR 278

Query:   253 PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS 312
              ++  I  +   A+  L+ +N+RLV+S+A+RY   G    DL+Q G +GL+R +EKFD +
Sbjct:   279 RDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYT 338

Query:   313 KGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE---RLGLIRNAKLRLEEKGVTPSV 369
             KG+K STY  WWIRQ ++RA+ + +RT+R+P H+ E   +LG I+  +L L++ G  P+ 
Sbjct:   339 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQR-EL-LQDLGREPTP 396

Query:   370 DRIAEYLNMSQKKVRNATEAIGKVFSLDR 398
             + +A+ ++++ +KV    +   +  SLD+
Sbjct:   397 EELAKEMDITPEKVLEIQQYAREPISLDQ 425

GO:0003677 "DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005618 "cell wall" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009405 "pathogenesis" evidence=IMP

GO:0009415 "response to water stimulus" evidence=IEP

GO:0016987 "sigma factor activity" evidence=IDA

GO:0040007 "growth" evidence=IMP

GO:0052572 "response to host immune response" evidence=IEP

UNIPROTKB|Q59563 mysB "RNA polymerase sigma factor" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 301 (111.0 bits), Expect = 4.7e-29, Sum P(2) = 4.7e-29
 Identities = 74/203 (36%), Positives = 112/203 (55%)

Query:   196 YVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPEL 255
             Y+ G+    LL  A  V L+K+I+ GL  + H L  ++RLG E     LAA +R      
Sbjct:    30 YLNGIGKTALLNAAGEVELAKRIEAGLYAE-HLLETRKRLG-ENRKRDLAAVVR------ 81

Query:   256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGF 315
                  +   AR  L+ +N+RLV+S+A+RY   G  + DL+Q G +GL+R +EKFD +KGF
Sbjct:    82 -----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGF 136

Query:   316 KISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAE 374
             K STY  WWIRQ ++R + + SRT+RLP HL E++  +   K  + +  G   + + +A 
Sbjct:   137 KFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDEELAA 196

Query:   375 YLNMSQKKVRNATEAIGKVFSLD 397
                +   K+ +  E      SLD
Sbjct:   197 ESGIPIDKINDLLEHSRDPVSLD 219

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

GO:0009410 "response to xenobiotic stimulus" evidence=IEP

GO:0016987 "sigma factor activity" evidence=IGI

GO:0019217 "regulation of fatty acid metabolic process" evidence=IDA

GO:0040007 "growth" evidence=IMP

GO:0043175 "RNA polymerase core enzyme binding" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0050708 "regulation of protein secretion" evidence=IDA

TIGR_CMR|GSU_3089 GSU_3089 "RNA polymerase sigma factor RpoD" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 312 (114.9 bits), Expect = 5.3e-29, Sum P(2) = 5.3e-29
 Identities = 73/207 (35%), Positives = 118/207 (57%)

Query:   199 GVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258
             GV ++ L   A    + K IK  LSL+D +   K+    E  ++++         EL   
Sbjct:   269 GVSADTLKEIAASEAVGKGIK--LSLEDAQKHEKKVRSAEKKLKKVEEESGFKARELSDA 326

Query:   259 LM-------ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDS 311
             L        +  LA+ +LV +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+ 
Sbjct:   327 LRAIDRGEAKSKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 386

Query:   312 SKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVD 370
              +G+K STY  WWIRQ ++RA+ + +RT+R+P H+ E +  LIR ++  ++E G  PS +
Sbjct:   387 QRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPE 446

Query:   371 RIAEYLNMSQKKVRNATEAIGKVFSLD 397
              IAE +N+   KVR   +   +  SL+
Sbjct:   447 EIAERMNLPLDKVRKVLKIAKEPISLE 473

GO:0006352 "DNA-dependent transcription, initiation" evidence=ISS

GO:0016987 "sigma factor activity" evidence=ISS

UNIPROTKB|Q84LK8 SIG6 "Sig6" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 309 (113.8 bits), Expect = 6.7e-29, Sum P(2) = 6.7e-29
 Identities = 80/280 (28%), Positives = 145/280 (51%)

Query:   110 ALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQ-- 167
             ALL  +  +L  Q   S   +V +   +++   K  V        +RR  SK++   +  
Sbjct:   174 ALLAEETDILATQLKASQLYSVDSSKSNEELQSKGQVFVRSTRLLERR--SKRRYAPRAS 231

Query:   168 --NKSILQQNGSKQLRSMISPELIQ--NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223
               + S    N  K+ +S     +++     K +++   + E LT  E   L  KI+  + 
Sbjct:   232 IADVSCSADNSKKKEKSKKYGRVLEPDEPFKLFLRDRETTEFLTAKEERHLFSKIQILMK 291

Query:   224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283
             +++   +L+ + G EP++ + A ++ +S  ELQS +      REK+  SN RLV+ +A++
Sbjct:   292 IEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARK 351

Query:   284 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343
             Y+  G D+ DLVQ G  GL++  EKF+ SKG +  TY YWWIRQ + +++ +NSR +RLP
Sbjct:   352 YEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLP 411

Query:   344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
               ++  L  +  A++    +G  P+   +A    ++ +K+
Sbjct:   412 ESVYALLRKVGKARMECIMEGEQPTNANVARRAGITIEKL 451

GO:0009536 "plastid" evidence=RCA

TIGR_CMR|BA_4515 BA_4515 "RNA polymerase sigma-43 factor" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 290 (107.1 bits), Expect = 5.2e-28, Sum P(2) = 5.2e-28
 Identities = 80/277 (28%), Positives = 145/277 (52%)

Query:   132 LTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISP--ELI 189
             + D P++    +  +T   V  +   L  K+ +L+  +   + NG +     +    E +
Sbjct:     1 MADKPARSKQIETEMTLEQVKEQLTELGKKRGVLTYEEIAERMNGFEIESDQMDEYYEYL 60

Query:   190 QNR---LKG-YVKGVVSEELLTHAEVVRLSK-KIKTGLSLDDH-KLRLKE--RLGCEPSM 241
               +   L G   +G  + ++    E   L+   +  G+ ++D  ++ LKE  R+    + 
Sbjct:    61 GEQGIDLVGDNDEGPNNHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVDLLSAE 120

Query:   242 EQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIG 301
             E++  + RI   + +        A+ +L  +N+RLV+SIA+RY   G    DL+Q G +G
Sbjct:   121 EEIRLATRIEEGDEE--------AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMG 172

Query:   302 LLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRL 360
             L++ +EKFD  KGFK STY  WWIRQ ++RA+ + +RT+R+P H+ E +  LIR  +  L
Sbjct:   173 LIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLL 232

Query:   361 EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD 397
             ++ G  PS + I E ++++ +KVR   +   +  SL+
Sbjct:   233 QDLGREPSPEEIGEEMDLAPEKVREILKIAQEPVSLE 269

GO:0006352 "DNA-dependent transcription, initiation" evidence=ISS

GO:0016987 "sigma factor activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O24629	SIGA_ARATH	No assigned EC number	0.6981	0.9472	0.7868	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	417
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	2e-60
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	5e-50
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	3e-44
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	3e-41
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	6e-41
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	3e-39
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	1e-36
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	4e-35
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	6e-33
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	7e-31
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	4e-30
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	5e-29
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	3e-23
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	2e-20
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	8e-19
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	2e-16
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	2e-16
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	1e-15
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	1e-15
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	6e-15
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	3e-14
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	4e-13
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	5e-12
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	1e-11
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	8e-11
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	2e-10
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	7e-10
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	1e-09
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	1e-09
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	1e-08
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	2e-08
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	3e-08
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	1e-07
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	3e-07
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	9e-05
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	9e-05
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	3e-04
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	0.003
PRK08295	208	PRK08295, PRK08295, RNA polymerase factor sigma-70	0.004

>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor, cyanobacterial RpoD-like family

 Score =  198 bits (505), Expect = 2e-60
 Identities = 81/195 (41%), Positives = 130/195 (66%), Gaps = 1/195 (0%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LLT  E + L+++++  + L++ +  L+E+LG EPS E+ AA+  +S  EL+  L +   
Sbjct: 15  LLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQR 74

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+EK++ +N+RLV+S+A++Y N G ++ DL+Q G +GL R +EKFD ++G+K STY YWW
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWW 134

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKV 383
           IRQG++RA+   SRT+RLP H+ E+L  I+  +  L ++ G TPS   IAE L +  ++V
Sbjct: 135 IRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQV 194

Query: 384 RNATEAIGKVFSLDR 398
           R   +   +  SLD 
Sbjct: 195 RELLQRARQPVSLDA 209

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

>gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated

 Score =  171 bits (435), Expect = 5e-50
 Identities = 79/194 (40%), Positives = 127/194 (65%), Gaps = 1/194 (0%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LLTH E +   K+++  ++L + +  L E LG EP+  + A + ++S  EL+S + E   
Sbjct: 22  LLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEA 81

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+ K+V +N+RLV+S+A++Y     D+ DL+Q G IG+ RG+EKFD +KG++ STY YWW
Sbjct: 82  AKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 141

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ E SRT+RLP H+ E+L  I+ A+ +L ++ G   ++  +AE L ++ K+V
Sbjct: 142 IRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQV 201

Query: 384 RNATEAIGKVFSLD 397
           R   E   +  SLD
Sbjct: 202 REYLERARQPLSLD 215

Length = 317

>gnl|CDD|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated

 Score =  157 bits (399), Expect = 3e-44
 Identities = 76/181 (41%), Positives = 116/181 (64%), Gaps = 1/181 (0%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LL   E + L++KI   L L++ + + +  LG EPS ++ A  + +  P+ +  LM    
Sbjct: 77  LLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRR 136

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+EK+V SN+RLV+SIA++Y N G    DL+Q G +GL+R  EKFD  KG+K STY  WW
Sbjct: 137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 196

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNA-KLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + SRT+RLP HL+E +  I+   K+  +E G  P+ + IAE + M+ +K+
Sbjct: 197 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 256

Query: 384 R 384
           R
Sbjct: 257 R 257

Length = 373

>gnl|CDD|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated

 Score =  148 bits (375), Expect = 3e-41
 Identities = 72/194 (37%), Positives = 123/194 (63%), Gaps = 1/194 (0%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LLTH + +   K+++  +SL + K  L ++LG EPS+ + A ++ +S  EL+  L +   
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++K++ +N+RLV++IA++Y     +  DL+Q G +GL RG+EKFD ++G+K STY YWW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+RLP H+ E+L  I+  +  L +K G + +   IA+ L +   ++
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQI 211

Query: 384 RNATEAIGKVFSLD 397
           R       +  SLD
Sbjct: 212 REYLSMARQPISLD 225

Length = 327

>gnl|CDD|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated

 Score =  149 bits (378), Expect = 6e-41
 Identities = 77/203 (37%), Positives = 121/203 (59%), Gaps = 23/203 (11%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRIS----RP------- 253
           ++         + IK  L L + + RL   LG  PS+E+ A +  IS    +P       
Sbjct: 94  IVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTLAEGKR 153

Query: 254 -----------ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGL 302
                      EL+ I  +   A+E ++ +N+RLV+S+A++Y N G ++ DLVQ G +GL
Sbjct: 154 RWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGL 213

Query: 303 LRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-E 361
            R +EKFD +KG++ STY YWWIRQG++RA+   SRT+RLP H+ E+L  I+ A+ ++ +
Sbjct: 214 ERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQ 273

Query: 362 EKGVTPSVDRIAEYLNMSQKKVR 384
           EKG TP+++ IA+ L M+  +VR
Sbjct: 274 EKGRTPTIEDIAQELEMTPTQVR 296

Length = 415

>gnl|CDD|213709 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal domain

 Score =  140 bits (355), Expect = 3e-39
 Identities = 57/134 (42%), Positives = 89/134 (66%), Gaps = 1/134 (0%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+++LV SN+RLV+SIA++Y N G    DL+Q G IGL++ +EKFD  KG+K STY  WW
Sbjct: 1   AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWW 60

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+R+P H+ E +  LI+  +   +E G  P+ + +AE + M  +KV
Sbjct: 61  IRQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKV 120

Query: 384 RNATEAIGKVFSLD 397
           R   +   +  SL+
Sbjct: 121 REIKKIAQEPISLE 134

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 [Transcription, Transcription factors]. Length = 238

>gnl|CDD|223642 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]

 Score =  136 bits (345), Expect = 1e-36
 Identities = 77/220 (35%), Positives = 118/220 (53%), Gaps = 21/220 (9%)

Query: 186 PELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSMEQL 244
             L  + ++ Y+  +    LL     V L+K+++    L +    L + +LG EPS    
Sbjct: 4   VRLSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERAR 63

Query: 245 AASLRISR--PELQSILM-----ECSL------------AREKLVMSNVRLVMSIAQRYD 285
             + R+S     +++  +     E +L            A++KLV SN+RLV+SIA++Y 
Sbjct: 64  RPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYT 123

Query: 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345
             G    DL+Q G IGL++ +EKFD  KGFK STY  WWIRQ ++RA+ + +RT+R+P H
Sbjct: 124 GRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 183

Query: 346 LHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVR 384
             E +  +R  K  L  E G  P+ + IAE L +S  KVR
Sbjct: 184 QVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVR 223

Length = 342

>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed

 Score =  131 bits (332), Expect = 4e-35
 Identities = 68/189 (35%), Positives = 112/189 (59%), Gaps = 14/189 (7%)

Query: 196 YVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPEL 255
           Y+ G+    LLT A+ V L+K+I+ GL   +H L  ++RL                + +L
Sbjct: 31  YLNGIGKTALLTAADEVELAKRIEAGL-YAEHLLETRKRLS------------EARKRDL 77

Query: 256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGF 315
            +++ +   AR  L+ +N+RLV+S+A+RY   G  + DL+Q G +GL+R +EKFD +KGF
Sbjct: 78  AAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGF 137

Query: 316 KISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAE 374
           K STY  WWIRQ ++R + + SRT+RLP HL E++  +   K  L ++ G   + + +AE
Sbjct: 138 KFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAE 197

Query: 375 YLNMSQKKV 383
              + ++K+
Sbjct: 198 ESGIPEEKI 206

Length = 324

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score =  129 bits (326), Expect = 6e-33
 Identities = 72/198 (36%), Positives = 113/198 (57%), Gaps = 22/198 (11%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LL   E V L+K+I+ GL  ++    L E    +P +          R +LQ I  +   
Sbjct: 225 LLNAEEEVELAKRIEAGLYAEE---LLAEGEKLDPEL----------RRDLQWIGRDGKR 271

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+  L+ +N+RLV+S+A+RY N G    DL+Q G +GL++ +EKFD +KG+K STY  WW
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 331

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+R+P H+ E +  L R  +  L+E G  P+ + +A+ +  + +KV
Sbjct: 332 IRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKV 391

Query: 384 RN----ATEAIGKVFSLD 397
           R       E I    SLD
Sbjct: 392 REIQKYNREPI----SLD 405

Length = 509

>gnl|CDD|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated

 Score =  121 bits (305), Expect = 7e-31
 Identities = 56/121 (46%), Positives = 84/121 (69%), Gaps = 1/121 (0%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+++L  +N+RLV+SIA+RY   G    DL+Q G +GL++ +EKFD  KGFK STY  WW
Sbjct: 130 AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 189

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+R+P H+ E +  LIR  +  L+E G  P+ + IAE ++M  +KV
Sbjct: 190 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKV 249

Query: 384 R 384
           R
Sbjct: 250 R 250

Length = 367

>gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS

 Score =  117 bits (294), Expect = 4e-30
 Identities = 67/188 (35%), Positives = 106/188 (56%), Gaps = 13/188 (6%)

Query: 214 LSKKIKTGLSLDDHKLRLKERLGCEPSM---EQLAASLRISRPELQSILMECSLAREKLV 270
             K        D  +L L+E +G +P +   E++A + R    + +        AR+ ++
Sbjct: 2   FKKAETETRVADVTQLYLRE-IGFKPLLTAEEEIAYARRALAGDFE--------ARKVMI 52

Query: 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVS 330
            SN+RLV+SIA+ Y N G  + DL++ G +GL+  +EKFD  +GF+ STY  WWIRQ + 
Sbjct: 53  ESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIE 112

Query: 331 RALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKVRNATEA 389
           RA++  +RT+RLP H+ + L +   A  +LE+K G  PSV+ IAE L+   + V      
Sbjct: 113 RAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLAL 172

Query: 390 IGKVFSLD 397
             ++ SLD
Sbjct: 173 NERITSLD 180

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) [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]. Length = 285

>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score =  115 bits (290), Expect = 5e-29
 Identities = 53/121 (43%), Positives = 78/121 (64%), Gaps = 1/121 (0%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AR++++ SN+RLV+ IA+RY N G  + DL++ G +GL+R +EKFD  +GF+ STY  WW
Sbjct: 87  ARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 146

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           IRQ + RA++  +RT+RLP H+ + L +   A   LE K    PS + IAE L+     V
Sbjct: 147 IRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDV 206

Query: 384 R 384
            
Sbjct: 207 S 207

Length = 325

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score =  101 bits (255), Expect = 3e-23
 Identities = 63/203 (31%), Positives = 113/203 (55%), Gaps = 31/203 (15%)

Query: 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIK-----TGLSLDDHKLRLKERLGCEPSMEQ 243
                K + + +V        E+ +L ++++     TGL++++    LKE         Q
Sbjct: 325 EIASGKPWSEFLVRVY----DEIKKLQQELEAIEEETGLTIEE----LKEIN------RQ 370

Query: 244 LAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL 303
           ++     +R            A++++V +N+RLV+SIA++Y N G    DL+Q G IGL+
Sbjct: 371 ISKGEAKAR-----------RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 419

Query: 304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEE 362
           + ++KF+  +G+K STY  WWIRQ ++R++ + +RT+R+P H+ E +  L R ++  L+E
Sbjct: 420 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQE 479

Query: 363 KGVTPSVDRIAEYLNMSQKKVRN 385
            G  P+ + +AE L M + KVR 
Sbjct: 480 IGREPTPEELAERLGMPEDKVRK 502

Length = 619

>gnl|CDD|234078 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

 Score = 89.2 bits (222), Expect = 2e-20
 Identities = 51/126 (40%), Positives = 74/126 (58%), Gaps = 1/126 (0%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AREKLV  N+ LV SIA+R+ N G    DLVQ G IGL++ I++FD S G K ST+    
Sbjct: 4   AREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPT 63

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           I   + R   +++  +R+P  L E    I  A   L ++ G +P++  IAE L +S+++V
Sbjct: 64  IMGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEV 123

Query: 384 RNATEA 389
             A EA
Sbjct: 124 VEALEA 129

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

>gnl|CDD|218138 pfam04542, Sigma70_r2, Sigma-70 region 2

 Score = 79.9 bits (198), Expect = 8e-19
 Identities = 33/71 (46%), Positives = 44/71 (61%)

Query: 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQG 328
           LV   + LV S+A+RY   GAD  DLVQ G +GLLR +E+FD  +G   ST++Y  IR  
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 329 VSRALVENSRT 339
           +  AL +  RT
Sbjct: 61  IIDALRKQRRT 71

Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation. Length = 71

>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed

 Score = 78.5 bits (194), Expect = 2e-16
 Identities = 53/139 (38%), Positives = 77/139 (55%), Gaps = 14/139 (10%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AREKL+  N+RLV+S+ QR++N G ++ DL Q G IGL++ I+ FD S+  K STY    
Sbjct: 38  AREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPM 97

Query: 325 IRQGVSRALVEN-----SRTLRLPNH--LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLN 377
           I   + R L +N     SR+LR   +  L  R  LI        E    P+V+ IA+ L 
Sbjct: 98  IIGEIRRYLRDNNPIRVSRSLRDIAYKALQVREKLIN-------ENSKEPTVEEIAKELE 150

Query: 378 MSQKKVRNATEAIGKVFSL 396
           + +++V  A +AI    SL
Sbjct: 151 VPREEVVFALDAIQDPVSL 169

Length = 258

>gnl|CDD|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated

 Score = 77.7 bits (192), Expect = 2e-16
 Identities = 51/133 (38%), Positives = 73/133 (54%), Gaps = 14/133 (10%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AR+ LV  N+RLV S+ QR+ N G +  DL Q G IGLL+ ++KFD S   K STY    
Sbjct: 33  ARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPM 92

Query: 325 IRQGVSRAL-----VENSRTLR-LPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLN 377
           I   + R L     V+ SR+L+   N        IR  K  L ++ G  P+++ +AEYL 
Sbjct: 93  IIGEIQRFLRDDGTVKVSRSLKETANK-------IRKDKDELSKELGREPTIEELAEYLG 145

Query: 378 MSQKKVRNATEAI 390
           ++ ++V  A EA 
Sbjct: 146 VTPEEVVLAQEAS 158

Length = 252

>gnl|CDD|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor

 Score = 75.5 bits (186), Expect = 1e-15
 Identities = 46/126 (36%), Positives = 72/126 (57%), Gaps = 2/126 (1%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AR+KL+  N+RLV SI +R+ N G +  DL Q G IGL++ I+KFD S   K STY    
Sbjct: 12  ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPM 71

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           I   + R L ++   +++   L E    IR  K  L ++ G  P+++ +AE L +S +++
Sbjct: 72  IMGEIKRFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEI 130

Query: 384 RNATEA 389
             A E+
Sbjct: 131 VMALES 136

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 [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 231

>gnl|CDD|224112 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription]

 Score = 75.8 bits (187), Expect = 1e-15
 Identities = 48/134 (35%), Positives = 76/134 (56%), Gaps = 5/134 (3%)

Query: 268 KLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR 326
           +L+   + LV SIA++++N   ++  DL+Q G+IGL++ IE++D SKG K STY    IR
Sbjct: 27  RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIR 86

Query: 327 QGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRN 385
             +   L +N  ++++P  L E    I  A   LE E G  P+ + IAE L + +++   
Sbjct: 87  GEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIE 145

Query: 386 ATEAIGK--VFSLD 397
           A  AI    + SLD
Sbjct: 146 ALLAINGSQLLSLD 159

Length = 247

>gnl|CDD|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor

 Score = 73.7 bits (181), Expect = 6e-15
 Identities = 55/140 (39%), Positives = 77/140 (55%), Gaps = 16/140 (11%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AREKL+  N+RLV+S+ QR++N G  + DL Q G IGL++ I+ FD S+  K STY    
Sbjct: 35  AREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 94

Query: 325 IRQGVSRALVEN-----SRTLRLPNH--LHERLGLI-RNAKLRLEEKGVTPSVDRIAEYL 376
           I   + R L +N     SR+LR   +  L  R  LI  N+K         P+V  IA+ L
Sbjct: 95  IIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRDKLISENSK--------EPTVSEIAKEL 146

Query: 377 NMSQKKVRNATEAIGKVFSL 396
            + Q++V  A +AI    SL
Sbjct: 147 KVPQEEVVFALDAIQDPVSL 166

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 [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 254

>gnl|CDD|236033 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed

 Score = 72.4 bits (178), Expect = 3e-14
 Identities = 23/62 (37%), Positives = 39/62 (62%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A  +++ +++RLV+S+A ++   G  M DL+Q G +GLL    +F+  +  + STY  WW
Sbjct: 41  ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWW 100

Query: 325 IR 326
           IR
Sbjct: 101 IR 102

Length = 289

>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH

 Score = 68.8 bits (169), Expect = 4e-13
 Identities = 41/124 (33%), Positives = 74/124 (59%), Gaps = 6/124 (4%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A +KLV+S++R V+ IA+ Y   G   ADL+Q G IGL++ +++FD  +G ++ ++   W
Sbjct: 36  AAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHW 95

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGL---IRNAKLRLEEKGVTPS-VDRIAEYLNMSQ 380
           I+  +   ++ N R +++     +R  L   +R  K RL +  + P  V+ IAE L +S+
Sbjct: 96  IKAEIHEYILRNWRLVKVATTKAQR-KLFFNLRKMKKRL-QGWLNPEEVEAIAEELGVSE 153

Query: 381 KKVR 384
           ++VR
Sbjct: 154 REVR 157

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 [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]. Length = 270

>gnl|CDD|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed

 Score = 66.0 bits (162), Expect = 5e-12
 Identities = 23/62 (37%), Positives = 41/62 (66%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A ++LV+S++R V+ IA+ Y   G   ADL+Q G IGL++ +++FD   G ++ ++   W
Sbjct: 49  AAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHW 108

Query: 325 IR 326
           I+
Sbjct: 109 IK 110

Length = 284

>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed

 Score = 64.2 bits (157), Expect = 1e-11
 Identities = 26/59 (44%), Positives = 39/59 (66%)

Query: 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
              AR  L+  N+RLV  I ++++N G D+ DL+  G IGL++ IE FD+ KG K++TY
Sbjct: 47  DEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATY 105

Length = 233

>gnl|CDD|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor

 Score = 61.3 bits (149), Expect = 8e-11
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
            AR  L+  N+RLV  I +++ N G D+ DL+  G IGL++ I+ FD  KG +++TY
Sbjct: 48  EARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATY 104

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 [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 227

>gnl|CDD|131987 TIGR02941, Sigma_B, RNA polymerase sigma-B factor

 Score = 60.7 bits (147), Expect = 2e-10
 Identities = 41/141 (29%), Positives = 68/141 (48%), Gaps = 3/141 (2%)

Query: 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           +   A+EKLV     LV SIA +Y   G    DLVQ G++GLL  I ++D S G     +
Sbjct: 26  QNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPF 85

Query: 321 VYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMS 379
               I   + R L + + ++ +P  + E    I+ A   L +    +P +  IA++L +S
Sbjct: 86  AIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLS 145

Query: 380 QKKVRNATEAIG--KVFSLDR 398
           +++V    E     +  S+D 
Sbjct: 146 EEEVLEIMEMGQSYRALSVDD 166

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus , Listeria and Bacillus. Length = 255

>gnl|CDD|146934 pfam04539, Sigma70_r3, Sigma-70 region 3

 Score = 54.9 bits (133), Expect = 7e-10
 Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNG 406
           E L  I+ A+  LE E G  P+ + IAE L +S++KVR   EA  +  SLD       +G
Sbjct: 1   ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDG 60

Query: 407 LPGETHH 413
             G+   
Sbjct: 61  ELGDLLE 67

Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme. Length = 78

>gnl|CDD|233885 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA/WhiG family

 Score = 57.7 bits (140), Expect = 1e-09
 Identities = 41/114 (35%), Positives = 55/114 (48%), Gaps = 12/114 (10%)

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV---SRALVENSRTLRLPNHL 346
           ++ DL+Q G+ GLL  IE++D S+G K  TY    IR  +    R L    R+LR     
Sbjct: 25  ELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQKARK 84

Query: 347 HERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLD 397
            ER      A   LE + G  P+ + IAE L M  K+ R A   I    + SLD
Sbjct: 85  LER------AIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLD 132

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

>gnl|CDD|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family

 Score = 56.2 bits (136), Expect = 1e-09
 Identities = 35/148 (23%), Positives = 56/148 (37%), Gaps = 31/148 (20%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A E+L    + LV   A+RY    AD  DLVQ   + LL  +++FD    FK   +++  
Sbjct: 2   AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFRI 59

Query: 325 IRQGVSRAL----------------VENSRTLRLPNHLHERLGLIRNAKLRLEEK----- 363
            R  +   L                +++  +        E    +R A  +L E+     
Sbjct: 60  ARNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVL 119

Query: 364 ------GVTPSVDRIAEYLNMSQKKVRN 385
                 G+  S   IAE L +S   V+ 
Sbjct: 120 VLRYLEGL--SYKEIAEILGISVGTVKR 145

This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this 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

>gnl|CDD|131882 TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor

 Score = 55.2 bits (133), Expect = 1e-08
 Identities = 27/75 (36%), Positives = 45/75 (60%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+  L+  N+RLV+ IA++++N G  + DLV  G IGL++ +  F+ SK  K++TY    
Sbjct: 53  AKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRC 112

Query: 325 IRQGVSRALVENSRT 339
           I   +   L  N++T
Sbjct: 113 IENEILMYLRRNNKT 127

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 [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 234

>gnl|CDD|236306 PRK08583, PRK08583, RNA polymerase sigma factor SigB; Validated

 Score = 54.3 bits (131), Expect = 2e-08
 Identities = 43/142 (30%), Positives = 69/142 (48%), Gaps = 5/142 (3%)

Query: 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           +   A+EKLV     LV S+A +Y    +   DLVQ G++GLL  I ++D S G     +
Sbjct: 26  QDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAF 85

Query: 321 VYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMS 379
               I   + R L + + ++ +P  + E    I+ A   L  E   +P +  IA+ L +S
Sbjct: 86  AVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVS 145

Query: 380 QKKVRNATEAIGK---VFSLDR 398
           +++V  A E  GK     S+D 
Sbjct: 146 EEEVLEAMEM-GKSYQALSVDH 166

Length = 257

>gnl|CDD|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed

 Score = 54.2 bits (131), Expect = 3e-08
 Identities = 46/122 (37%), Positives = 67/122 (54%), Gaps = 10/122 (8%)

Query: 266 REKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           R +LV  N+ LV   A R+ N  ++   DLVQ G +GL+R IE+FD SKG   S++   +
Sbjct: 27  RNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPY 86

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAK-----LRLEEKGVTPSVDRIAEYLNMS 379
           IR  +   L + S T+R+P    E   L R AK     LR +E G  P+   IA+ L++S
Sbjct: 87  IRGEIQHYLRDKSPTVRIPRRWQE---LQRQAKKVRQELR-QELGRQPTDQEIAQALDIS 142

Query: 380 QK 381
            +
Sbjct: 143 LE 144

Length = 256

>gnl|CDD|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed

 Score = 52.1 bits (125), Expect = 1e-07
 Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 1/119 (0%)

Query: 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI 325
           R+++V   + L   IA+R+D  G    DLVQ   +GL+  + +FD   G    ++    I
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTI 101

Query: 326 RQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
              V R   +NS ++++P  L E    +  A   L ++ G  P+   +A  L M +++V
Sbjct: 102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEV 160

Length = 264

>gnl|CDD|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed

 Score = 51.0 bits (123), Expect = 3e-07
 Identities = 21/56 (37%), Positives = 37/56 (66%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
            R  L+  N+RLV+ IA++++N G ++ DL+  G IGL++ +  F+  K  K++TY
Sbjct: 53  VRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATY 108

Length = 234

>gnl|CDD|235770 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed

 Score = 43.5 bits (103), Expect = 9e-05
 Identities = 39/124 (31%), Positives = 61/124 (49%), Gaps = 9/124 (7%)

Query: 266 REKLVMSNVRLVMSIAQRYD-NMGADM--ADLVQGGLIGLLRGIEKFDSSKGFKISTYVY 322
           RE L++    LV  +A R    M  ++   DLV  G+ GL+  IEKFD  +  K  TY  
Sbjct: 33  REYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAV 92

Query: 323 WWIRQGVSRALVENSRTL-RLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQ 380
             IR     A+ +  R++  +P  + ++   I  A   LE + G TPS + IA+ L +S 
Sbjct: 93  TRIRG----AIFDELRSIDWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISL 148

Query: 381 KKVR 384
           ++  
Sbjct: 149 EEYN 152

Length = 268

>gnl|CDD|235901 PRK06986, fliA, flagellar biosynthesis sigma factor; Validated

 Score = 43.3 bits (103), Expect = 9e-05
 Identities = 33/121 (27%), Positives = 54/121 (44%), Gaps = 26/121 (21%)

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTY----VYW----WIRQG--VSRALVENSRT 339
           D+ DL+Q G+IGLL    ++D  +G    TY    +       +R    V R++  N+R 
Sbjct: 37  DLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDWVPRSVRRNAR- 95

Query: 340 LRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSL 396
                        +  A  +LE E G  P+   +AE L +S ++ R       I ++FS+
Sbjct: 96  ------------EVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSI 143

Query: 397 D 397
           D
Sbjct: 144 D 144

Length = 236

>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated

 Score = 42.0 bits (99), Expect = 3e-04
 Identities = 26/92 (28%), Positives = 45/92 (48%), Gaps = 4/92 (4%)

Query: 293 DLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGL 352
           DL   G++GL   +EKFD S+  K  TY  + IR  +   L +      LP  + E+   
Sbjct: 54  DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED---WLPRSMREKTKK 110

Query: 353 IRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           +  A  +LE++     +   +A  L M++++V
Sbjct: 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEV 142

Length = 251

>gnl|CDD|235644 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed

 Score = 38.8 bits (90), Expect = 0.003
 Identities = 38/147 (25%), Positives = 73/147 (49%), Gaps = 12/147 (8%)

Query: 266 REKLVMSNVRLVMSIAQRY-DNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVY 322
           R+ L+   + LV ++A R    M +     DL   G+ GL+R +E+FD  K  +   Y  
Sbjct: 25  RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84

Query: 323 WWIRQGVSRALVENSRTLR-LPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQ 380
           + I+     A++++ R    +P  +H++   + +A   L +  G  P+   + EYLN+SQ
Sbjct: 85  FLIKA----AIIDDLRKQDWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQ 140

Query: 381 KKVRN--ATEAIGKVFSLDREAFPSLN 405
           +++    ++     + SL+ E FP  +
Sbjct: 141 QELSGWFSSARPALILSLNEE-FPCQS 166

Length = 257

>gnl|CDD|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated

 Score = 38.0 bits (89), Expect = 0.004
 Identities = 16/38 (42%), Positives = 23/38 (60%)

Query: 276 LVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSK 313
            V + A+ Y  +GAD  D+VQ G+IGL + I  +D  K
Sbjct: 36  FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDK 73

Length = 208

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	417
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	99.97
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	99.96
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.96
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	99.96
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.96
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.95
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	99.95
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	99.95
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	99.95
PRK08215	258	sporulation sigma factor SigG; Reviewed	99.94
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	99.93
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	99.93
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	99.92
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	99.92
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	99.91
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	99.9
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	99.9
PRK05572	252	sporulation sigma factor SigF; Validated	99.9
PRK08583	257	RNA polymerase sigma factor SigB; Validated	99.89
PRK07670	251	RNA polymerase sigma factor SigD; Validated	99.87
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.87
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	99.85
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	99.84
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.82
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	99.82
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.82
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.78
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.77
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.76
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.75
PRK12513	194	RNA polymerase sigma factor; Provisional	99.75
PRK11922	231	RNA polymerase sigma factor; Provisional	99.74
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.74
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.73
PRK12514	179	RNA polymerase sigma factor; Provisional	99.73
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.73
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.72
PRK12524	196	RNA polymerase sigma factor; Provisional	99.72
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.72
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.72
PRK12534	187	RNA polymerase sigma factor; Provisional	99.72
PRK12531	194	RNA polymerase sigma factor; Provisional	99.72
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.72
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.71
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.71
PRK12537	182	RNA polymerase sigma factor; Provisional	99.71
PRK12519	194	RNA polymerase sigma factor; Provisional	99.71
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.7
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.7
PRK12538	233	RNA polymerase sigma factor; Provisional	99.7
PRK12536	181	RNA polymerase sigma factor; Provisional	99.7
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.69
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.69
PRK12526	206	RNA polymerase sigma factor; Provisional	99.69
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.69
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.69
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.69
PRK12539	184	RNA polymerase sigma factor; Provisional	99.68
PRK12542	185	RNA polymerase sigma factor; Provisional	99.67
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.66
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.66
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.66
PRK12515	189	RNA polymerase sigma factor; Provisional	99.66
PRK12512	184	RNA polymerase sigma factor; Provisional	99.66
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.65
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.65
PRK12520	191	RNA polymerase sigma factor; Provisional	99.64
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.64
PRK12522	173	RNA polymerase sigma factor; Provisional	99.64
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.64
PRK12543	179	RNA polymerase sigma factor; Provisional	99.63
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.63
PRK12516	187	RNA polymerase sigma factor; Provisional	99.63
PRK12540	182	RNA polymerase sigma factor; Provisional	99.63
PRK12518	175	RNA polymerase sigma factor; Provisional	99.62
PRK11924	179	RNA polymerase sigma factor; Provisional	99.62
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.62
PRK12547	164	RNA polymerase sigma factor; Provisional	99.61
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.6
PRK12535	196	RNA polymerase sigma factor; Provisional	99.6
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.6
PRK12541	161	RNA polymerase sigma factor; Provisional	99.6
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.59
PRK12529	178	RNA polymerase sigma factor; Provisional	99.59
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.58
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.58
PRK12533	216	RNA polymerase sigma factor; Provisional	99.57
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.57
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.56
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.56
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.55
PRK12517	188	RNA polymerase sigma factor; Provisional	99.55
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.54
PRK12528	161	RNA polymerase sigma factor; Provisional	99.54
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.53
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.53
PRK12532	195	RNA polymerase sigma factor; Provisional	99.53
PRK12545	201	RNA polymerase sigma factor; Provisional	99.52
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.52
PRK12530	189	RNA polymerase sigma factor; Provisional	99.51
PRK12546	188	RNA polymerase sigma factor; Provisional	99.51
PRK12544	206	RNA polymerase sigma factor; Provisional	99.5
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.5
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.5
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.5
PRK12511	182	RNA polymerase sigma factor; Provisional	99.48
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.46
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.42
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.4
PRK12525	168	RNA polymerase sigma factor; Provisional	99.4
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.39
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.37
PRK09191	261	two-component response regulator; Provisional	99.31
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.3
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.3
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.22
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.2
PF07638	185	Sigma70_ECF: ECF sigma factor	98.83
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	98.53
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	97.61
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	97.59
PRK05901	509	RNA polymerase sigma factor; Provisional	97.58
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	97.55
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	97.43
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	97.31
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	97.3
PRK07598	415	RNA polymerase sigma factor SigC; Validated	97.27
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	97.26
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	97.24
PRK05949	327	RNA polymerase sigma factor; Validated	97.23
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	97.14
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	97.13
PRK07405	317	RNA polymerase sigma factor SigD; Validated	96.98
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	96.96
PRK07670	251	RNA polymerase sigma factor SigD; Validated	96.89
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	96.87
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	96.86
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	96.74
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	96.69
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	96.48
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	96.44
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	96.17
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	96.16
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	96.15
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	96.08
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	96.06
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	95.95
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	95.85
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	95.82
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	95.52
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	95.42
PRK08215	258	sporulation sigma factor SigG; Reviewed	95.36
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	95.22
PRK05572	252	sporulation sigma factor SigF; Validated	94.21
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	93.47
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	91.79
PRK08583	257	RNA polymerase sigma factor SigB; Validated	90.5
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	90.31
PRK06930	170	positive control sigma-like factor; Validated	90.24
PHA02547	179	55 RNA polymerase sigma factor; Provisional	89.66
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	89.33
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	87.64
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	87.01
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	86.76
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	86.47
PRK00118	104	putative DNA-binding protein; Validated	85.75
PF06971	50	Put_DNA-bind_N: Putative DNA-binding protein N-ter	85.68
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	85.55
PHA02591	83	hypothetical protein; Provisional	84.89
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	84.29
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	83.98
PF10668	60	Phage_terminase: Phage terminase small subunit; In	82.64
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	82.22
PRK04217	110	hypothetical protein; Provisional	82.15
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	81.36
COG4941	415	Predicted RNA polymerase sigma factor containing a	81.13
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	80.5

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=1.1e-40  Score=342.73  Aligned_cols=215  Identities=37%  Similarity=0.645  Sum_probs=201.1

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCc--------------------chhHHHHHHHhhCCCCchHHHHHHhc-
Q 014852          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLR-  249 (417)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~--------------------l~~~~~~l~~~lg~eps~~e~A~~~~-  249 (417)
                      |.++.||.+|++.|+||++||++|.++++.+..                    |++.+.+|++.+|++|+..+||.++| 
T Consensus        60 d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~  139 (415)
T PRK07598         60 DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADI  139 (415)
T ss_pred             ChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence            799999999999999999999999999999988                    88899999999999999999996555 


Q ss_pred             ---------------------CChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhh
Q 014852          250 ---------------------ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK  308 (417)
Q Consensus       250 ---------------------~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAier  308 (417)
                                           ++.++|...+..|..|+++||.+|+++|+++|++|.+++.+++||+|||++|||+|+++
T Consensus       140 ~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravek  219 (415)
T PRK07598        140 SLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK  219 (415)
T ss_pred             cHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence                                 45555556667788999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHH
Q 014852          309 FDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNAT  387 (417)
Q Consensus       309 FD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL  387 (417)
                      |||.+|++|+||++||||+.|.+++.++.+.+++|.++.+.+++++++...|. .+||.||..|||+.|||++++|+.++
T Consensus       220 FDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l  299 (415)
T PRK07598        220 FDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVL  299 (415)
T ss_pred             cCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999984 68999999999999999999999999


Q ss_pred             HHhCcccccccccCCCCC
Q 014852          388 EAIGKVFSLDREAFPSLN  405 (417)
Q Consensus       388 ~rark~LSLD~~~~~s~~  405 (417)
                      ..++..+|||.++..+.+
T Consensus       300 ~~~~~~~SLd~~vg~~~d  317 (415)
T PRK07598        300 LRVPRSVSLETKVGKDKD  317 (415)
T ss_pred             HHccCCcccccccCCCcc
Confidence            999999999998875544

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=3e-39  Score=328.92  Aligned_cols=215  Identities=37%  Similarity=0.590  Sum_probs=206.7

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (417)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI  270 (417)
                      +.+..||++|+++|+||++||.+|+++++.|..+++.+..|.+.+|++|+..+||..+|++..+|+.++..|..|++.||
T Consensus        63 d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li  142 (373)
T PRK07406         63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV  142 (373)
T ss_pred             CHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHH
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHH
Q 014852          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (417)
Q Consensus       271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~  350 (417)
                      .+|+++|+++|++|.+++.+++||+|||+||||+++++||+.+|++|+|||+||||+.|.++|+++.+.+++|.++.+..
T Consensus       143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~  222 (373)
T PRK07406        143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI  222 (373)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852          351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN  405 (417)
Q Consensus       351 ~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~  405 (417)
                      .++.++...|. .+||.||.+|||+.||+++++|..++..+...+|||.+...+.+
T Consensus       223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~  278 (373)
T PRK07406        223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEED  278 (373)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCc
Confidence            99999999995 58999999999999999999999998888889999999865443

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family

Probab=100.00  E-value=1.1e-38  Score=315.14  Aligned_cols=211  Identities=39%  Similarity=0.660  Sum_probs=203.0

Q ss_pred             hHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 014852          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (417)
Q Consensus       192 ~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe  271 (417)
                      .+..||++|...|+||++||.+|+++++.|..+++.+..|.+.+|++|+..+||++++++..+|...+..|..|++.||.
T Consensus         2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~   81 (298)
T TIGR02997         2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK   81 (298)
T ss_pred             cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHH
Q 014852          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG  351 (417)
Q Consensus       272 ~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~  351 (417)
                      +|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+||++||||+.|.+++.++.+.+++|.++.....
T Consensus        82 ~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~  161 (298)
T TIGR02997        82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLN  161 (298)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH-HHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCC
Q 014852          352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFP  402 (417)
Q Consensus       352 kI~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~  402 (417)
                      +++++...+ ..+|+.||.+|||+.||+++++|..++......+|||.+...
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~  213 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGD  213 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCC
Confidence            999998888 458999999999999999999999999999899999998754

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).

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=1.4e-38  Score=319.14  Aligned_cols=216  Identities=33%  Similarity=0.608  Sum_probs=207.3

Q ss_pred             hhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 014852          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (417)
Q Consensus       190 ~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~L  269 (417)
                      .|.+..|+++|+..|+||++||.+|+++++.|..+++.+..|...+|++|+..+||..+++++.+|...+..|..|++.|
T Consensus        17 ~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~L   96 (327)
T PRK05949         17 ADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKM   96 (327)
T ss_pred             CCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHH
Confidence            37888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHH
Q 014852          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER  349 (417)
Q Consensus       270 Ie~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~  349 (417)
                      |.+|+++|+++|++|.+++.+++||+||||+|||+++++||+++|++|+|||+||||+.|.+++.++.+.+|+|.++.+.
T Consensus        97 i~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~  176 (327)
T PRK05949         97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK  176 (327)
T ss_pred             HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-HHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852          350 LGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN  405 (417)
Q Consensus       350 ~~kI~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~  405 (417)
                      ++.++++...+ ..+||+||.+|||+.||+++++|..++..+...+|||.+..++.+
T Consensus       177 ~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~  233 (327)
T PRK05949        177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQD  233 (327)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCC
Confidence            99999999998 568999999999999999999999999999999999998765433

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=1.9e-37  Score=309.53  Aligned_cols=214  Identities=37%  Similarity=0.642  Sum_probs=205.4

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (417)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI  270 (417)
                      +.+..||++|+..|+||++||.+|+++++.|..+++.+..|.+.+|++|+..+||.++++++.+|...+..|..|++.||
T Consensus         8 ~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~   87 (317)
T PRK07405          8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV   87 (317)
T ss_pred             cHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHH
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999989999999


Q ss_pred             HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHH
Q 014852          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (417)
Q Consensus       271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~  350 (417)
                      ..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+|||+||||+.|.++|.++.+.+|+|.++....
T Consensus        88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~  167 (317)
T PRK07405         88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL  167 (317)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCC
Q 014852          351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSL  404 (417)
Q Consensus       351 ~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~  404 (417)
                      .+++++...+. .+|+.||.+|||+.+|++.++|..++......+|||.+..++.
T Consensus       168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~  222 (317)
T PRK07405        168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQ  222 (317)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCC
Confidence            99999999984 5899999999999999999999999999889999998875443

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=7.8e-36  Score=313.42  Aligned_cols=203  Identities=34%  Similarity=0.568  Sum_probs=182.3

Q ss_pred             hhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 014852          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (417)
Q Consensus       190 ~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~L  269 (417)
                      .+.+..||++|+.+|+||++||.+|+++++.|+.+++..   .       ...+|+   .....+|+..+..+..|++.|
T Consensus       210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~---~~~~~~l~~~~~~g~~Ar~~L  276 (509)
T PRK05901        210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLD---PELRRDLQWIGRDGKRAKNHL  276 (509)
T ss_pred             ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccch---hhhhhhhhhhccchHHHHHHH
Confidence            478999999999999999999999999999998744421   1       112233   224567888888899999999


Q ss_pred             HHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHH
Q 014852          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER  349 (417)
Q Consensus       270 Ie~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~  349 (417)
                      |.+|++||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+||||+.|.++|+++.+.+|+|.++.+.
T Consensus       277 I~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~  356 (509)
T PRK05901        277 LEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVET  356 (509)
T ss_pred             HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852          350 LGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN  405 (417)
Q Consensus       350 ~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~  405 (417)
                      .++|.++...|. .+||.||.+|||+.||++++.|..++......+|||.++..+.+
T Consensus       357 i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~  413 (509)
T PRK05901        357 INKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGD  413 (509)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCc
Confidence            999999999994 68999999999999999999999999988899999998865544

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=1.6e-34  Score=289.67  Aligned_cols=202  Identities=34%  Similarity=0.585  Sum_probs=179.8

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (417)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI  270 (417)
                      +.+..||++|+.+|+||++||.+|+++++.|..++..          +|...+++..   ...+|+..+..|..|++.||
T Consensus        26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~----------~~~~~~~~~~---~~~~l~~~~~~~~~A~~~Lv   92 (324)
T PRK07921         26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL----------LETRKRLSEA---RKRDLAAVVRDGEAARRHLL   92 (324)
T ss_pred             ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh----------hccccccchh---HHHHHHHHHhcCHHHHHHHH
Confidence            5788999999999999999999999999998764433          1111111111   34578888889999999999


Q ss_pred             HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHH
Q 014852          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (417)
Q Consensus       271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~  350 (417)
                      ..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||+.|.++|+++.+.+++|.++.+..
T Consensus        93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~  172 (324)
T PRK07921         93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQV  172 (324)
T ss_pred             HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852          351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN  405 (417)
Q Consensus       351 ~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~  405 (417)
                      +++.++...|. .+||.||.+|||+.||+++++|..++..+...+|||.+...+.+
T Consensus       173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~  228 (324)
T PRK07921        173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEE  228 (324)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCC
Confidence            99999999995 68999999999999999999999999888889999998754433

>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]

Probab=100.00  E-value=3.2e-34  Score=287.40  Aligned_cols=223  Identities=36%  Similarity=0.531  Sum_probs=196.3

Q ss_pred             hhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHH-hhCCCCchH---------------HHHHHhcCCh-
Q 014852          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRISR-  252 (417)
Q Consensus       190 ~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~-~lg~eps~~---------------e~A~~~~~s~-  252 (417)
                      .+.+..|+..++..++++.+++..+.+.+.....+......+.. .++..|+..               +++..+...+ 
T Consensus         8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee   87 (342)
T COG0568           8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE   87 (342)
T ss_pred             hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence            47889999999999999999999999999887776666667766 677888876               4444444444 


Q ss_pred             HHHHHHhhhh---HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhH
Q 014852          253 PELQSILMEC---SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV  329 (417)
Q Consensus       253 ~eLr~~l~~~---~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i  329 (417)
                      ..|..++..+   ..|..+||.+|+++|++||++|.++|..+.||||||+|||++|+++|||++|++|+|||+||||+.|
T Consensus        88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI  167 (342)
T COG0568          88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI  167 (342)
T ss_pred             HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence            5566667655   4499999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhccccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCC
Q 014852          330 SRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLP  408 (417)
Q Consensus       330 ~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~~~~  408 (417)
                      .++|.++.+.+|+|.|+.+..+++.++...|. +.+++|+++|||+.||++.++|+..+.++..++|||.+++.+.++..
T Consensus       168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l  247 (342)
T COG0568         168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL  247 (342)
T ss_pred             HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence            99999999999999999999999999999995 46999999999999999999999999999999999999987765544


Q ss_pred             CCcc
Q 014852          409 GETH  412 (417)
Q Consensus       409 ~d~l  412 (417)
                      ++-+
T Consensus       248 ~d~l  251 (342)
T COG0568         248 GDFL  251 (342)
T ss_pred             HHHh
Confidence            4433

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=8.7e-33  Score=281.07  Aligned_cols=177  Identities=37%  Similarity=0.616  Sum_probs=168.5

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHH
Q 014852          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK  268 (417)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~  268 (417)
                      ..+.++.||++|+..|+||++++.+|+++++.||.                                        .|++.
T Consensus        94 ~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~----------------------------------------~A~~~  133 (367)
T PRK09210         94 INDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE----------------------------------------EAKQR  133 (367)
T ss_pred             cCcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH----------------------------------------HHHHH
Confidence            35799999999999999999999999999999987                                        89999


Q ss_pred             HHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHH
Q 014852          269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE  348 (417)
Q Consensus       269 LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e  348 (417)
                      ||..|+++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+|||+||||+.|.++|+++.+.+++|.++.+
T Consensus       134 Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~  213 (367)
T PRK09210        134 LAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE  213 (367)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852          349 RLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN  405 (417)
Q Consensus       349 ~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~  405 (417)
                      ..+++.++...|. .+||.||.+|||+.||+++++|++++..+...+|||.++..+.+
T Consensus       214 ~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~  271 (367)
T PRK09210        214 TINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDD  271 (367)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCc
Confidence            9999999999984 68999999999999999999999999998889999998865544

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=99.97  E-value=1.1e-30  Score=281.45  Aligned_cols=178  Identities=32%  Similarity=0.608  Sum_probs=164.5

Q ss_pred             hHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 014852          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (417)
Q Consensus       192 ~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe  271 (417)
                      .+..||+++...+.|++++...++++++.|+.                                     .+..|+++||.
T Consensus       345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~-------------------------------------~~~~a~~~Li~  387 (619)
T PRK05658        345 KLQQELEAIEEETGLTIEELKEINRQISKGEA-------------------------------------KARRAKKEMVE  387 (619)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHhccch-------------------------------------hhhHHHHHHHH
Confidence            55678888888899999999999999998875                                     12268999999


Q ss_pred             HhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHH
Q 014852          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG  351 (417)
Q Consensus       272 ~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~  351 (417)
                      .|++||+++|++|.++|++++||+|||+|||++|+++|||.+|++|+|||+||||++|.++|+++.+.+++|.++.+..+
T Consensus       388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~  467 (619)
T PRK05658        388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN  467 (619)
T ss_pred             HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH-HHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCC
Q 014852          352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNG  406 (417)
Q Consensus       352 kI~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~~  406 (417)
                      ++.++...| .++||+||.+|||+.||+|+++|+.++..+..++|||.+..++.+.
T Consensus       468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~  523 (619)
T PRK05658        468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDS  523 (619)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCC
Confidence            999999998 5689999999999999999999999999999999999998665543

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=99.96  E-value=2.1e-28  Score=241.53  Aligned_cols=174  Identities=24%  Similarity=0.351  Sum_probs=151.1

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHH-ccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 014852          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (417)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k-~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~L  269 (417)
                      +.+..||++|...|+||+++|.+|+++++ .||.                                        .|++.|
T Consensus         6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~~gd~----------------------------------------~A~~~L   45 (289)
T PRK07500          6 SADRSMIRSAMKAPYLEREEEHALAYRWKDHRDE----------------------------------------DALHRI   45 (289)
T ss_pred             hHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHH
Confidence            46677999999999999999999999974 7887                                        899999


Q ss_pred             HHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHH-
Q 014852          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE-  348 (417)
Q Consensus       270 Ie~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e-  348 (417)
                      |..|+|+|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+|||+|||++.|.++++++.+.+|+|.+... 
T Consensus        46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~  125 (289)
T PRK07500         46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQK  125 (289)
T ss_pred             HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999998888899988554 


Q ss_pred             -HHHHHHHHHHHHH----HcCCCccHHHHHHHcCCCHHHHHHHHHH-hCcccccccccCCCC
Q 014852          349 -RLGLIRNAKLRLE----EKGVTPSVDRIAEYLNMSQKKVRNATEA-IGKVFSLDREAFPSL  404 (417)
Q Consensus       349 -~~~kI~~a~~~L~----e~gRepS~eEIAe~LGIS~etVr~aL~r-ark~LSLD~~~~~s~  404 (417)
                       ...++.++...+.    .+++.||.+|||+.||+++++|..++.. ....+|||.+..++.
T Consensus       126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~  187 (289)
T PRK07500        126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEED  187 (289)
T ss_pred             HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCC
Confidence             2234444444442    4789999999999999999999877543 447899999876443

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.96  E-value=3.4e-28  Score=239.42  Aligned_cols=176  Identities=30%  Similarity=0.471  Sum_probs=153.2

Q ss_pred             cchhhhhhhHHHHHHhhcccCCCCHHHHHHHHHHH-HccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhh
Q 014852          184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC  262 (417)
Q Consensus       184 ~~~e~~~~~~~~yl~~i~~~~lLt~~eE~eLirk~-k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~  262 (417)
                      .+|+   +.+..|++++...|++++++|.+|+.+. +.||.                                       
T Consensus        10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~---------------------------------------   47 (284)
T PRK06596         10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL---------------------------------------   47 (284)
T ss_pred             CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence            4555   5888999999999999999999999984 68887                                       


Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (417)
Q Consensus       263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl  342 (417)
                       .|++.||..|+++|+++|++|.+++.+++||+|||++||++|+++||+++|++|+|||+|||++.|.++++++.+.+++
T Consensus        48 -~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~  126 (284)
T PRK06596         48 -EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKV  126 (284)
T ss_pred             -HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeec
Confidence             8999999999999999999999999999999999999999999999999999999999999999999999998777888


Q ss_pred             CccHHH--HHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC-cccccccccCCC
Q 014852          343 PNHLHE--RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG-KVFSLDREAFPS  403 (417)
Q Consensus       343 p~~~~e--~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar-k~LSLD~~~~~s  403 (417)
                      |.+...  ....+.++...+. .++.||.+|||+.||+++++|.+++.... ..+|||.+..++
T Consensus       127 p~~~~~~~~~~~~~~~~~~l~-~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~  189 (284)
T PRK06596        127 ATTKAQRKLFFNLRKAKKRLG-WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDD  189 (284)
T ss_pred             cchHHHHHHHHHHHHHHHHhc-cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCC
Confidence            887532  3344555555554 46889999999999999999999876544 688999987543

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=99.96  E-value=1.2e-27  Score=240.09  Aligned_cols=177  Identities=35%  Similarity=0.571  Sum_probs=164.1

Q ss_pred             hhhhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHH
Q 014852          187 ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR  266 (417)
Q Consensus       187 e~~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Ar  266 (417)
                      +.+.+.+++|+++|+..|+||++++..|+++++.||.                                        .|+
T Consensus        49 ~~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~   88 (325)
T PRK05657         49 QRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AAR   88 (325)
T ss_pred             cccccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHH
Confidence            3455899999999999999999999999999999998                                        899


Q ss_pred             HHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccH
Q 014852          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL  346 (417)
Q Consensus       267 e~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~  346 (417)
                      +.||.+|.++|+++|++|++++.+++||+||||||+|+++++||+.+|++|+||++||||..|.++++++.+.+++|.++
T Consensus        89 ~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~  168 (325)
T PRK05657         89 QRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHV  168 (325)
T ss_pred             HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCC
Q 014852          347 HERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS  403 (417)
Q Consensus       347 ~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s  403 (417)
                      ...++.+.++...|. ..++.|+.+|||+.||++++.|+.++......+|||.+...+
T Consensus       169 ~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~  226 (325)
T PRK05657        169 VKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGD  226 (325)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCC
Confidence            888777888888885 478999999999999999999999998777788999876543

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.96  E-value=1.6e-27  Score=232.55  Aligned_cols=171  Identities=29%  Similarity=0.496  Sum_probs=147.2

Q ss_pred             hHHHHHHhhcccCCCCHHHHHHHHHH-HHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852          192 RLKGYVKGVVSEELLTHAEVVRLSKK-IKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (417)
Q Consensus       192 ~~~~yl~~i~~~~lLt~~eE~eLirk-~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI  270 (417)
                      .+..||+++..+|+|+++++.+|+++ .+.||.                                        .|++.||
T Consensus         2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~~gd~----------------------------------------~a~~~Lv   41 (270)
T TIGR02392         2 SLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDL----------------------------------------DAAKKLV   41 (270)
T ss_pred             hHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHH
Confidence            46789999999999999999999998 568887                                        8999999


Q ss_pred             HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHH--H
Q 014852          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH--E  348 (417)
Q Consensus       271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~--e  348 (417)
                      ..|+++|+++|++|.+++.+++||+|||++||++|+++||+++|++|+|||+|||+++|.+++++..+.+++|....  +
T Consensus        42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~  121 (270)
T TIGR02392        42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK  121 (270)
T ss_pred             HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999998876678886643  3


Q ss_pred             HHHHHHHHHHHHHHcCCCc-cHHHHHHHcCCCHHHHHHHHHHhC-cccccccccCCC
Q 014852          349 RLGLIRNAKLRLEEKGVTP-SVDRIAEYLNMSQKKVRNATEAIG-KVFSLDREAFPS  403 (417)
Q Consensus       349 ~~~kI~~a~~~L~e~gRep-S~eEIAe~LGIS~etVr~aL~rar-k~LSLD~~~~~s  403 (417)
                      ...++..+...+. .++.| +.+|||+.||+++++|.+++.... ..+|||.+..++
T Consensus       122 ~~~~~~~~~~~~~-~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~  177 (270)
T TIGR02392       122 LFFNLRKMKKRLQ-GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDD  177 (270)
T ss_pred             HHHHHHHHHHHHh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCC
Confidence            3445555555553 12555 699999999999999999876554 478999987553

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.

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=99.95  E-value=1.6e-27  Score=232.48  Aligned_cols=140  Identities=26%  Similarity=0.368  Sum_probs=131.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp  343 (417)
                      .++++||..|+++|+++|++|.++|.+.+||+|||+|||++|+++|||++|++|+|||+||||+.|.++++++.+.+++|
T Consensus        40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P  119 (264)
T PRK07122         40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP  119 (264)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccCCC
Q 014852          344 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPS  403 (417)
Q Consensus       344 ~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~r--ark~LSLD~~~~~s  403 (417)
                      .++.+...++.++...|. .+|+.||.+|||+.||+++++|.+++..  ....+|||.+..++
T Consensus       120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~  182 (264)
T PRK07122        120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSG  182 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCC
Confidence            999999999999999995 6899999999999999999999998865  34689999987543

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=99.95  E-value=1e-26  Score=224.61  Aligned_cols=162  Identities=33%  Similarity=0.443  Sum_probs=151.2

Q ss_pred             cccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHH
Q 014852          201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI  280 (417)
Q Consensus       201 ~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sI  280 (417)
                      ...|+|+++++.+|+.+++.||.                                        .|++.|+..|.++|+++
T Consensus        11 ~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~~   50 (254)
T TIGR02850        11 SKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLSV   50 (254)
T ss_pred             cCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHH
Confidence            56799999999999999999987                                        89999999999999999


Q ss_pred             HHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHH
Q 014852          281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL  360 (417)
Q Consensus       281 A~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L  360 (417)
                      |++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++++.. .+++|.+..+...++.++...|
T Consensus        51 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~l  129 (254)
T TIGR02850        51 IQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKL  129 (254)
T ss_pred             HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999965 7899999999989999998888


Q ss_pred             H-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCC
Q 014852          361 E-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS  403 (417)
Q Consensus       361 ~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s  403 (417)
                      . ++|+.||.+|||+.||+++++|..++......+|||++...+
T Consensus       130 ~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~  173 (254)
T TIGR02850       130 ISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYND  173 (254)
T ss_pred             HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCC
Confidence            4 589999999999999999999999999888889999887543

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.

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=99.95  E-value=3.2e-27  Score=225.92  Aligned_cols=140  Identities=41%  Similarity=0.699  Sum_probs=132.4

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc
Q 014852          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN  344 (417)
Q Consensus       265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~  344 (417)
                      |+++||..|+++|+++|++|.+++.+++||+|||+|||++|+++|||.+|++|+|||+||||+.|.++++++.+.+++|.
T Consensus         1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~   80 (238)
T TIGR02393         1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV   80 (238)
T ss_pred             CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCC
Q 014852          345 HLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSL  404 (417)
Q Consensus       345 ~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~  404 (417)
                      ++.+..+++.++...|. ..|+.||.+|||+.||++.++|.+++......+|||.+...+.
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~  141 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEE  141 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCC
Confidence            99999999999999995 5899999999999999999999999888888999999875443

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.

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=99.95  E-value=2.2e-26  Score=223.09  Aligned_cols=140  Identities=32%  Similarity=0.444  Sum_probs=129.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCC-CCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~-g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl  342 (417)
                      .|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||++||++.|.++++++...+++
T Consensus        25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr~  104 (256)
T PRK07408         25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRI  104 (256)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeeee
Confidence            899999999999999999999865 6679999999999999999999999999999999999999999999999999999


Q ss_pred             CccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccCCC
Q 014852          343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPS  403 (417)
Q Consensus       343 p~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~r--ark~LSLD~~~~~s  403 (417)
                      |.++.+..+++.++...|. .+|++||.+|||+.||+++++|..++..  ....+|||.+...+
T Consensus       105 pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~  168 (256)
T PRK07408        105 PRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQD  168 (256)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCC
Confidence            9999999999999999995 5899999999999999999999998653  34688999987543

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=99.94  E-value=1.7e-25  Score=216.53  Aligned_cols=162  Identities=32%  Similarity=0.457  Sum_probs=150.0

Q ss_pred             cccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHH
Q 014852          201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI  280 (417)
Q Consensus       201 ~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sI  280 (417)
                      ...|+|+++++..|+.+++.||.                                        .|++.|+..|.++|+++
T Consensus        14 ~~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~   53 (258)
T PRK08215         14 SKLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNLRLVLSV   53 (258)
T ss_pred             CCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence            35689999999999999999987                                        89999999999999999


Q ss_pred             HHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHH
Q 014852          281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL  360 (417)
Q Consensus       281 A~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L  360 (417)
                      |++|.+++.+++||+|||++|||+++++||+.+|.+|.||+++||++.|.+++++.. .+++|.+......++.++...+
T Consensus        54 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l  132 (258)
T PRK08215         54 IQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKL  132 (258)
T ss_pred             HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999985 7899999998888888888888


Q ss_pred             H-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCC
Q 014852          361 E-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS  403 (417)
Q Consensus       361 ~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s  403 (417)
                      . ..|+.|+..|||+.||+++++|...+......+|||.+..++
T Consensus       133 ~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~  176 (258)
T PRK08215        133 INENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHD  176 (258)
T ss_pred             HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCC
Confidence            4 589999999999999999999999998887888999887544

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=99.93  E-value=2.4e-25  Score=215.68  Aligned_cols=161  Identities=34%  Similarity=0.487  Sum_probs=147.3

Q ss_pred             CCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHH
Q 014852          204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR  283 (417)
Q Consensus       204 ~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~R  283 (417)
                      +.++..+...++...+.|+.                                        .++ .||++|+|||.++|++
T Consensus         4 ~~~~~~e~~~~~~~~~~g~~----------------------------------------~~~-~Li~~ylpLV~~ia~k   42 (247)
T COG1191           4 QPLSKEEEEKLLEYYAEGDE----------------------------------------EAR-RLIERYLPLVKSIARK   42 (247)
T ss_pred             cccchHHHHHHHHHHHhcCH----------------------------------------HHH-HHHHHHHHHHHHHHHH
Confidence            45677777788888888887                                        888 9999999999999999


Q ss_pred             ccCCCC-ChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-
Q 014852          284 YDNMGA-DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-  361 (417)
Q Consensus       284 y~~~g~-e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-  361 (417)
                      |.+.+. +.|||+|.|+|||++|+++||+++|.+|+|||.++|+++|++++|++. .+++|+.+++..+++..+++.|. 
T Consensus        43 ~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~  121 (247)
T COG1191          43 FENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQ  121 (247)
T ss_pred             HHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-CccCcHHHHHHHHHHHHHHHHHHH
Confidence            998776 999999999999999999999999999999999999999999999999 99999999999999999999995 


Q ss_pred             HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCCCCCC
Q 014852          362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNG  406 (417)
Q Consensus       362 e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~~s~~~  406 (417)
                      ++||+||..|||+.|||+.+.|..++....  ..+|+|+....+++.
T Consensus       122 el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~  168 (247)
T COG1191         122 ELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDD  168 (247)
T ss_pred             HhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhcccccc
Confidence            699999999999999999999999998876  788999877654443

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=99.93  E-value=9e-25  Score=214.60  Aligned_cols=175  Identities=35%  Similarity=0.578  Sum_probs=163.0

Q ss_pred             hhhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHH
Q 014852          188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE  267 (417)
Q Consensus       188 ~~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are  267 (417)
                      .+.+.+++||++|..+|.|+.+++.+|+++++.||.                                        .|++
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~~   49 (285)
T TIGR02394        10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EARK   49 (285)
T ss_pred             CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence            567899999999999999999999999999999998                                        8999


Q ss_pred             HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHH
Q 014852          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH  347 (417)
Q Consensus       268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~  347 (417)
                      .||..|.++|+++|.+|.+++.+++||+||||||||+++++||+.+|++|+||+.|+++..+.++++++.+.+++|..+.
T Consensus        50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~~  129 (285)
T TIGR02394        50 VMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVI  129 (285)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCC
Q 014852          348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFP  402 (417)
Q Consensus       348 e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~  402 (417)
                      +..+.+.+....+. ..++.|+..++|+.||++++.|..++..+.+.+|+|.+...
T Consensus       130 ~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~  185 (285)
T TIGR02394       130 KELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDD  185 (285)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCC
Confidence            88888777776664 46899999999999999999999999888888999876543

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).

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=99.92  E-value=1.2e-23  Score=202.90  Aligned_cols=162  Identities=27%  Similarity=0.330  Sum_probs=148.3

Q ss_pred             CCCCHHHHHHHHHHHHc-cCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHH
Q 014852          204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (417)
Q Consensus       204 ~lLt~~eE~eLirk~k~-Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~  282 (417)
                      |.|++.++.+|+.+++. ||.                                        .|++.|+..|.++|+.+|+
T Consensus         8 ~~l~~~~~~~li~~~~~~gd~----------------------------------------~a~~~l~~~y~~~v~~~a~   47 (255)
T TIGR02941         8 TNLTKEDVIQWIAEFQQNQNG----------------------------------------EAQEKLVDHYQNLVYSIAY   47 (255)
T ss_pred             CCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence            67999999999999988 576                                        8999999999999999999


Q ss_pred             HccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-
Q 014852          283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-  361 (417)
Q Consensus       283 Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-  361 (417)
                      +|.+++.++|||+||||++||+++++|++..|.+|.||+++||+|.|.+++++....+++|..+.+...++..+...+. 
T Consensus        48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~  127 (255)
T TIGR02941        48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTD  127 (255)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999998888999999999999999999985 


Q ss_pred             HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCCCCC
Q 014852          362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLN  405 (417)
Q Consensus       362 e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~~s~~  405 (417)
                      .+|+.|+..|||+.||++.+.+..++....  ..+|||.++..+++
T Consensus       128 ~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~  173 (255)
T TIGR02941       128 HLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD  173 (255)
T ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence            579999999999999999999998877653  57899988765433

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=99.92  E-value=1e-23  Score=204.71  Aligned_cols=136  Identities=25%  Similarity=0.391  Sum_probs=123.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcc---CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~---~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      .|++.||..|+|+|+++|++|.   ..+.+.+||+|||+||||+|+++|||++|++|+||+.+|||++|.+++++..   
T Consensus        23 ~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~---   99 (257)
T PRK05911         23 EYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD---   99 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence            7999999999999999999985   2456899999999999999999999999999999999999999999999876   


Q ss_pred             ccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCC
Q 014852          341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFP  402 (417)
Q Consensus       341 rlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~~  402 (417)
                      ++|.++.+..+++..+...|. .+||.||.+|||+.||+++++|..++..+.  ..+|||.+...
T Consensus       100 ~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~  164 (257)
T PRK05911        100 WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPC  164 (257)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCC
Confidence            489999999999999999885 589999999999999999999999987665  36899987643

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=99.91  E-value=1.5e-23  Score=199.05  Aligned_cols=141  Identities=35%  Similarity=0.437  Sum_probs=131.1

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir  341 (417)
                      +..|++.|+..|.++|+++|.+|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.++++++. .++
T Consensus         9 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~i~   87 (231)
T TIGR02885         9 DKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIK   87 (231)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-CeE
Confidence            3489999999999999999999999999999999999999999999999999889999999999999999999986 789


Q ss_pred             cCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCC
Q 014852          342 LPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS  403 (417)
Q Consensus       342 lp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s  403 (417)
                      +|.++.+...++.++...|. ++|+.||.+|||+.||+++++|..++..+....|||.+..++
T Consensus        88 ~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~  150 (231)
T TIGR02885        88 VSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQD  150 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCC
Confidence            99999999999999988885 579999999999999999999999988888889999877543

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.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=99.90  E-value=9.5e-23  Score=198.49  Aligned_cols=159  Identities=28%  Similarity=0.362  Sum_probs=141.5

Q ss_pred             hcccCCCCHHHHHHHHHHHH-ccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHH
Q 014852          200 VVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM  278 (417)
Q Consensus       200 i~~~~lLt~~eE~eLirk~k-~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~  278 (417)
                      -+.+|+||.++|.+|+++++ .||.                                        .|++.|+..|.++|+
T Consensus         6 ~~~~~~~~~~~e~~l~~~~~~~~d~----------------------------------------~a~~~l~~~y~~lv~   45 (268)
T PRK06288          6 SGKIPKYAQQDETELWREYKKTGDP----------------------------------------KIREYLILKYSPLVK   45 (268)
T ss_pred             cCCCccccchHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHH
Confidence            36789999999999999976 4565                                        899999999999999


Q ss_pred             HHHHHcc-C--CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHH
Q 014852          279 SIAQRYD-N--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRN  355 (417)
Q Consensus       279 sIA~Ry~-~--~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~  355 (417)
                      .+|++|. +  .+.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|+..   ++|.++......+.+
T Consensus        46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~  122 (268)
T PRK06288         46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIER  122 (268)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHH
Confidence            9999986 2  567899999999999999999999998899999999999999999998653   689998888889999


Q ss_pred             HHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccC
Q 014852          356 AKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAF  401 (417)
Q Consensus       356 a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~  401 (417)
                      +...|. .+++.||.+|||+.||++.+.|..++..+.  ..+|||++..
T Consensus       123 ~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~  171 (268)
T PRK06288        123 AIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWF  171 (268)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhc
Confidence            999995 589999999999999999999999987653  5689988764

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=99.90  E-value=8.3e-23  Score=193.23  Aligned_cols=139  Identities=39%  Similarity=0.485  Sum_probs=130.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (417)
Q Consensus       263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl  342 (417)
                      ..|++.|+..|.++|+++|++|.+++.++|||+|||++|||+++++||+.+|.+|+||+++||++.|.++++++.+.+++
T Consensus         2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri   81 (227)
T TIGR02980         2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV   81 (227)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999888999


Q ss_pred             CccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCc--ccccccccC
Q 014852          343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGK--VFSLDREAF  401 (417)
Q Consensus       343 p~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark--~LSLD~~~~  401 (417)
                      |.++.+...++.++...+. ..|+.|+..|+|+.||+++++|.+++.....  .+|||++..
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~  143 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIE  143 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCC
Confidence            9999999999999999884 5789999999999999999999998887765  889998875

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.

>PRK05572 sporulation sigma factor SigF; Validated

Probab=99.90  E-value=2.8e-22  Score=193.39  Aligned_cols=165  Identities=36%  Similarity=0.452  Sum_probs=151.3

Q ss_pred             HHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHH
Q 014852          197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRL  276 (417)
Q Consensus       197 l~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~L  276 (417)
                      ++.-...|.|+++++.+|+.+++.|+.                                        .|++.|+..|.++
T Consensus         5 ~~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~   44 (252)
T PRK05572          5 VKNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRL   44 (252)
T ss_pred             hccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHH
Confidence            345567899999999999999999987                                        8999999999999


Q ss_pred             HHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHH
Q 014852          277 VMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNA  356 (417)
Q Consensus       277 V~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a  356 (417)
                      |+++|++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||++.|.+++++.. .+++|..+.....++.++
T Consensus        45 v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~  123 (252)
T PRK05572         45 VWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKD  123 (252)
T ss_pred             HHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999988889999999999999999999874 779999999999999999


Q ss_pred             HHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCC
Q 014852          357 KLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFP  402 (417)
Q Consensus       357 ~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~  402 (417)
                      ...+. +.||.|+..|||+.||++++.|..++.......||+.+..+
T Consensus       124 ~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~  170 (252)
T PRK05572        124 KDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHE  170 (252)
T ss_pred             HHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCccc
Confidence            98884 57999999999999999999999998887788899887653

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=99.89  E-value=8.5e-22  Score=190.20  Aligned_cols=160  Identities=28%  Similarity=0.342  Sum_probs=146.1

Q ss_pred             CCCCHHHHHHHHHHHHc-cCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHH
Q 014852          204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (417)
Q Consensus       204 ~lLt~~eE~eLirk~k~-Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~  282 (417)
                      |.|+++++.+|+.+++. ||.                                        .|++.|+..|.++|+++|+
T Consensus         8 ~~l~~~e~~~li~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~a~   47 (257)
T PRK08583          8 TKLTKEEVNKWIAEYQENQDE----------------------------------------EAQEKLVKHYKNLVESLAY   47 (257)
T ss_pred             CcCChHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHH
Confidence            77999999999999885 787                                        8999999999999999999


Q ss_pred             HccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-
Q 014852          283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-  361 (417)
Q Consensus       283 Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-  361 (417)
                      +|.+++.+++||+||||++||+++++||+..|.+|.||+++||+|.|.+++++....+++|.++.+..+++..+...+. 
T Consensus        48 ~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~  127 (257)
T PRK08583         48 KYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTT  127 (257)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999998889999999999999999999998889999999999999999988885 


Q ss_pred             HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccCCC
Q 014852          362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPS  403 (417)
Q Consensus       362 e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~~s  403 (417)
                      ..++.|+..|+|+.+|++.+.|..++....  ..+|+|.+...+
T Consensus       128 ~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~  171 (257)
T PRK08583        128 ELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEAD  171 (257)
T ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCC
Confidence            578999999999999999999988876543  578898877544

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=99.87  E-value=2.4e-21  Score=186.84  Aligned_cols=136  Identities=25%  Similarity=0.375  Sum_probs=123.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccC---CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~---~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      .|++.||..|.++|+++|++|.+   ++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.++++++.   
T Consensus        22 ~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~---   98 (251)
T PRK07670         22 DAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED---   98 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence            89999999999999999999965   688999999999999999999999999999999999999999999999865   


Q ss_pred             ccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccCC
Q 014852          341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFP  402 (417)
Q Consensus       341 rlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~r--ark~LSLD~~~~~  402 (417)
                      ++|....+...+++++...+. ..|+.|+.+|||+.||+++++|+.++..  ....+|||++...
T Consensus        99 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~  163 (251)
T PRK07670         99 WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHD  163 (251)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccC
Confidence            688888888888888888884 5899999999999999999999999864  3468899988643

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.87  E-value=2.2e-21  Score=184.97  Aligned_cols=163  Identities=28%  Similarity=0.364  Sum_probs=136.1

Q ss_pred             hHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHH
Q 014852          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (417)
Q Consensus       192 ~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe  271 (417)
                      ++..|+.++...|+||++++..|+..++.|+.                                        .|++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence            68899999999999999999999999999987                                        89999999


Q ss_pred             HhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-c--------
Q 014852          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L--------  342 (417)
Q Consensus       272 ~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-l--------  342 (417)
                      .|.++|+++|.+|.+++.+++|++||+||++|+++++|++++|.+|.||+++|++|.+++++|+..+..+ .        
T Consensus        57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~~~~~~~~~~~  136 (233)
T PRK05803         57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGV  136 (233)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccccCCCccccccC
Confidence            9999999999999999999999999999999999999999888899999999999999999987653210 0        


Q ss_pred             -------------Cc---cHH------HHHHHHHHHHHHHHHcC-------------CCccHHHHHHHcCCCHHHHHHHH
Q 014852          343 -------------PN---HLH------ERLGLIRNAKLRLEEKG-------------VTPSVDRIAEYLNMSQKKVRNAT  387 (417)
Q Consensus       343 -------------p~---~~~------e~~~kI~~a~~~L~e~g-------------RepS~eEIAe~LGIS~etVr~aL  387 (417)
                                   +.   ...      .....+..++..|++..             .+.|++|||+.||+|.++|++++
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~  216 (233)
T PRK05803        137 DKEGNEISLIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIE  216 (233)
T ss_pred             CCCcCcccHHHHccCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence                         00   000      11234666666664322             34589999999999999999999


Q ss_pred             HHhCccc
Q 014852          388 EAIGKVF  394 (417)
Q Consensus       388 ~rark~L  394 (417)
                      +++++.+
T Consensus       217 ~rA~~kL  223 (233)
T PRK05803        217 KRALKKL  223 (233)
T ss_pred             HHHHHHH
Confidence            8887654

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=99.85  E-value=1.2e-20  Score=180.73  Aligned_cols=136  Identities=20%  Similarity=0.270  Sum_probs=119.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccC---CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~---~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      .-...|+..|+|+|..+|++|..   .+.+.+||+|||+||||+|+++||+..| +|+||+++||+|.|.+++++..   
T Consensus        15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~---   90 (231)
T PRK12427         15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD---   90 (231)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC---
Confidence            34568899999999999999874   4679999999999999999999998666 8999999999999999998854   


Q ss_pred             ccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHH--hCcccccccccCCC
Q 014852          341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPS  403 (417)
Q Consensus       341 rlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~r--ark~LSLD~~~~~s  403 (417)
                      +.|..+....+++.++...|. .+|++||.+|||+.||+++++|.+++..  +...+|||++..++
T Consensus        91 ~~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~  156 (231)
T PRK12427         91 WRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALE  156 (231)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCC
Confidence            468888888899999999984 5899999999999999999999998764  34688999987554

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family

Probab=99.84  E-value=3.8e-20  Score=175.14  Aligned_cols=130  Identities=33%  Similarity=0.464  Sum_probs=117.2

Q ss_pred             HHHHhHHHHHHHHHHccC---CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCcc
Q 014852          269 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH  345 (417)
Q Consensus       269 LIe~yl~LV~sIA~Ry~~---~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~  345 (417)
                      |+..|.++|+++|.+|.+   ++.+++||+||||+|||+++++||+++|.+|+||+++||+|.+.+++++..   ++|..
T Consensus         1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~   77 (224)
T TIGR02479         1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS   77 (224)
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence            688999999999999985   789999999999999999999999999999999999999999999998764   58888


Q ss_pred             HHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccC
Q 014852          346 LHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAF  401 (417)
Q Consensus       346 ~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~  401 (417)
                      .....+++.++...|. .+|+.|+.+|||+.||++++.|..++..+.  ..+|+|+...
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~  136 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLE  136 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCccc
Confidence            8888999999999995 589999999999999999999999987554  4678887554

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.

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.82  E-value=1.6e-19  Score=171.75  Aligned_cols=163  Identities=26%  Similarity=0.367  Sum_probs=131.7

Q ss_pred             hHHHHHHhhcc-cCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHH
Q 014852          192 RLKGYVKGVVS-EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (417)
Q Consensus       192 ~~~~yl~~i~~-~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LI  270 (417)
                      ++-+|+-.-++ .+.|++.++.+|+.+++.|+.                                        .|++.|+
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~   54 (227)
T TIGR02846        15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLI   54 (227)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHH
Confidence            44567666554 456999999999999999997                                        8999999


Q ss_pred             HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-c-------
Q 014852          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L-------  342 (417)
Q Consensus       271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-l-------  342 (417)
                      +.|.+.|+++|.+|.++..++||++||+|+++|+++++|+++.+.+|.||++++++|.+++++|+..+..+ .       
T Consensus        55 ~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~~~~~~~~~~  134 (227)
T TIGR02846        55 ERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGEVSLQDPIG  134 (227)
T ss_pred             HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhccccceecccccc
Confidence            99999999999999999999999999999999999999999888789999999999999999987654211 0       


Q ss_pred             --------------Cc---c------HHHHHHHHHHHHHHHHHcC-------------CCccHHHHHHHcCCCHHHHHHH
Q 014852          343 --------------PN---H------LHERLGLIRNAKLRLEEKG-------------VTPSVDRIAEYLNMSQKKVRNA  386 (417)
Q Consensus       343 --------------p~---~------~~e~~~kI~~a~~~L~e~g-------------RepS~eEIAe~LGIS~etVr~a  386 (417)
                                    +.   .      ..+....+..++..|++..             .+.|++|||+.||+|+++|+..
T Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~  214 (227)
T TIGR02846       135 VDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRI  214 (227)
T ss_pred             CCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHH
Confidence                          00   0      0011233666677764322             3458999999999999999999


Q ss_pred             HHHhCccc
Q 014852          387 TEAIGKVF  394 (417)
Q Consensus       387 L~rark~L  394 (417)
                      ++++++.+
T Consensus       215 ~~rAl~~L  222 (227)
T TIGR02846       215 EKRALMKL  222 (227)
T ss_pred             HHHHHHHH
Confidence            99987654

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.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=99.82  E-value=2.4e-19  Score=171.07  Aligned_cols=138  Identities=28%  Similarity=0.400  Sum_probs=120.7

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHcc---CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852          261 ECSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (417)
Q Consensus       261 ~~~~Are~LIe~yl~LV~sIA~Ry~---~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~  337 (417)
                      +|..++++|+..|.++|+++|.+|.   +++.+++||+||||+|||+++++||+..|.+|.||+++||+|.|.++++++.
T Consensus         5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~   84 (236)
T PRK06986          5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD   84 (236)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence            4567899999999999999999997   6789999999999999999999999998889999999999999999999875


Q ss_pred             cccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccC
Q 014852          338 RTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAF  401 (417)
Q Consensus       338 r~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~  401 (417)
                         ++|..+......+.++...+. ..+++|+.+|||+.||++++.|..++....  ..+|++....
T Consensus        85 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~  148 (236)
T PRK06986         85 ---WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRG  148 (236)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccc
Confidence               367777776677777777774 579999999999999999999999887643  4668887643

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.82  E-value=1.9e-19  Score=171.31  Aligned_cols=159  Identities=26%  Similarity=0.443  Sum_probs=129.2

Q ss_pred             HHHhhccc-CCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhH
Q 014852          196 YVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV  274 (417)
Q Consensus       196 yl~~i~~~-~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl  274 (417)
                      |+++.... +.+++..+.+|+.+++.||.                                        .|++.|+..|.
T Consensus        23 ~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y~   62 (234)
T PRK08301         23 YIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERNL   62 (234)
T ss_pred             HhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHhH
Confidence            66666444 44888888999999999987                                        89999999999


Q ss_pred             HHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc---c--C------
Q 014852          275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR---L--P------  343 (417)
Q Consensus       275 ~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir---l--p------  343 (417)
                      ++|+.+|.+|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+++++|++.+...   .  +      
T Consensus        63 ~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~~~~~~~~~~~~~~~  142 (234)
T PRK08301         63 RLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKAEVSFDEPLNIDWD  142 (234)
T ss_pred             HHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccccccccccccccccC
Confidence            9999999999999999999999999999999999999887789999999999999999997654211   0  0      


Q ss_pred             ------------c-cH------H-HHHHHHHHHHHHHHHc-------------CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852          344 ------------N-HL------H-ERLGLIRNAKLRLEEK-------------GVTPSVDRIAEYLNMSQKKVRNATEAI  390 (417)
Q Consensus       344 ------------~-~~------~-e~~~kI~~a~~~L~e~-------------gRepS~eEIAe~LGIS~etVr~aL~ra  390 (417)
                                  . ..      . .....+..++..|++.             ..+.|++|||+.||||+++|++.++++
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA  222 (234)
T PRK08301        143 GNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRI  222 (234)
T ss_pred             CCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence                        0 00      0 0123467777777442             235699999999999999999999998


Q ss_pred             Cccc
Q 014852          391 GKVF  394 (417)
Q Consensus       391 rk~L  394 (417)
                      ++.+
T Consensus       223 ~~~L  226 (234)
T PRK08301        223 IKRL  226 (234)
T ss_pred             HHHH
Confidence            7654

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.78  E-value=2.4e-18  Score=164.43  Aligned_cols=159  Identities=29%  Similarity=0.445  Sum_probs=127.6

Q ss_pred             HHHhhc-ccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhH
Q 014852          196 YVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV  274 (417)
Q Consensus       196 yl~~i~-~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl  274 (417)
                      |+.+-. .-+.|++.++.+|+..++.|+.                                        .|++.|+..|.
T Consensus        23 ~~~~~~~~~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~   62 (234)
T TIGR02835        23 YIGGSEALPPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNL   62 (234)
T ss_pred             HhcccccCCCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhH
Confidence            444433 3366888888899999999887                                        89999999999


Q ss_pred             HHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-cC----------
Q 014852          275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-LP----------  343 (417)
Q Consensus       275 ~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-lp----------  343 (417)
                      +.|+++|.+|.+++.++|||+||+|+++|+++++|++..+++|.||++++++|.+++++++..+... .+          
T Consensus        63 ~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~~~~~~~~~~~~~~  142 (234)
T TIGR02835        63 RLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRSEVSFDEPLNVDWD  142 (234)
T ss_pred             HHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccCcccccccccCCCC
Confidence            9999999999999999999999999999999999998887789999999999999999997654211 00          


Q ss_pred             ------------c-----cH---HHHHHHHHHHHHHHHHc-------------CCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852          344 ------------N-----HL---HERLGLIRNAKLRLEEK-------------GVTPSVDRIAEYLNMSQKKVRNATEAI  390 (417)
Q Consensus       344 ------------~-----~~---~e~~~kI~~a~~~L~e~-------------gRepS~eEIAe~LGIS~etVr~aL~ra  390 (417)
                                  .     ..   ......+..++..|++.             +.+.|++|||+.||+|+++|+.+++++
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra  222 (234)
T TIGR02835       143 GNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRI  222 (234)
T ss_pred             CCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence                        0     00   01123467777777431             145799999999999999999999988


Q ss_pred             Cccc
Q 014852          391 GKVF  394 (417)
Q Consensus       391 rk~L  394 (417)
                      ++.+
T Consensus       223 ~~~L  226 (234)
T TIGR02835       223 LKRL  226 (234)
T ss_pred             HHHH
Confidence            7644

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.

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.77  E-value=1.6e-18  Score=160.26  Aligned_cols=153  Identities=11%  Similarity=0.083  Sum_probs=123.6

Q ss_pred             cccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHH
Q 014852          201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI  280 (417)
Q Consensus       201 ~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sI  280 (417)
                      ...|+..+.++..|+..+..|+.                                        .|++.|++.|.++|+++
T Consensus         7 ~~~~~~~~~~~~~li~~~~~g~~----------------------------------------~a~~~l~~~y~~~l~~~   46 (194)
T PRK09646          7 MTGPPAESPDLDALLRRVARGDQ----------------------------------------DAFAELYDRTSSRVYGL   46 (194)
T ss_pred             ccCCCCCcccHHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence            34566666677788888888876                                        89999999999999999


Q ss_pred             HHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc---------Cc---cH--
Q 014852          281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL---------PN---HL--  346 (417)
Q Consensus       281 A~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl---------p~---~~--  346 (417)
                      |.+|+++..++||++||+||++|+++++|++.+| .|.+|++.+++|.++++++.+.+..+.         ..   ..  
T Consensus        47 ~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (194)
T PRK09646         47 VRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVDRVRSEQAASQREVRYGARNVDPAFDQVAE  125 (194)
T ss_pred             HHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHHHHHhhccccccccccccccccccccchHH
Confidence            9999999999999999999999999999998776 899999999999999999876532110         00   00  


Q ss_pred             ----HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          347 ----HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       347 ----~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                          .+....+..++..|++..|.         .|++|||+.||+|+++|+..++++++.+
T Consensus       126 ~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~L  186 (194)
T PRK09646        126 EVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRL  186 (194)
T ss_pred             HHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHHHHH
Confidence                11223466777777554444         3999999999999999999999998754

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.76  E-value=8e-18  Score=154.44  Aligned_cols=148  Identities=18%  Similarity=0.129  Sum_probs=119.7

Q ss_pred             CCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHcc
Q 014852          206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD  285 (417)
Q Consensus       206 Lt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~  285 (417)
                      +|+.+...|+..++.|+.                                        .|++.|+..|.+.|+.+|.++.
T Consensus         6 ~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~l~~~~~~~~   45 (189)
T PRK09648          6 DTGEELDALVAEAVAGDR----------------------------------------RALREVLEIIRPLVVRYCRARL   45 (189)
T ss_pred             CCchHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHh
Confidence            477777788888888887                                        8999999999999999999987


Q ss_pred             CC----CCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-----Cc------c-----
Q 014852          286 NM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-----PN------H-----  345 (417)
Q Consensus       286 ~~----g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-----p~------~-----  345 (417)
                      ++    +.+++|++||+|+++|+++.+|++.. .+|.||++.+++|.+++++++..+....     +.      .     
T Consensus        46 ~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~-~~~~~wl~~i~~n~~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~  124 (189)
T PRK09648         46 GGVERPGLSADDVAQEVCLAVITALPRYRDQG-RPFLAFVYGIAAHKVADAHRAAGRDKAVPTEEVPERPSDDAGPEERA  124 (189)
T ss_pred             cccccCCCCHHHHHHHHHHHHHHHHHHHhccC-CcHHHHHHHHHHHHHHHHHHHhCCCccccccccccccccCCCHHHHH
Confidence            64    46899999999999999999998653 4899999999999999999986653211     10      0     


Q ss_pred             -HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          346 -LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       346 -~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                       ..+....+..++..|++..|++         +++|||+.||+|+.+|+..++++++.|
T Consensus       125 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L  183 (189)
T PRK09648        125 LRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARL  183 (189)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence             1112234677777776655553         999999999999999999999988654

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.75  E-value=1.2e-17  Score=152.99  Aligned_cols=130  Identities=14%  Similarity=0.134  Sum_probs=107.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc--
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR--  341 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir--  341 (417)
                      .|++.|+..|.++|+.+|.++++++.+++|++||+|+++|+++.+|++.. .+|.+|++++++|.+.++++++.....  
T Consensus        20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~-~~f~~wl~~ia~n~~~d~~R~~~~~~~~~   98 (186)
T PRK05602         20 AAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGE-ARFDTWLHRVVLNLCYDRLRRRREVPVED   98 (186)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCCC-CcHHHHHHHHHHHHHHHHHHhcCCCCccc
Confidence            89999999999999999999999999999999999999999999999863 489999999999999999987653210  


Q ss_pred             cCc---------c---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 LPN---------H---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 lp~---------~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+.         .   ..+....+..++..|++..|+         .+++|||+.||+|..+|+..++++++.+
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L  172 (186)
T PRK05602         99 APDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRAL  172 (186)
T ss_pred             ccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence            110         0   012234467777777655554         3999999999999999999999998765

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=1.7e-17  Score=152.90  Aligned_cols=129  Identities=14%  Similarity=0.120  Sum_probs=107.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp  343 (417)
                      .|++.|+..|.+.|+++|.++.++..++||++||+|+++|+++.+|++..  .|.+|++++++|.+++++++..+....+
T Consensus        26 ~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~~~~~~R~~~~~~~~~  103 (194)
T PRK12513         26 AAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNLLIDHWRRHGARQAPS  103 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            89999999999999999999999999999999999999999999999754  7999999999999999998776432211


Q ss_pred             c------------c--------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 N------------H--------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ~------------~--------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .            .        ..+....+..++..|++..|.+         |++|||+.||+|+++|++.++++++.+
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L  183 (194)
T PRK12513        104 LDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKL  183 (194)
T ss_pred             cccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            0            0        0112245777788886655553         999999999999999999999998765

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.74  E-value=2.1e-17  Score=157.52  Aligned_cols=152  Identities=19%  Similarity=0.206  Sum_probs=127.3

Q ss_pred             cccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHH
Q 014852          201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI  280 (417)
Q Consensus       201 ~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sI  280 (417)
                      ...|+|++..+..|+.+++.|+.                                        .|++.|+..|.+.|+++
T Consensus         7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~   46 (231)
T PRK11922          7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT   46 (231)
T ss_pred             CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence            45688999999999999999987                                        89999999999999999


Q ss_pred             HHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc----------------
Q 014852          281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN----------------  344 (417)
Q Consensus       281 A~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~----------------  344 (417)
                      +.++.++..++|||+||+|+++|+++++|++..  .|.||++++++|.+++++|+..+....+.                
T Consensus        47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~~--~~~~wL~~iarn~~~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~  124 (231)
T PRK11922         47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGDA--SLSTWLSRIVLNEALGRLRRRRRLVNLAEMVMASTIAGGERTPLA  124 (231)
T ss_pred             HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCCc--hhHHHHHHHHHHHHHHHHHhhcccccchhcccccccccccccccC
Confidence            999999999999999999999999999999863  89999999999999999987664322110                


Q ss_pred             ----c------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          345 ----H------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       345 ----~------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                          .      ..+....+..++..|++..|++         |++|||+.||+|.++|+++++++++.+
T Consensus       125 ~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kL  193 (231)
T PRK11922        125 DPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLL  193 (231)
T ss_pred             cccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence                0      0112234777888886655553         999999999999999999999998655

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.74  E-value=1.5e-17  Score=154.05  Aligned_cols=131  Identities=28%  Similarity=0.347  Sum_probs=102.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp  343 (417)
                      .|++.|++.|.++|+.+|.+|.++..++||++||+|+++|+++.+|++.+|.+|.||++.++++.+.++++...+..+.+
T Consensus        24 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~~r~~~r~~~~~  103 (208)
T PRK08295         24 EALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKHIP  103 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhhhhcccc
Confidence            89999999999999999999999999999999999999999999999987679999999999999999887543321110


Q ss_pred             -----------------------------ccH------HHHHHHH-HHHHHHHHHcCC--------CccHHHHHHHcCCC
Q 014852          344 -----------------------------NHL------HERLGLI-RNAKLRLEEKGV--------TPSVDRIAEYLNMS  379 (417)
Q Consensus       344 -----------------------------~~~------~e~~~kI-~~a~~~L~e~gR--------epS~eEIAe~LGIS  379 (417)
                                                   ...      .+....+ ..++..|++..|        +.|++|||+.||+|
T Consensus       104 ~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l~~e~~s~~EIA~~lgis  183 (208)
T PRK08295        104 LNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELYLDGKSYQEIAEELNRH  183 (208)
T ss_pred             ccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCHHHHHHHHCCC
Confidence                                         000      0011122 223345443333        34999999999999


Q ss_pred             HHHHHHHHHHhCccc
Q 014852          380 QKKVRNATEAIGKVF  394 (417)
Q Consensus       380 ~etVr~aL~rark~L  394 (417)
                      +++|+.+++++++.+
T Consensus       184 ~~tV~~~l~rar~~L  198 (208)
T PRK08295        184 VKSIDNALQRVKRKL  198 (208)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999998765

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.73  E-value=4.3e-17  Score=149.76  Aligned_cols=131  Identities=26%  Similarity=0.345  Sum_probs=102.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .|++.|+..|.+.|+.+|.++.++..+++||+||+|+++|+++.+|++..+.+|.||++++|++.+.++++...+..+. 
T Consensus        19 ~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~~~~r~~~~~~~~~   98 (198)
T TIGR02859        19 HALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIKTATRQKHIP   98 (198)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            8999999999999999999999999999999999999999999999998767999999999999888777643211000 


Q ss_pred             -------------------------------CccH---HHHHHHHHHHHHHH-HHcCC--------CccHHHHHHHcCCC
Q 014852          343 -------------------------------PNHL---HERLGLIRNAKLRL-EEKGV--------TPSVDRIAEYLNMS  379 (417)
Q Consensus       343 -------------------------------p~~~---~e~~~kI~~a~~~L-~e~gR--------epS~eEIAe~LGIS  379 (417)
                                                     |...   .+....+.+++..| ++..+        +.|++|||+.||+|
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~~~~s~~eIA~~l~~s  178 (198)
T TIGR02859        99 LNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYLDGKSYQEIACDLNRH  178 (198)
T ss_pred             hhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence                                           0000   11123355666664 22222        24999999999999


Q ss_pred             HHHHHHHHHHhCccc
Q 014852          380 QKKVRNATEAIGKVF  394 (417)
Q Consensus       380 ~etVr~aL~rark~L  394 (417)
                      +++|+.+++++++.+
T Consensus       179 ~~tV~~~l~r~r~~L  193 (198)
T TIGR02859       179 VKSIDNALQRVKRKL  193 (198)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999998765

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.

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=2.9e-17  Score=149.24  Aligned_cols=130  Identities=14%  Similarity=0.063  Sum_probs=105.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-cc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-RL  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i-rl  342 (417)
                      .|+..|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++..+ .|.||++.+++|.+++++++..+.. ..
T Consensus        19 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R~~~~~~~~~   97 (179)
T PRK12514         19 DAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLRARKAVAVDI   97 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhcCCccccc
Confidence            899999999999999999999999999999999999999999999997554 7999999999999999998755321 00


Q ss_pred             ------------CccH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 ------------PNHL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 ------------p~~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                  |...   .+....+..++..|++..|+         .|++|||+.||+|+++|+..++++++.+
T Consensus        98 ~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L  173 (179)
T PRK12514         98 DEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKL  173 (179)
T ss_pred             ccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence                        0000   11223466777777654444         3999999999999999999999998765

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.73  E-value=2.2e-17  Score=145.90  Aligned_cols=129  Identities=19%  Similarity=0.187  Sum_probs=105.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL---  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i---  340 (417)
                      .||+.|++.|.++|++++.++ ++..++||++||+|+++|+++++|++..| +|.+|++.+++|.++++++++.+..   
T Consensus         4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~~~   81 (154)
T PRK06759          4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQEKC   81 (154)
T ss_pred             ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence            689999999999999999987 45679999999999999999999998776 8999999999999999999874211   


Q ss_pred             ---ccCcc---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 ---RLPNH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 ---rlp~~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                         ..|..   ..+....+..++..|++..|.         .|++|||+.||+|+++|+.++.++++.+
T Consensus        82 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~L  150 (154)
T PRK06759         82 VCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKM  150 (154)
T ss_pred             cccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence               11222   222345577777777654444         4999999999999999999999998654

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.72  E-value=5.9e-17  Score=148.97  Aligned_cols=144  Identities=17%  Similarity=0.225  Sum_probs=117.0

Q ss_pred             cCChHHHHHHhhh----hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHH
Q 014852          249 RISRPELQSILME----CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW  324 (417)
Q Consensus       249 ~~s~~eLr~~l~~----~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~  324 (417)
                      .+++++|...++.    +..|++.|+..|.+.|+++|.+|.++..+++|++||+|+++|+++++|++. + +|.||++++
T Consensus         7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~-~-~~~~wl~~i   84 (188)
T PRK09640          7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK-S-KFKTWLYSI   84 (188)
T ss_pred             CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC-C-cchHHHHHH
Confidence            3456666666653    688999999999999999999999999999999999999999999999964 3 899999999


Q ss_pred             HHhhHHHHHHhhccccccC---------c---c---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCH
Q 014852          325 IRQGVSRALVENSRTLRLP---------N---H---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQ  380 (417)
Q Consensus       325 IR~~i~~~Ird~~r~irlp---------~---~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~  380 (417)
                      ++|.+++++++..+.....         .   .   ..+....+..++..|++..|++         +++|||+.||||.
T Consensus        85 a~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~  164 (188)
T PRK09640         85 TYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGL  164 (188)
T ss_pred             HHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCH
Confidence            9999999998754321111         0   0   1122355788888887666654         9999999999999


Q ss_pred             HHHHHHHHHhCccc
Q 014852          381 KKVRNATEAIGKVF  394 (417)
Q Consensus       381 etVr~aL~rark~L  394 (417)
                      ++|+..+.+|++.+
T Consensus       165 ~tV~~~l~Ra~~~L  178 (188)
T PRK09640        165 SATKMRYKRALDKL  178 (188)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999998654

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=2.5e-17  Score=152.52  Aligned_cols=130  Identities=19%  Similarity=0.233  Sum_probs=106.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-c-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-R-  341 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i-r-  341 (417)
                      .|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+.+.+|++..+ .|.||+++++++.++++++++.+.. . 
T Consensus        26 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~Rk~~~~~~~~  104 (196)
T PRK12524         26 AAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEA-RVSTWLYRVVCNLCTDRLRRRRRASVDL  104 (196)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhccccccc-hHHHHHHHHHHHHHHHHHHhhcCCCCCc
Confidence            899999999999999999999999999999999999999999999986444 8999999999999999998754321 1 


Q ss_pred             --cC------c---c---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 --LP------N---H---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 --lp------~---~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                        .+      .   .   ..+....+..++..|++..|.         .+++|||+.||+|..+|+++++++++.+
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L  180 (196)
T PRK12524        105 DDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRAL  180 (196)
T ss_pred             cccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence              00      0   0   011224467777777654443         4999999999999999999999998766

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.72  E-value=4.9e-17  Score=149.48  Aligned_cols=147  Identities=20%  Similarity=0.250  Sum_probs=119.1

Q ss_pred             CCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHcc
Q 014852          206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD  285 (417)
Q Consensus       206 Lt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~  285 (417)
                      ||+..+..|+..++.||.                                        .+++.|+..|.+.|+.+++++.
T Consensus         2 ~~~~~~~~ll~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~~~~~~   41 (193)
T PRK11923          2 LTQEEDQQLVERVQRGDK----------------------------------------RAFDLLVLKYQHKILGLIVRFV   41 (193)
T ss_pred             CccccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHh
Confidence            566666778888888887                                        8999999999999999999999


Q ss_pred             CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc---c--C------------cc---
Q 014852          286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR---L--P------------NH---  345 (417)
Q Consensus       286 ~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir---l--p------------~~---  345 (417)
                      ++..+++|++||+|+++|+++.+|++..  .|.+|++++++|.++++++++.+...   .  .            ..   
T Consensus        42 ~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (193)
T PRK11923         42 HDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESP  119 (193)
T ss_pred             CCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHHHhcCCCccccccccchhhhcccccccCcCCH
Confidence            9999999999999999999999999875  69999999999999999986543211   0  0            00   


Q ss_pred             -----HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          346 -----LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       346 -----~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                           ..+....+..++..|++..|.+         +++|||+.||+|+++|+..+.++++.|
T Consensus       120 e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~L  182 (193)
T PRK11923        120 ERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAREAI  182 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                 0011234666777776555543         999999999999999999999998755

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.72  E-value=3.2e-17  Score=149.65  Aligned_cols=130  Identities=15%  Similarity=0.167  Sum_probs=106.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-c
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-l  342 (417)
                      .|++.|+..|.+.|+.++.++.+++.+++|++||+|+++|+++++|++..+ .|.+|++++++|.+++++++..+... +
T Consensus        23 ~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~rk~~~~~~~~  101 (186)
T PRK13919         23 EALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAVDHVRRRAARPQPL  101 (186)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHHHHHHhhhcccccc
Confidence            899999999999999999999988899999999999999999999997654 79999999999999999987653211 1


Q ss_pred             ------C------cc-----HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 ------P------NH-----LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 ------p------~~-----~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                            +      ..     .......+..++..|++..|.+         +++|||+.||+|+++|+..++++++.+
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~L  179 (186)
T PRK13919        102 EPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRL  179 (186)
T ss_pred             cccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence                  0      00     0111234677777776545443         999999999999999999999998765

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=3.2e-17  Score=149.98  Aligned_cols=130  Identities=15%  Similarity=0.068  Sum_probs=106.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc--
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR--  341 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir--  341 (417)
                      .+++.|+..|.+.|+++|.++.++..++||++||+|+++|+++++|++.++ .|.||++++++|.+++++++..+...  
T Consensus        25 ~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~R~~~~~~~~~  103 (187)
T PRK12534         25 HAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHLRANAPQRRNV  103 (187)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhcccccccc
Confidence            899999999999999999999999999999999999999999999998765 79999999999999999987643210  


Q ss_pred             ----cC---------cc---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 ----LP---------NH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 ----lp---------~~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                          .+         ..   ..+....+..++..|++..+.         .+++|||+.||+|+++|+.+++++++.|
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~L  181 (187)
T PRK12534        104 ALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKL  181 (187)
T ss_pred             cccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence                00         00   112234566777777554333         4999999999999999999999998765

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=3.9e-17  Score=151.02  Aligned_cols=130  Identities=15%  Similarity=0.114  Sum_probs=105.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-cc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-RL  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i-rl  342 (417)
                      .+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++..+ .|.||++++++|.+++++++..+.. ..
T Consensus        27 ~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~Rk~~~~~~~~  105 (194)
T PRK12531         27 QAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLRKQKGKDLHI  105 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHHHhccccccc
Confidence            899999999999999999999999889999999999999999999997655 7999999999999999998765321 10


Q ss_pred             ------Cc---------c-HH---HHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 ------PN---------H-LH---ERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 ------p~---------~-~~---e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                            +.         . ..   .....+..++..|++..|.         .+++|||+.||||+++|+..++++++.+
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~~~L  185 (194)
T PRK12531        106 HADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKL  185 (194)
T ss_pred             chhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence                  00         0 00   1123466667777554444         3999999999999999999999998765

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.72  E-value=4.7e-17  Score=149.95  Aligned_cols=130  Identities=18%  Similarity=0.176  Sum_probs=104.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCC---CCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~---g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      .|++.|+..|.+.|+.++.++.++   ..++||++||+|+++|+++++|+++.+ .|.||++++++|.+.++++++.+..
T Consensus        18 ~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~~d~~rk~~~~~   96 (189)
T PRK06811         18 KALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKAIDYKRKLTKNN   96 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHHHHHHHHhcccc
Confidence            899999999999999999999875   357999999999999999999997655 8999999999999999998766432


Q ss_pred             ccC---c-------c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 RLP---N-------H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 rlp---~-------~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...   .       .      ..+....+..++..|++..|.         .+++|||+.||+|..+|++.+.++++.+
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~L  175 (189)
T PRK06811         97 EIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKL  175 (189)
T ss_pred             ccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            211   0       0      111223466777777554443         4999999999999999999999998654

>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family

Probab=99.71  E-value=4.5e-17  Score=145.69  Aligned_cols=132  Identities=15%  Similarity=0.067  Sum_probs=107.3

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir  341 (417)
                      +..|++.|+..|.+.++.++.++.++..++||++||+|+++|+++++|+...+ +|.+|++++++|.++++++.+.+...
T Consensus         9 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~~   87 (170)
T TIGR02952         9 EEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHPL   87 (170)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence            33899999999999999999999988899999999999999999999997655 89999999999999999997654322


Q ss_pred             cCc-----------cH------HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 LPN-----------HL------HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 lp~-----------~~------~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+.           ..      .+....+..++..|++..|.         .+++|||+.||||+++|+..++++++.+
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~L  166 (170)
T TIGR02952        88 FSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIKKL  166 (170)
T ss_pred             CcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            110           00      11224466777777654444         3999999999999999999999998654

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.

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.71  E-value=7.1e-17  Score=146.79  Aligned_cols=129  Identities=19%  Similarity=0.161  Sum_probs=105.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp  343 (417)
                      .|+.+|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++.+|++..  +|.||++++++|.+.+++++..+.....
T Consensus        18 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~~~rk~~~~~~~~   95 (187)
T TIGR02948        18 NAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTIDRLRKRKPDFYLD   95 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHhhccccccc
Confidence            89999999999999999999999999999999999999999999999876  7999999999999999998754321100


Q ss_pred             c-------------------c---H---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHH
Q 014852          344 N-------------------H---L---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEA  389 (417)
Q Consensus       344 ~-------------------~---~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~r  389 (417)
                      .                   .   .   .+....+.+++..|++..|.+         +++|||+.||+|+++|+..+++
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~~v~~~l~R  175 (187)
T TIGR02948        96 DEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEILDLPVGTVKTRIHR  175 (187)
T ss_pred             ccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            0                   0   0   011233666777776555443         9999999999999999999999


Q ss_pred             hCccc
Q 014852          390 IGKVF  394 (417)
Q Consensus       390 ark~L  394 (417)
                      +++.+
T Consensus       176 ar~~L  180 (187)
T TIGR02948       176 GREAL  180 (187)
T ss_pred             HHHHH
Confidence            98755

This sigma factor is restricted to certain lineages of the order Bacillales.

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.71  E-value=5.1e-17  Score=148.67  Aligned_cols=130  Identities=21%  Similarity=0.239  Sum_probs=107.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp  343 (417)
                      .|++.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|++..+ .|.+|++++++|.+++++++..+.....
T Consensus        23 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~r~~~~~~~~~  101 (182)
T PRK12537         23 RALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLALNVLRDTRREVVLD  101 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhccccCccc
Confidence            899999999999999999999999999999999999999999999987554 7999999999999999999876432211


Q ss_pred             c----------cH------HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 N----------HL------HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ~----------~~------~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .          ..      .+....+..++..|++..|.         .+++|||+.||||+++|+..++++++.+
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~L  177 (182)
T PRK12537        102 DDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKAL  177 (182)
T ss_pred             cchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHHHH
Confidence            0          00      11223466777777654444         3999999999999999999999998654

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.71  E-value=8.2e-17  Score=148.11  Aligned_cols=129  Identities=22%  Similarity=0.229  Sum_probs=104.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .|++.|+..|.+.|+.++.++.++..+++|++||+|+++|+. ..|++..+ .|.||++++++|.++++++++.+.... 
T Consensus        29 ~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~Rk~~~~~~~~  106 (194)
T PRK12519         29 AALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLRSRRSRQRLL  106 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHHhcccccchh
Confidence            899999999999999999999999999999999999999976 67887665 899999999999999999876542110 


Q ss_pred             -----------Cc-c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 -----------PN-H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 -----------p~-~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                 +. .      ..+....+..++..|++..++         .+++|||+.||+|+.+|+..++++++.+
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L  185 (194)
T PRK12519        107 ERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKL  185 (194)
T ss_pred             hhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence                       00 0      011224467777777654444         3999999999999999999999988654

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.70  E-value=1.5e-16  Score=151.95  Aligned_cols=120  Identities=19%  Similarity=0.205  Sum_probs=100.9

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCC--CChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc---c
Q 014852          265 AREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR---T  339 (417)
Q Consensus       265 Are~LIe~yl~LV~sIA~Ry~~~g--~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r---~  339 (417)
                      .+++||..|.|+|.++|.+|+++.  .+.||++|+|+||||+|+++||+++|.+|.|||.++|++++.+++|+..+   .
T Consensus        10 ~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k~~~~   89 (218)
T TIGR02895        10 EREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQKYQNL   89 (218)
T ss_pred             HHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhcccccCe
Confidence            399999999999999999998664  58999999999999999999999999999999999999999999999873   4


Q ss_pred             cccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHH------cCCCHHHHH
Q 014852          340 LRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEY------LNMSQKKVR  384 (417)
Q Consensus       340 irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~------LGIS~etVr  384 (417)
                      +++|+...+....+..+...+. ..++.++.+||+..      .||+.+.+-
T Consensus        90 v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv  141 (218)
T TIGR02895        90 LYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELV  141 (218)
T ss_pred             eeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHh
Confidence            4677665555556666666664 46888888888764      488877763

Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).

>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family

Probab=99.70  E-value=1e-16  Score=144.45  Aligned_cols=129  Identities=18%  Similarity=0.146  Sum_probs=106.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp  343 (417)
                      .|++.|+..|.+.|++++.++.++..++||++||+|+.+|+.+.+|++..  +|.||++.+++|.+++++++..+....+
T Consensus        16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~~   93 (169)
T TIGR02954        16 PAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECIDLLKKKKKVIPFD   93 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHHHHHHhcCCcCccc
Confidence            89999999999999999999999999999999999999999999999754  7999999999999999998765432211


Q ss_pred             cc----------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 NH----------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ~~----------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ..          ..+....+..++..|++..|+         .|++|||+.||+|+++|+..+.++++.+
T Consensus        94 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L  163 (169)
T TIGR02954        94 PNTSIEKGECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKL  163 (169)
T ss_pred             cccccccchhhhchHHHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            10          011123566777777655554         3999999999999999999999998754

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 certain Bacillus and Clostridium species.

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.70  E-value=9.3e-17  Score=154.12  Aligned_cols=130  Identities=21%  Similarity=0.228  Sum_probs=107.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc--c
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--R  341 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i--r  341 (417)
                      .|++.|+..|.+.|+.++.+++++..++||++||+|+++|+.+++|++..+ .|.+|++++++|.+++++|++.+..  .
T Consensus        63 ~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~~~~~~~~  141 (233)
T PRK12538         63 AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKPRTENVDA  141 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhhccccccc
Confidence            899999999999999999999999999999999999999999999987655 7999999999999999998753211  0


Q ss_pred             c-------CccH-----HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 L-------PNHL-----HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 l-------p~~~-----~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .       +...     .+....+..++..|++..|++         +++|||+.||+|+++|+..++++++.|
T Consensus       142 ~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kL  215 (233)
T PRK12538        142 VPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQL  215 (233)
T ss_pred             ccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            1       1100     112234677788886655553         999999999999999999999998755

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.70  E-value=2e-16  Score=144.60  Aligned_cols=129  Identities=16%  Similarity=0.159  Sum_probs=105.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcc-CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYD-NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~-~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl  342 (417)
                      .|++.|+..|.+.|+.++.++. ++..++||++||+|+.+|+.++.|++..  +|.+|++.+++|.+++++|+..+....
T Consensus        21 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~~--~~~~wl~~iarN~~~d~~Rk~~~~~~~   98 (181)
T PRK12536         21 AAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRADQ--PLTAWVHAIARYKLMDFLRSRARREAL   98 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHHHhccccc
Confidence            8999999999999999999876 4578999999999999999999999753  799999999999999999986432211


Q ss_pred             C--------------ccHHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 P--------------NHLHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 p--------------~~~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .              ....+....+..++..|++..+.+         +++|||+.||+|+++|+..++++++.+
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar~~L  173 (181)
T PRK12536         99 HDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKAL  173 (181)
T ss_pred             cCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            0              011223345777777776555543         999999999999999999999998765

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.69  E-value=1.4e-16  Score=147.40  Aligned_cols=129  Identities=18%  Similarity=0.203  Sum_probs=107.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp  343 (417)
                      .+++.|++.|.+.|++++.++.++..++||++||+|+.+|+.+++|++..  +|.+|++++++|.+++++|+..+....+
T Consensus        27 ~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~~d~~Rk~~~~~~~~  104 (192)
T PRK09643         27 YAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDRLRRAKARPTVP  104 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHHHHHHHccccCCCCC
Confidence            89999999999999999999999999999999999999999999999764  7999999999999999998765322111


Q ss_pred             -----------ccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 -----------NHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 -----------~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                 ...   .+....+..++..|++..|.+         +++|||+.||+|..+|+..++++++.+
T Consensus       105 ~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl~rar~~L  178 (192)
T PRK09643        105 LDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARL  178 (192)
T ss_pred             ccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence                       111   122345777777886655543         999999999999999999999998765

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.69  E-value=1.6e-16  Score=143.57  Aligned_cols=129  Identities=16%  Similarity=0.147  Sum_probs=106.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp  343 (417)
                      .|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++..  +|.+|++.+++|.+++++++..+.....
T Consensus        18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~   95 (176)
T PRK09638         18 AALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRS--KFSTWLISIASRLYKDHLRKQKREKLRL   95 (176)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCcc--cHHHHHHHHHHHHHHHHHHHhccccchh
Confidence            89999999999999999999999999999999999999999999998753  8999999999999999999765422110


Q ss_pred             ----------c--c---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 ----------N--H---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ----------~--~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                .  .   .......+..++..|++..|.+         +++|||+.||+|+.+|+..+.++++.+
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l  170 (176)
T PRK09638         96 QRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQL  170 (176)
T ss_pred             hhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence                      0  0   1112345677777776655553         999999999999999999999988654

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.69  E-value=1.7e-16  Score=148.55  Aligned_cols=130  Identities=18%  Similarity=0.156  Sum_probs=106.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .++++|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|++.++ .|.||++++++|.+++++++..+.... 
T Consensus        38 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~~~~~  116 (206)
T PRK12526         38 QAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAKKEQN  116 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccccccc
Confidence            899999999999999999999999899999999999999999999998766 699999999999999999876532110 


Q ss_pred             ------C--c-------c---HHH--HHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          343 ------P--N-------H---LHE--RLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       343 ------p--~-------~---~~e--~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                            +  .       .   ...  ....+..++..|++..|.         .|++|||+.||+|+.+|+..++++++.
T Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~  196 (206)
T PRK12526        117 LGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAK  196 (206)
T ss_pred             cccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                  0  0       0   000  113466777777554444         399999999999999999999999876


Q ss_pred             c
Q 014852          394 F  394 (417)
Q Consensus       394 L  394 (417)
                      +
T Consensus       197 L  197 (206)
T PRK12526        197 L  197 (206)
T ss_pred             H
Confidence            5

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.69  E-value=1.8e-16  Score=145.99  Aligned_cols=130  Identities=16%  Similarity=0.139  Sum_probs=106.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .|++.|+..|.+.++.++. +.++..++||++||+|+.+|+.+++|++..  .|.+|++++++|.+++++++..+.... 
T Consensus        24 ~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~~--~~~~Wl~~Iarn~~~d~~Rk~~~~~~~~  100 (185)
T PRK09649         24 RALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSARS--SARTWLLAIARHVVADHIRHVRSRPRTT  100 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCccc--hHHHHHHHHHHHHHHHHHHHhccccccc
Confidence            8999999999999999995 577788999999999999999999999653  899999999999999999875432211 


Q ss_pred             ----Ccc---------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          343 ----PNH---------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       343 ----p~~---------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                          +..         ..+....+..++..|++..|++         |++|||+.||+|+++|+..+.++++.+--
T Consensus       101 ~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~  176 (185)
T PRK09649        101 RGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLA  176 (185)
T ss_pred             cccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence                110         0122345777888887666654         99999999999999999999999987643

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.69  E-value=2.7e-16  Score=143.35  Aligned_cols=129  Identities=20%  Similarity=0.226  Sum_probs=105.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++..  +|.+|++++++|.+++++++..+.... 
T Consensus        20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~--~~~~wl~~iarn~~~~~~r~~~r~~~~~   97 (190)
T TIGR02939        20 QAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGDS--AFYTWLYRIAVNTAKNHLVAQGRRPPTS   97 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCCC--ccHhHHHHHHHHHHHHHHHHhccCCCcc
Confidence            89999999999999999999999999999999999999999999999763  799999999999999999765432210 


Q ss_pred             ---------------------Ccc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHH
Q 014852          343 ---------------------PNH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEA  389 (417)
Q Consensus       343 ---------------------p~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~r  389 (417)
                                           |..   ..+....+..++..|++..|.+         +++|||+.||+++.+|++.+++
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tv~~~l~r  177 (190)
T TIGR02939        98 DVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIARIMDCPVGTVRSRIFR  177 (190)
T ss_pred             cccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence                                 000   0111234666777776555543         9999999999999999999999


Q ss_pred             hCccc
Q 014852          390 IGKVF  394 (417)
Q Consensus       390 ark~L  394 (417)
                      +++.|
T Consensus       178 ar~~L  182 (190)
T TIGR02939       178 AREAI  182 (190)
T ss_pred             HHHHH
Confidence            98765

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 RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.69  E-value=2.9e-16  Score=142.82  Aligned_cols=129  Identities=22%  Similarity=0.189  Sum_probs=105.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .|++.|+..|.++|+.+|.++.++..+++|++||+|++||+++++|++..  .|.+|++++++|.+++++++..+.... 
T Consensus        18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R~~~~~~~~~   95 (187)
T PRK09641         18 NAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLRKRKPDYYLD   95 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHHhcCcccccc
Confidence            89999999999999999999999999999999999999999999999754  799999999999999999876532110 


Q ss_pred             ---------------Cc---c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHH
Q 014852          343 ---------------PN---H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEA  389 (417)
Q Consensus       343 ---------------p~---~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~r  389 (417)
                                     +.   .      ..+....+..++..|++..++         .+++|||+.||||+++|++.+++
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~~lgis~~~v~~~l~R  175 (187)
T PRK09641         96 AEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHR  175 (187)
T ss_pred             ccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHHHHCCCHHHHHHHHHH
Confidence                           00   0      011123466677777554444         39999999999999999999999


Q ss_pred             hCccc
Q 014852          390 IGKVF  394 (417)
Q Consensus       390 ark~L  394 (417)
                      +++.+
T Consensus       176 ar~~L  180 (187)
T PRK09641        176 GREAL  180 (187)
T ss_pred             HHHHH
Confidence            98654

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.68  E-value=5.3e-16  Score=142.20  Aligned_cols=129  Identities=21%  Similarity=0.187  Sum_probs=104.9

Q ss_pred             HHHHHHHHHhHHHHHHHHH----HccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccc
Q 014852          264 LAREKLVMSNVRLVMSIAQ----RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT  339 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~----Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~  339 (417)
                      .||+.|+..|.+.|+.++.    ++.++..+++|++||+|+.+|+.++.|++..  .|.+|++++++|.+++++++..+.
T Consensus        21 ~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~d~~R~~~~~   98 (184)
T PRK12539         21 AAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLIDHLRRTRAS   98 (184)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHHHHHHHHhcc
Confidence            8999999999999999976    5557889999999999999999999999764  799999999999999999875532


Q ss_pred             c-ccC---------cc---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          340 L-RLP---------NH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       340 i-rlp---------~~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      . ..+         ..   ..+....+..++..|++..|+         .+++|||+.||+|+++|+..++++++.+
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~L  175 (184)
T PRK12539         99 LADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLKAL  175 (184)
T ss_pred             ccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            1 111         00   122334577778888665554         3999999999999999999999998754

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=1.4e-16  Score=145.98  Aligned_cols=134  Identities=18%  Similarity=0.147  Sum_probs=109.6

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       261 ~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      ++..|++.|+..|.+.|+.+|.+++++..++||++||+|+.+|+++.+|++..+..|.||++++++|.+++++++..+..
T Consensus         6 gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~   85 (185)
T PRK12542          6 NDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHE   85 (185)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            45589999999999999999999999999999999999999999999998754448999999999999999998865432


Q ss_pred             cc----C--------ccH------HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          341 RL----P--------NHL------HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       341 rl----p--------~~~------~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                      ..    +        ...      ......+..++..|++..|++         +++|||+.||+|+++|+..+.++++.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~  165 (185)
T PRK12542         86 TFLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKR  165 (185)
T ss_pred             hhhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            11    0        000      011234677777887656554         99999999999999999999999876


Q ss_pred             c
Q 014852          394 F  394 (417)
Q Consensus       394 L  394 (417)
                      +
T Consensus       166 L  166 (185)
T PRK12542        166 V  166 (185)
T ss_pred             H
Confidence            5

>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]

Probab=99.66  E-value=6.9e-16  Score=141.35  Aligned_cols=135  Identities=24%  Similarity=0.251  Sum_probs=112.4

Q ss_pred             HhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852          258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (417)
Q Consensus       258 ~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~  337 (417)
                      ....+..++..++..|.+.++.++.+++++..++|||+||+|+.+|+++..| ...+ .|.||++++++|.+++++|+..
T Consensus         9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~~-~~~~wl~~Ia~n~~iD~~R~~~   86 (182)
T COG1595           9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGRS-SFKAWLYRIARNLAIDRLRKRK   86 (182)
T ss_pred             HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CCCC-chHHHHHHHHHHHHHHHHHHhc
Confidence            3445668999999999999999999999988899999999999999999999 4444 8999999999999999999776


Q ss_pred             ccccc-C-------------ccH-----HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHH
Q 014852          338 RTLRL-P-------------NHL-----HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEA  389 (417)
Q Consensus       338 r~irl-p-------------~~~-----~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~r  389 (417)
                      +.... .             ...     .+....+..++..|++..|++         |++|||+.||||+++|+..+++
T Consensus        87 r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~r  166 (182)
T COG1595          87 RRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHR  166 (182)
T ss_pred             ccccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            53221 0             001     233456888888887766664         9999999999999999999999


Q ss_pred             hCccc
Q 014852          390 IGKVF  394 (417)
Q Consensus       390 ark~L  394 (417)
                      ++..+
T Consensus       167 a~~~l  171 (182)
T COG1595         167 ARKKL  171 (182)
T ss_pred             HHHHH
Confidence            98755

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.66  E-value=4.1e-16  Score=139.95  Aligned_cols=131  Identities=24%  Similarity=0.189  Sum_probs=104.4

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir  341 (417)
                      +..|++.|+..|.++|+.++.+|.+++.+++|++||++++||+++++|+ . +.+|.||++.++++.+.+++++..+...
T Consensus         8 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~-~-~~~~~~~l~~~~~~~~~~~~r~~~~~~~   85 (182)
T PRK09652          8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR-G-GAAFYTWLYRIARNTAINYLRKQGRRPP   85 (182)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC-C-CcchHHHHHHHHHHHHHHHHHcccCCCC
Confidence            4489999999999999999999999999999999999999999999999 3 3489999999999999999987654322


Q ss_pred             cC-------c---------c---H------HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHH
Q 014852          342 LP-------N---------H---L------HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNAT  387 (417)
Q Consensus       342 lp-------~---------~---~------~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL  387 (417)
                      .+       .         .   .      .+....+..++..|++..|.         .+++|||+.||+|+.+|+..+
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l  165 (182)
T PRK09652         86 ASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI  165 (182)
T ss_pred             ccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            11       0         0   0      01223455666666443333         399999999999999999999


Q ss_pred             HHhCccc
Q 014852          388 EAIGKVF  394 (417)
Q Consensus       388 ~rark~L  394 (417)
                      +++++.+
T Consensus       166 ~ra~~~L  172 (182)
T PRK09652        166 FRAREAL  172 (182)
T ss_pred             HHHHHHH
Confidence            9988654

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=99.66  E-value=4.6e-16  Score=141.44  Aligned_cols=129  Identities=19%  Similarity=0.187  Sum_probs=100.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCC-----ChhhhhhhHHHHHHH-HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~-----e~EDLIQEG~IgLik-AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~  337 (417)
                      .|++.|+..|.+.|+.+|.+|.++..     +++|++||+|+.+|+ ...+|++. + .|.+|++.+++|.+++++++..
T Consensus        17 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~-~-~~~~wl~~i~~n~~~d~~R~~~   94 (183)
T TIGR02999        17 AARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR-A-HFFAAAAKAMRRILVDHARRRR   94 (183)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch-H-HHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999998877     899999999999998 78889754 3 7999999999999999998754


Q ss_pred             cccc------c------Cc---cHHHHHHHHHHHHHH---HHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHh
Q 014852          338 RTLR------L------PN---HLHERLGLIRNAKLR---LEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAI  390 (417)
Q Consensus       338 r~ir------l------p~---~~~e~~~kI~~a~~~---L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~ra  390 (417)
                      +..+      .      +.   ...+....+..+...   |++..|+         .|++|||+.||||+++|+..++++
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Ra  174 (183)
T TIGR02999        95 AQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFA  174 (183)
T ss_pred             HHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            3211      0      00   111222233444344   6554444         399999999999999999999999


Q ss_pred             Cccc
Q 014852          391 GKVF  394 (417)
Q Consensus       391 rk~L  394 (417)
                      ++.+
T Consensus       175 r~~L  178 (183)
T TIGR02999       175 RAWL  178 (183)
T ss_pred             HHHH
Confidence            8654

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=6.1e-16  Score=142.14  Aligned_cols=129  Identities=16%  Similarity=0.146  Sum_probs=105.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .|++.|+..|.+.++.++.++.++..+++|++||+|+.+|+++.+|++..  .|.||++++++|.+.+++++..+.... 
T Consensus        22 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~   99 (189)
T PRK12515         22 TAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRS--QVSTWLLSIARFKALSALRRRKHEEIDD   99 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--ChHHHHHHHHHHHHHHHHHccCCCCCcc
Confidence            89999999999999999999999999999999999999999999999753  899999999999999999875432110 


Q ss_pred             ------Cc------cH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 ------PN------HL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 ------p~------~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                            +.      ..   .+....+..++..|++..|+         .+++|||+.||+|+++|++.+.++++.+
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~Rar~~L  175 (189)
T PRK12515        100 EAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKL  175 (189)
T ss_pred             ccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence                  00      00   01123466677777654544         3999999999999999999999998765

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=1.2e-15  Score=139.16  Aligned_cols=129  Identities=19%  Similarity=0.162  Sum_probs=105.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccC----CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT  339 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~----~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~  339 (417)
                      .|++.|+..|.+.|+.+|.++++    +..+++|++||+|+.+|+..++|+...  .|.+|++.+++|.+.++++++.+.
T Consensus        22 ~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~~--~~~~wl~~i~rn~~~d~~Rr~~~~   99 (184)
T PRK12512         22 AAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPGA--PFAPWLFAIARNKLIDALRRRGRR   99 (184)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCccc--cHHHHHHHHHHHHHHHHHHhhccc
Confidence            89999999999999999999875    346899999999999999999998743  799999999999999999876543


Q ss_pred             ccc---------Ccc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          340 LRL---------PNH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       340 irl---------p~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...         +..   .......+.+++..|++..|++         +++|||+.||+|..+|+..++++++.+
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~~~L  175 (184)
T PRK12512        100 VFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL  175 (184)
T ss_pred             ccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            221         111   1122355777777776655553         999999999999999999999998765

>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family

Probab=99.65  E-value=6.9e-16  Score=136.82  Aligned_cols=128  Identities=16%  Similarity=0.173  Sum_probs=105.0

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-C
Q 014852          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-P  343 (417)
Q Consensus       265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-p  343 (417)
                      |++.++..|.+.|+.+|.++.++..++||++||+++.+|+++++|++..  .|.+|++++++|.++++++++.+.... .
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~~   79 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVFD   79 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccccC
Confidence            7899999999999999999999999999999999999999999999764  799999999999999999986643221 0


Q ss_pred             cc----------------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 NH----------------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ~~----------------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ..                ..+....+..++..|++..+.         .+++|||+.||||.++|+..++++++.+
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~L  155 (159)
T TIGR02989        80 DELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRL  155 (159)
T ss_pred             HHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            00                011223366667777554443         3999999999999999999999998765

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.65  E-value=9e-16  Score=140.24  Aligned_cols=131  Identities=12%  Similarity=0.124  Sum_probs=107.7

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir  341 (417)
                      +..|++.|+..|.+.|++++.+++++..+++|++||+|+.+|+++++|++..  .|.+|++++++|.+++++|+..+...
T Consensus        14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n~~~d~~Rk~~~~~~   91 (179)
T PRK09415         14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAINHCKDYLKSWHNKKV   91 (179)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHHHHHHHHHhhccccc
Confidence            4479999999999999999999999999999999999999999999998753  79999999999999999987532211


Q ss_pred             cC---------------cc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 LP---------------NH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 lp---------------~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+               ..   ..+....+..++..|++..|++         |++|||+.||||+++|+..+.++++.+
T Consensus        92 ~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~L  171 (179)
T PRK09415         92 IVTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELL  171 (179)
T ss_pred             cccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            10               00   1122345677777787666664         999999999999999999999998765

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=6.6e-16  Score=142.17  Aligned_cols=128  Identities=15%  Similarity=0.137  Sum_probs=106.0

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc
Q 014852          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN  344 (417)
Q Consensus       265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~  344 (417)
                      +|+.|+..|.+.|+.+|.+++++..++||++||.|+.+|+.+++|++..  +|.||++++++|.+++++++..+......
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            6899999999999999999999999999999999999999999998654  79999999999999999998654322110


Q ss_pred             ------------------------------cH------HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCC
Q 014852          345 ------------------------------HL------HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMS  379 (417)
Q Consensus       345 ------------------------------~~------~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS  379 (417)
                                                    ..      .+....+..++..|++..|.+         |++|||+.||+|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis  160 (191)
T PRK12520         81 DDADEQSDDDLFDALFAADGHYREPPSDWGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQIT  160 (191)
T ss_pred             cccccchhhhhhhhhcccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence                                          00      011234677777786655554         999999999999


Q ss_pred             HHHHHHHHHHhCccc
Q 014852          380 QKKVRNATEAIGKVF  394 (417)
Q Consensus       380 ~etVr~aL~rark~L  394 (417)
                      +++|+..++++++.+
T Consensus       161 ~~tV~~~l~Rar~~L  175 (191)
T PRK12520        161 ATNAWVLLYRARMRL  175 (191)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999998765

>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1

Probab=99.64  E-value=1.2e-15  Score=147.78  Aligned_cols=129  Identities=15%  Similarity=0.058  Sum_probs=105.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHH-------HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhh
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR-------GIEKFDSSKGFKISTYVYWWIRQGVSRALVEN  336 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLik-------AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~  336 (417)
                      .||..|++.|.+.|+.++.+++++..++||++||+|+.+|.       .+++|++..  .|.||++++++|.++++++++
T Consensus        39 ~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~--~~~tWL~~Ia~N~~id~lRk~  116 (244)
T TIGR03001        39 AALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRG--PLLSWVRIVATRIALELQAQE  116 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCC--chHhHHHHHHHHHHHHHHHHh
Confidence            89999999999999999999999999999999999999994       788899753  799999999999999999876


Q ss_pred             ccccccC---------------ccH-H------HHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHH
Q 014852          337 SRTLRLP---------------NHL-H------ERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRN  385 (417)
Q Consensus       337 ~r~irlp---------------~~~-~------e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~  385 (417)
                      .+...+.               ... .      +....+.+++..|++..|++         |++|||+.||||+++|+.
T Consensus       117 ~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~  196 (244)
T TIGR03001       117 RRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGLSMDRIGAMYQVHRSTVSR  196 (244)
T ss_pred             cccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Confidence            5422110               000 0      12234777888887655553         999999999999999999


Q ss_pred             HHHHhCccc
Q 014852          386 ATEAIGKVF  394 (417)
Q Consensus       386 aL~rark~L  394 (417)
                      .++++++.+
T Consensus       197 rl~RAr~~L  205 (244)
T TIGR03001       197 WVAQARERL  205 (244)
T ss_pred             HHHHHHHHH
Confidence            999988654

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=1.4e-15  Score=137.75  Aligned_cols=129  Identities=16%  Similarity=0.116  Sum_probs=105.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      ..+++|+..|.++|+.+|.+|.++..++||++||+|+.+|+++++|++..  +|.+|++.+++|.+++++|++.+.... 
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~   80 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI   80 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            46899999999999999999999999999999999999999999999864  899999999999999999876542110 


Q ss_pred             --------------------Ccc--HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          343 --------------------PNH--LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       343 --------------------p~~--~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                                          +..  ..+....+..++..|++..+.         .+++|||+.||+|+++|+..+.+++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~  160 (173)
T PRK12522         81 LDLFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAK  160 (173)
T ss_pred             ccccchhhhhhhccccCCCChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence                                000  011223466777777654444         3999999999999999999999998


Q ss_pred             ccc
Q 014852          392 KVF  394 (417)
Q Consensus       392 k~L  394 (417)
                      +.|
T Consensus       161 ~~L  163 (173)
T PRK12522        161 KQM  163 (173)
T ss_pred             HHH
Confidence            765

>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family

Probab=99.64  E-value=1.4e-15  Score=140.30  Aligned_cols=130  Identities=17%  Similarity=0.157  Sum_probs=107.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (417)
Q Consensus       263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl  342 (417)
                      ..+|+.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+.+|++..  +|.+|++++++|.+++++++..+....
T Consensus        10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~~--~~~~wL~~iarN~~~d~~Rk~~~~~~~   87 (193)
T TIGR02947        10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGT--NLKAWLYRILTNTYINSYRKAQRRPQQ   87 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCCC--cchHHHHHHHHHHHHHHHHHhcCCccc
Confidence            478999999999999999999999999999999999999999999998654  799999999999999999876543211


Q ss_pred             C--c------------c------HH-------HHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHH
Q 014852          343 P--N------------H------LH-------ERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNA  386 (417)
Q Consensus       343 p--~------------~------~~-------e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~a  386 (417)
                      .  .            .      ..       .....+..++..|++..|++         |++|||+.||||+++|+..
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~  167 (193)
T TIGR02947        88 SDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSR  167 (193)
T ss_pred             ccchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHH
Confidence            0  0            0      00       11245677888887666654         9999999999999999999


Q ss_pred             HHHhCccc
Q 014852          387 TEAIGKVF  394 (417)
Q Consensus       387 L~rark~L  394 (417)
                      ++++++.+
T Consensus       168 l~Rar~~L  175 (193)
T TIGR02947       168 LHRGRKQL  175 (193)
T ss_pred             HHHHHHHH
Confidence            99998755

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=1.3e-15  Score=139.03  Aligned_cols=132  Identities=17%  Similarity=0.138  Sum_probs=107.4

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       261 ~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      ++..|+..|+..|.+.|+.++.+|+++..+++|++||+|+.+|+++.+|++..  .|.+|++.+++|.+.++++...+..
T Consensus         4 ~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~   81 (179)
T PRK12543          4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRF   81 (179)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccc
Confidence            34579999999999999999999999999999999999999999999999875  7999999999999999887644211


Q ss_pred             c---------------cCccH--HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 R---------------LPNHL--HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 r---------------lp~~~--~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      +               .|...  .+....+..++..|++..|++         |++|||+.||||+++|+..++++++.+
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~L  161 (179)
T PRK12543         82 RIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKL  161 (179)
T ss_pred             ccccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            1               11111  122345677777776655543         999999999999999999999988655

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.63  E-value=1.3e-15  Score=137.40  Aligned_cols=132  Identities=15%  Similarity=0.099  Sum_probs=106.6

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir  341 (417)
                      +..+++.|+..|.+.|+++|.+++++..++||++||.|+.+|+..++|++..+ .|.+|++++++|.+++++++..+...
T Consensus         7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~Rk~~~~~~   85 (173)
T PRK09645          7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGR-SARAWLFTVARNLVIDERRSARARPV   85 (173)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhhccccc
Confidence            44799999999999999999999998899999999999999999999975433 79999999999999999987543211


Q ss_pred             --------cCc-----cHH--HHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 --------LPN-----HLH--ERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 --------lp~-----~~~--e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                              .+.     ...  .....+..++..|++..|++         +++|||+.||+|+++|+..++++++.+
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L  162 (173)
T PRK09645         86 EGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRAL  162 (173)
T ss_pred             ccccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence                    110     111  11234677777776655553         999999999999999999999998654

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=1.7e-15  Score=140.18  Aligned_cols=131  Identities=11%  Similarity=0.137  Sum_probs=107.9

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir  341 (417)
                      +..+|..|+..|.+.++.+|.+++++..++||++||.|+.+|+..++|+...  .|.+|++++++|.++++++++.+...
T Consensus         8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~~   85 (187)
T PRK12516          8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREVQ   85 (187)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence            4479999999999999999999999999999999999999999999998654  79999999999999999998654221


Q ss_pred             cCc------------c-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 LPN------------H-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 lp~------------~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...            . .......+..++..|++..|++         +++|||+.||||+++|+..+.++++.|
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~L  160 (187)
T PRK12516         86 DTDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRL  160 (187)
T ss_pred             ccccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            100            0 1112345777888886655553         999999999999999999999998655

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=1.8e-15  Score=139.40  Aligned_cols=150  Identities=16%  Similarity=0.194  Sum_probs=116.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .++..++..|.+.|+++|.+++++..++||++||+|+.+|+..++|++..  .|.+|++++++|.++++++++.+.... 
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~   82 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVEDA   82 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhcccccccc
Confidence            57889999999999999999999999999999999999999999998764  799999999999999999876542210 


Q ss_pred             -----------Ccc-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc--ccccc
Q 014852          343 -----------PNH-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF--SLDRE  399 (417)
Q Consensus       343 -----------p~~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L--SLD~~  399 (417)
                                 +.. .......+..++..|++..|++         |++|||+.||+|+++|+..++++++.|  .|...
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~  162 (182)
T PRK12540         83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVD  162 (182)
T ss_pred             cccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence                       000 1112245677788886655553         999999999999999999999998765  22211


Q ss_pred             cCCCCCCCCCCccccccC
Q 014852          400 AFPSLNGLPGETHHIHCG  417 (417)
Q Consensus       400 ~~~s~~~~~~d~l~d~l~  417 (417)
                      .  ..+..++++..+++|
T Consensus       163 ~--~~~~~~~~~~~~~~~  178 (182)
T PRK12540        163 G--AEDFGPDDTVRAVIG  178 (182)
T ss_pred             c--ccccCCCcccccccC
Confidence            1  222356677777776

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.62  E-value=2.8e-15  Score=135.37  Aligned_cols=129  Identities=17%  Similarity=0.129  Sum_probs=102.8

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-
Q 014852          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-  341 (417)
Q Consensus       263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-  341 (417)
                      ..|++.|+..|.+.|+.++.++.+ ..+++|++||+|+.+|+.++.|++..  .|.+|++++++|.+++++|+..+... 
T Consensus        10 ~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~~~~~   86 (175)
T PRK12518         10 RQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNPA--YFSTWLYRITWNVATDARRQFAQRPSR   86 (175)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCcc--cHHHHHHHHHHHHHHHHHHHhhccccc
Confidence            389999999999999999999874 47899999999999999999999753  79999999999999999987543110 


Q ss_pred             ---cC--------c--c-H--HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 ---LP--------N--H-L--HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 ---lp--------~--~-~--~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                         .+        .  . .  .+....+..++..|++..|.+         |++|||+.||+|+++|+..++++++.+
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L  164 (175)
T PRK12518         87 IQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQL  164 (175)
T ss_pred             hhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence               00        0  0 0  011133566677776655553         999999999999999999999998765

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.62  E-value=3.8e-15  Score=133.33  Aligned_cols=130  Identities=19%  Similarity=0.127  Sum_probs=104.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (417)
Q Consensus       263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl  342 (417)
                      ..|++.|++.|.+.|+++|.++.++..+++|++||+|++||+++++|+ .. ..|.+|++.++++.+.++++...+....
T Consensus        12 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~-~~-~~~~~~l~~i~~~~~~d~~r~~~~~~~~   89 (179)
T PRK11924         12 KEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-GK-GSARTWLLTIARNVCYDLLRRRRREKAV   89 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC-Cc-chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            389999999999999999999999999999999999999999999999 33 3899999999999999999875543211


Q ss_pred             Cc-------------c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 PN-------------H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 p~-------------~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ..             .      ..+....+..++..|++..+.         .+++|||+.||+|..+|++.++++++.+
T Consensus        90 ~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~l  169 (179)
T PRK11924         90 LSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLL  169 (179)
T ss_pred             CcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            00             0      111223456666666544443         3999999999999999999999988654

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.62  E-value=3.8e-15  Score=148.89  Aligned_cols=130  Identities=23%  Similarity=0.224  Sum_probs=106.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc--
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR--  341 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir--  341 (417)
                      .+++.|+..|.+.|+++|.+++++..++||++||.|+.+|+.+++|++..  .|.+|++++++|.+++++|++.+...  
T Consensus        19 ~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~   96 (339)
T PRK08241         19 DAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRS--SLRTWLYRIATNVCLDALEGRARRPLPT   96 (339)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhcccccc--chHHHHHHHHHHHHHHHHHhhccccCcc
Confidence            89999999999999999999999999999999999999999999998543  79999999999999999987543210  


Q ss_pred             -c-----------------------Cc-----------cH---HHH-HHHHHHHHHHHHHcCCCc---------cHHHHH
Q 014852          342 -L-----------------------PN-----------HL---HER-LGLIRNAKLRLEEKGVTP---------SVDRIA  373 (417)
Q Consensus       342 -l-----------------------p~-----------~~---~e~-~~kI~~a~~~L~e~gRep---------S~eEIA  373 (417)
                       .                       +.           ..   .+. ...+..++..|++..|++         +++|||
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA  176 (339)
T PRK08241         97 DLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLGWSAAEVA  176 (339)
T ss_pred             ccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHhhCCCHHHHH
Confidence             0                       00           00   011 123667788887666664         999999


Q ss_pred             HHcCCCHHHHHHHHHHhCcccc
Q 014852          374 EYLNMSQKKVRNATEAIGKVFS  395 (417)
Q Consensus       374 e~LGIS~etVr~aL~rark~LS  395 (417)
                      +.||+|+++|+..++++++.+.
T Consensus       177 ~~lgis~~tVk~~l~RAr~~Lr  198 (339)
T PRK08241        177 ELLDTSVAAVNSALQRARATLA  198 (339)
T ss_pred             HHhCCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999987664

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.61  E-value=4.7e-15  Score=133.54  Aligned_cols=130  Identities=12%  Similarity=0.128  Sum_probs=106.8

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (417)
Q Consensus       263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl  342 (417)
                      ...|..|+..|.+.|+.+|.++.++..++||++||+|+.+|+...+|+...  .|.+|++++++|.+++++++..+....
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~   82 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQD   82 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            478999999999999999999999999999999999999999999998654  799999999999999999876542211


Q ss_pred             C---------cc----HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 P---------NH----LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 p---------~~----~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .         ..    .......+..++..|++..|++         +++|||+.||||+++|++.++++++.+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L  156 (164)
T PRK12547         83 SDGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRL  156 (164)
T ss_pred             ccccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            0         00    0112345677788886655553         999999999999999999999998654

>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family

Probab=99.60  E-value=4.6e-15  Score=132.37  Aligned_cols=131  Identities=15%  Similarity=0.081  Sum_probs=106.8

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-  340 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i-  340 (417)
                      +..+++.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|+. .+ .|.+|++.+++|.+++++++..+.. 
T Consensus         4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~-~~-~~~~wl~~i~~n~~~d~~rk~~~~~~   81 (162)
T TIGR02983         4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD-PD-APDAYVRRVLVNLARSRWRRRRLLEL   81 (162)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC-cc-cHHHHHHHHHHHHHHHHHHhhccccc
Confidence            45899999999999999999999999999999999999999999999964 33 8999999999999999998765311 


Q ss_pred             ---ccCc----c---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 ---RLPN----H---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 ---rlp~----~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                         ..+.    .   .......+..++..|++..|++         +++|||+.||+|+++|+..+.++++.+
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~L  154 (162)
T TIGR02983        82 PTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL  154 (162)
T ss_pred             cccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence               0010    0   1123345777777776655543         999999999999999999999998765

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.60  E-value=7.7e-15  Score=136.86  Aligned_cols=128  Identities=10%  Similarity=0.049  Sum_probs=103.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .+++.|+..|.+.++.++. +.++..++||++||.|+.+|+..++|++..  .|.+|++.+++|.+++++|+..+..+. 
T Consensus        25 ~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~~  101 (196)
T PRK12535         25 AALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAARS--SARTWLLSLARRVWVDNIRHDMARPRKS  101 (196)
T ss_pred             HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccCCCcc
Confidence            8999999999999999975 567888999999999999999999998643  799999999999999999975432110 


Q ss_pred             -------------Ccc--HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 -------------PNH--LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 -------------p~~--~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                   |..  ..+....+..++..|++..|++         +++|||+.||+|+++|+..++++++.|
T Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~~L  177 (196)
T PRK12535        102 ATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADL  177 (196)
T ss_pred             cccccccccccCCcchhHHHHHHHHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence                         000  1112245677777776655554         999999999999999999999998654

>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1

Probab=99.60  E-value=2.6e-15  Score=132.00  Aligned_cols=128  Identities=22%  Similarity=0.214  Sum_probs=101.7

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc--
Q 014852          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL--  342 (417)
Q Consensus       265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl--  342 (417)
                      |++.|+..|.+.|+.++.++.++..++||++||+|+++|+.+.+|++..  +|.+|++.++++.+.+++++..+....  
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~~~~~   79 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEEKYQE   79 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Confidence            7899999999999999999999989999999999999999999998754  899999999999999988876532110  


Q ss_pred             --------------Ccc---HHHHHHHHHHHHHHHHHcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 --------------PNH---LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 --------------p~~---~~e~~~kI~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                    |..   ..+....+..++..|++..+         +.++.|||+.||+|+.+|+..++++++.+
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~L  157 (161)
T TIGR02985        80 EILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALKEL  157 (161)
T ss_pred             HHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                          000   01122345666665543333         34999999999999999999999997654

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.60  E-value=6.3e-15  Score=131.75  Aligned_cols=129  Identities=13%  Similarity=0.105  Sum_probs=104.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc
Q 014852          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (417)
Q Consensus       263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl  342 (417)
                      ..|++.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|++.   .|.||++++++|.+++++++..+....
T Consensus         4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~   80 (161)
T PRK12541          4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT   80 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc
Confidence            47999999999999999999999999999999999999999999999863   599999999999999999876532111


Q ss_pred             ----------Ccc-----HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 ----------PNH-----LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 ----------p~~-----~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                +..     ..+....+..++..|++..|.+         +++|||+.||+|+++|+..++++++.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L  156 (161)
T PRK12541         81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKET  156 (161)
T ss_pred             chhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                      000     1112233455666676555543         999999999999999999999998755

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=99.59  E-value=6.3e-15  Score=126.28  Aligned_cols=128  Identities=28%  Similarity=0.353  Sum_probs=102.7

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc------
Q 014852          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR------  338 (417)
Q Consensus       265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r------  338 (417)
                      |++.|+..|.++|+++++++..++.+++|++||++++++++++.|++.  .+|.+|+..++++.+.+++++..+      
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~~~~~~~   79 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRRELD   79 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhccCCcchh
Confidence            789999999999999999999988999999999999999999999998  489999999999999999988763      


Q ss_pred             cc-cc------Ccc---HHHHHHHHHHHHHHHHHcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          339 TL-RL------PNH---LHERLGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       339 ~i-rl------p~~---~~e~~~kI~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .. ..      +..   .......+..++..|++..+         +.+..|||+.||+|+.+|++++.++++.+
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl  154 (158)
T TIGR02937        80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL  154 (158)
T ss_pred             hhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            00 00      000   11223445666666643332         34999999999999999999999987543

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.

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=4e-15  Score=136.02  Aligned_cols=134  Identities=13%  Similarity=-0.005  Sum_probs=105.1

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHccC--CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc
Q 014852          261 ECSLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR  338 (417)
Q Consensus       261 ~~~~Are~LIe~yl~LV~sIA~Ry~~--~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r  338 (417)
                      ++..+|+.|+..|.+.|+.++.++++  +..++||++||.|+.+|+..++|+......|.||++++++|.+++++++..+
T Consensus        10 ~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~~   89 (178)
T PRK12529         10 ADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQSL   89 (178)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence            44589999999999999998665555  4678999999999999999999985433489999999999999999987542


Q ss_pred             ccc-------c-------Ccc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852          339 TLR-------L-------PNH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGK  392 (417)
Q Consensus       339 ~ir-------l-------p~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark  392 (417)
                      ...       .       |..   ..+....|..++..|++..|.+         |++|||+.||+|+++|+..++++..
T Consensus        90 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl~  169 (178)
T PRK12529         90 ELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYV  169 (178)
T ss_pred             HhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            110       0       111   1123345788888887766664         9999999999999999999998875


Q ss_pred             cc
Q 014852          393 VF  394 (417)
Q Consensus       393 ~L  394 (417)
                      .+
T Consensus       170 ~~  171 (178)
T PRK12529        170 TC  171 (178)
T ss_pred             HH
Confidence            43

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.58  E-value=7.1e-15  Score=132.13  Aligned_cols=126  Identities=10%  Similarity=0.058  Sum_probs=103.2

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC--
Q 014852          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP--  343 (417)
Q Consensus       266 re~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp--  343 (417)
                      ++.|++.|.+.|+.+|.++.++..++||++||+|+.+|+.+++|++.   .|.+|++++++|.+.+++++..+.....  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~~~   79 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVGTD   79 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccchh
Confidence            67899999999999999999999999999999999999999999863   6999999999999999999866432111  


Q ss_pred             ----------ccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 ----------NHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ----------~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                ...   .+....+..++..|++..|++         +++|||+.||+|+++|+.+++++++.+
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~L  152 (165)
T PRK09644         80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRL  152 (165)
T ss_pred             HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                      110   112245666777776555553         999999999999999999999998765

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=99.58  E-value=8.1e-15  Score=145.17  Aligned_cols=131  Identities=21%  Similarity=0.201  Sum_probs=107.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir  341 (417)
                      +..|++.|+..|.+.|+++|.+++++..++||++||.|+.+|+.+++|++..  .|.+|++++++|.+++++|++.+...
T Consensus         3 d~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~   80 (324)
T TIGR02960         3 DGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRS--SVRTWLYRIATNACLDALEARQRRPR   80 (324)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCccc--chHHHHHHHHHHHHHHHHHhccCCcC
Confidence            3479999999999999999999999999999999999999999999999753  79999999999999999987543211


Q ss_pred             --------------------------cCc-----------c-----H-HHH-HHHHHHHHHHHHHcCCCc---------c
Q 014852          342 --------------------------LPN-----------H-----L-HER-LGLIRNAKLRLEEKGVTP---------S  368 (417)
Q Consensus       342 --------------------------lp~-----------~-----~-~e~-~~kI~~a~~~L~e~gRep---------S  368 (417)
                                                .+.           .     . .+. ...+..++..|++..|.+         +
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s  160 (324)
T TIGR02960        81 PVGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWR  160 (324)
T ss_pred             ccccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCCC
Confidence                                      000           0     0 111 123667788887666664         9


Q ss_pred             HHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          369 VDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       369 ~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ++|||+.||+|+++|++.++++++.|
T Consensus       161 ~~EIA~~lgis~~tV~~~l~Rar~~L  186 (324)
T TIGR02960       161 AAETAELLGTSTASVNSALQRARATL  186 (324)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999999998765

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.

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.57  E-value=1.5e-14  Score=137.47  Aligned_cols=131  Identities=15%  Similarity=0.149  Sum_probs=107.3

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       261 ~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      ....+|+.|+..|.+.++.++.++.++..++||++||+|+.+|+.+++|++.   .|.+|++++++|.++++++++.+..
T Consensus        15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~   91 (216)
T PRK12533         15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAH   91 (216)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccc
Confidence            4457999999999999999999999999999999999999999999999853   5999999999999999998764321


Q ss_pred             c------cC------------cc------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHH
Q 014852          341 R------LP------------NH------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNAT  387 (417)
Q Consensus       341 r------lp------------~~------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL  387 (417)
                      .      ..            ..      ..+....+..++..|++..|++         |++|||+.||||+++|+..+
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L  171 (216)
T PRK12533         92 EVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRL  171 (216)
T ss_pred             cccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence            1      00            00      1122345777777886655554         99999999999999999999


Q ss_pred             HHhCccc
Q 014852          388 EAIGKVF  394 (417)
Q Consensus       388 ~rark~L  394 (417)
                      +++++.|
T Consensus       172 ~RAr~~L  178 (216)
T PRK12533        172 ARARRRL  178 (216)
T ss_pred             HHHHHHH
Confidence            9998765

>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1

Probab=99.57  E-value=1.8e-14  Score=130.99  Aligned_cols=133  Identities=19%  Similarity=0.115  Sum_probs=103.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcc----CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYD----NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~----~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~  337 (417)
                      +..|++.|+..|.+.|+.+|++|.    ++..++||++||+|+.+|+++.+|++..+.+|.+|++++++|.+.+++++..
T Consensus         5 ~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~   84 (189)
T TIGR02984         5 DQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRHL   84 (189)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHHH
Confidence            458999999999999999999874    3567899999999999999999999765558999999999999999998651


Q ss_pred             ----ccc----cc-----------------------Ccc---HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHH
Q 014852          338 ----RTL----RL-----------------------PNH---LHERLGLIRNAKLRLEEKGVT---------PSVDRIAE  374 (417)
Q Consensus       338 ----r~i----rl-----------------------p~~---~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe  374 (417)
                          +..    .+                       |..   ..+....+..++..|++..|.         .+++|||+
T Consensus        85 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eIA~  164 (189)
T TIGR02984        85 GAQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEVAE  164 (189)
T ss_pred             HHHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHHHH
Confidence                100    00                       000   011223466666666544433         39999999


Q ss_pred             HcCCCHHHHHHHHHHhCccc
Q 014852          375 YLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       375 ~LGIS~etVr~aL~rark~L  394 (417)
                      .||||+++|+..++++++.+
T Consensus       165 ~lgis~~~v~~~l~Ra~~~L  184 (189)
T TIGR02984       165 RMDRSEGAVSMLWVRGLARL  184 (189)
T ss_pred             HHCcCHHHHHHHHHHHHHHH
Confidence            99999999999999988654

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.56  E-value=7.8e-15  Score=132.90  Aligned_cols=128  Identities=16%  Similarity=0.099  Sum_probs=102.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL---  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i---  340 (417)
                      .|+..|+..|.+.|+.++.+++++..+++|++||+|+.+|+. ..|....  .|.+|++++++|.++++++++.+..   
T Consensus        10 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~~--~~~~wL~~Iarn~~~d~~Rk~~~~~~~~   86 (172)
T PRK12523         10 ELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTPR--EPRAFLAAVAKGLMFDHFRRAALEQAYL   86 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcch--hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            799999999999999999999999999999999999999986 4566442  7999999999999999998754311   


Q ss_pred             -c---c-----C--ccH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 -R---L-----P--NHL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 -r---l-----p--~~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                       .   .     +  ...   .+....+..++..|++..|.         .+++|||+.||+|+++|+..+.++++.+
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~  163 (172)
T PRK12523         87 AELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQC  163 (172)
T ss_pred             HHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence             0   0     0  110   12224567777777654544         3999999999999999999999988765

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.56  E-value=8e-15  Score=130.78  Aligned_cols=121  Identities=15%  Similarity=0.078  Sum_probs=97.6

Q ss_pred             HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc-c-------
Q 014852          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR-L-------  342 (417)
Q Consensus       271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir-l-------  342 (417)
                      +.|.+.|+.+|.+++++..++||++||+|+.+|+++++|++.   .|.||++++++|.+++++++..+... .       
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~   78 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEELSLCKETE   78 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccccccchhhh
Confidence            578999999999999999999999999999999999999863   59999999999999999987653211 0       


Q ss_pred             --------CccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 --------PNHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 --------p~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                              |...   .+....+..++..|++..|.+         |++|||+.||+|+++|++.++++++.+
T Consensus        79 ~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L  150 (160)
T PRK09642         79 ENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWI  150 (160)
T ss_pred             hhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                    0000   111234677777776655553         999999999999999999999998755

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.55  E-value=1.6e-14  Score=129.14  Aligned_cols=127  Identities=17%  Similarity=0.107  Sum_probs=101.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp  343 (417)
                      .+++.|++.|.+.|+.+|.++.++..+++|++||+|+.+|++  .|++.  ..|.+|++++++|.+.+++++..+.....
T Consensus         3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~~--~~~~~wl~~i~rn~~~d~~rk~~~~~~~~   78 (166)
T PRK09639          3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKGI--ENEKGWLIKSARNVAYNYLRSEKRRRARI   78 (166)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hcccc--cchHHHHHHHHHHHHHHHHHHhccccccc
Confidence            689999999999999999999999999999999999999999  67654  38999999999999999998766432110


Q ss_pred             ---------------cc---HHHHHHHHHHHHHHHHHcCC--------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 ---------------NH---LHERLGLIRNAKLRLEEKGV--------TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ---------------~~---~~e~~~kI~~a~~~L~e~gR--------epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                     ..   ..+....+..++..|++..|        ..+++|||+.||+|+.+|+..+.++++.+
T Consensus        79 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~g~s~~eIA~~lgis~~tV~~~i~ra~~~L  155 (166)
T PRK09639         79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKF  155 (166)
T ss_pred             cchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                           00   01122346666666654333        34999999999999999999999998654

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.55  E-value=2.9e-14  Score=131.93  Aligned_cols=132  Identities=17%  Similarity=0.149  Sum_probs=106.2

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       261 ~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      .+..+++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.++.|++..  .|.+|++++++|.+.+.++...+..
T Consensus        20 ~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~~~~~~r~~~~~~   97 (188)
T PRK12517         20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRENARRFERKQFDL   97 (188)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHHHHHHHHHhccCc
Confidence            45689999999999999999999999999999999999999999999998753  7999999999999887765543211


Q ss_pred             -cc-----C-----cc-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 -RL-----P-----NH-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 -rl-----p-----~~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                       ..     +     .. .......+..++..|++..|.+         +++|||+.||||+.+|+..++++++.+
T Consensus        98 ~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L  172 (188)
T PRK12517         98 VDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQL  172 (188)
T ss_pred             cCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence             00     0     00 1111234777888887655553         999999999999999999999998765

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.54  E-value=2.4e-14  Score=126.31  Aligned_cols=122  Identities=20%  Similarity=0.194  Sum_probs=98.3

Q ss_pred             HHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-------
Q 014852          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-------  342 (417)
Q Consensus       270 Ie~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-------  342 (417)
                      +++|.+.|+.++.+++++..+++|++||+|+.+|+.+++|++  + +|.||++.++++.+.+++++..+....       
T Consensus         1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~--~-~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~   77 (154)
T TIGR02950         1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD--S-SIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGD   77 (154)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC--C-chHHHHHHHHHHHHHHHHHHhhhhccccHhhhhh
Confidence            357899999999999999999999999999999999999997  3 899999999999999999875432211       


Q ss_pred             --------CccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 --------PNHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 --------p~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                              |...   .+....+..++..|++..+++         +++|||+.||+|+.+|+..++++++.+
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~L  149 (154)
T TIGR02950        78 LEQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKEL  149 (154)
T ss_pred             ccccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                    0000   112245777788886655543         999999999999999999999998654

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.54  E-value=2.5e-14  Score=127.95  Aligned_cols=128  Identities=15%  Similarity=0.073  Sum_probs=102.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL---  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i---  340 (417)
                      .|++.|++.|.+.|+.++.+++++..++||++||.|+.+|+..+.|++.   .|.+|++++++|.+++++++..+..   
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~~   80 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLERAYL   80 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            6899999999999999999999999999999999999999998887642   6999999999999999998754211   


Q ss_pred             ----ccCc----c------HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 ----RLPN----H------LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 ----rlp~----~------~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                          ..+.    .      ..+....+..++..|++..|++         +++|||+.||+|+++|+..++++++.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~  157 (161)
T PRK12528         81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC  157 (161)
T ss_pred             HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                0110    0      0122245667777776655543         999999999999999999999987643

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.53  E-value=4.4e-14  Score=129.94  Aligned_cols=127  Identities=19%  Similarity=0.163  Sum_probs=102.4

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc-
Q 014852          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN-  344 (417)
Q Consensus       266 re~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~-  344 (417)
                      ++.|++.|.+.|+.++.++.++..++||++||.|+.+|+.+..|+...  +|.+|++++++|.+++++++..+....+. 
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~~--~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~   80 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGS--SIKSWLYQIANNTIIDFYRKKNRSEELPDD   80 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhcccc--chHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence            678999999999999999999999999999999999999999998643  89999999999999999987654332211 


Q ss_pred             -------c----HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          345 -------H----LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       345 -------~----~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                             .    ..+....+..++..|++..|.         .+++|||+.||+|+++|+..+.++++.+
T Consensus        81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~L  150 (181)
T PRK09637         81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKL  150 (181)
T ss_pred             hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence                   1    112223455666666554444         3999999999999999999999988654

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.53  E-value=4.5e-14  Score=132.67  Aligned_cols=130  Identities=19%  Similarity=0.190  Sum_probs=105.1

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc-
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL-  340 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i-  340 (417)
                      +..+++.|+..|.+.++.++.++.++..+++|++||+|+.+|+...+|++  + +|.+|++++++|.+++++++..+.. 
T Consensus        26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~~~  102 (203)
T PRK09647         26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARIRM  102 (203)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccCcc
Confidence            44799999999999999999999999999999999999999999999985  3 6999999999999999998764311 


Q ss_pred             -ccC-----------c--cH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 -RLP-----------N--HL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 -rlp-----------~--~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                       ..+           .  ..   .+....+..++..|++..+.         .+++|||+.||||+++|++.+.++++.|
T Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~L  182 (203)
T PRK09647        103 EALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL  182 (203)
T ss_pred             ccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence             000           0  00   11223466667777554444         3999999999999999999999998765

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.53  E-value=3.8e-14  Score=130.85  Aligned_cols=126  Identities=15%  Similarity=0.219  Sum_probs=100.3

Q ss_pred             HHHHHHhHHHHHHHHHHccCCCCC-hhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC--
Q 014852          267 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP--  343 (417)
Q Consensus       267 e~LIe~yl~LV~sIA~Ry~~~g~e-~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp--  343 (417)
                      +..+..|.+.|+.+|.+++++..+ +||++||+|+.+|+++++|++. + +|.+|++++++|.++++++++.+.....  
T Consensus         8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~-~-~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~   85 (195)
T PRK12532          8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR-A-LVNSWLFAILKNKIIDALRQIGRQRKVFTL   85 (195)
T ss_pred             hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc-c-hHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence            456788999999999999998888 9999999999999999999865 3 8999999999999999999865422110  


Q ss_pred             --------------------------------cc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCC
Q 014852          344 --------------------------------NH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMS  379 (417)
Q Consensus       344 --------------------------------~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS  379 (417)
                                                      ..   ..+....+..++..|++..|++         |++|||+.||+|
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~lgis  165 (195)
T PRK12532         86 LDDELLDEAFESHFSQNGHWTPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGIS  165 (195)
T ss_pred             ccccccchhhhhhhccccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHHCCC
Confidence                                            00   0111234667777776555443         999999999999


Q ss_pred             HHHHHHHHHHhCccc
Q 014852          380 QKKVRNATEAIGKVF  394 (417)
Q Consensus       380 ~etVr~aL~rark~L  394 (417)
                      +++|+..++++++.+
T Consensus       166 ~~tVk~~l~Rar~~L  180 (195)
T PRK12532        166 TSNYHTIMHRARESL  180 (195)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999998654

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.52  E-value=3.6e-14  Score=132.42  Aligned_cols=124  Identities=15%  Similarity=0.115  Sum_probs=99.8

Q ss_pred             HHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC---c-
Q 014852          269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---N-  344 (417)
Q Consensus       269 LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp---~-  344 (417)
                      ++..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|++..  .|.||++++++|.+++++++..+....+   . 
T Consensus        13 ~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~~   90 (201)
T PRK12545         13 YLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALDAE   90 (201)
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccccccc
Confidence            488899999999999999999999999999999999999999764  7999999999999999999765432110   0 


Q ss_pred             ----------------------------cHH------HHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHH
Q 014852          345 ----------------------------HLH------ERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQK  381 (417)
Q Consensus       345 ----------------------------~~~------e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~e  381 (417)
                                                  ...      +....+..++..|++..|.         .+++|||+.||+|++
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~  170 (201)
T PRK12545         91 LDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTAN  170 (201)
T ss_pred             cchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence                                        000      1112356677777654544         399999999999999


Q ss_pred             HHHHHHHHhCccc
Q 014852          382 KVRNATEAIGKVF  394 (417)
Q Consensus       382 tVr~aL~rark~L  394 (417)
                      +|+..+.++++.|
T Consensus       171 tVk~~l~RAr~~L  183 (201)
T PRK12545        171 HCSVLLYRARTRL  183 (201)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998755

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.52  E-value=3.7e-13  Score=130.18  Aligned_cols=77  Identities=17%  Similarity=0.220  Sum_probs=71.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCC--ChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~--e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      .|++.|+..|.|+|+++|.+++++..  +++|++||||+++|+++++|++++|.+|.+|++++|+|.+++++|++.+..
T Consensus        18 ~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDylRk~~~~~   96 (237)
T PRK08311         18 ELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRKESKHN   96 (237)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHhhccc
Confidence            89999999999999999999998765  599999999999999999999998889999999999999999999877643

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.51  E-value=5.4e-14  Score=129.91  Aligned_cols=125  Identities=11%  Similarity=0.109  Sum_probs=99.9

Q ss_pred             HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-----
Q 014852          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-----  342 (417)
Q Consensus       268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-----  342 (417)
                      .-|..|.+.++.+|.+++++..++||++||+|+.+|+.+++|++..  +|.+|++++++|.+++++|++.+....     
T Consensus        11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~~   88 (189)
T PRK12530         11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESELIE   88 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcccccc
Confidence            3467788999999999999999999999999999999999998764  799999999999999999976542211     


Q ss_pred             ---C-----------------cc--H-------HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHH
Q 014852          343 ---P-----------------NH--L-------HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVR  384 (417)
Q Consensus       343 ---p-----------------~~--~-------~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr  384 (417)
                         +                 ..  .       .+....+..++..|++..|++         |++|||+.||+|+++|+
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk  168 (189)
T PRK12530         89 EDSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLH  168 (189)
T ss_pred             cccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHHH
Confidence               0                 00  0       011123567778887655554         99999999999999999


Q ss_pred             HHHHHhCccc
Q 014852          385 NATEAIGKVF  394 (417)
Q Consensus       385 ~aL~rark~L  394 (417)
                      ..++++++.+
T Consensus       169 ~~l~RAr~~L  178 (189)
T PRK12530        169 VLLYRARLQL  178 (189)
T ss_pred             HHHHHHHHHH
Confidence            9999998754

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.51  E-value=1.3e-13  Score=128.04  Aligned_cols=128  Identities=16%  Similarity=0.194  Sum_probs=103.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      ++++.|.. |.+.|+++|.++.++..++||++||.|+.+|+.+..|+...  .|.+|++++++|.+++++++..+.... 
T Consensus         8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~~--~~~awL~~ia~n~~~d~~Rk~~r~~~~~   84 (188)
T PRK12546          8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGT--NLRAWLFTILRNTFYSDRRKHKREVPDP   84 (188)
T ss_pred             hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCCc--chHHHHHHHHHHHHHHHHHHhcccccCc
Confidence            56777766 77999999999999999999999999999999999998643  799999999999999999886642210 


Q ss_pred             C-----------cc-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 P-----------NH-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 p-----------~~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .           .. .......+..++..|++..|.+         +++|||+.||||+.+|+..++++++.+
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~L  157 (188)
T PRK12546         85 EGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARL  157 (188)
T ss_pred             ccccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            0           00 0112245677888887655554         999999999999999999999998654

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.50  E-value=6.9e-14  Score=131.68  Aligned_cols=126  Identities=13%  Similarity=0.124  Sum_probs=100.7

Q ss_pred             HHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC---
Q 014852          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---  343 (417)
Q Consensus       267 e~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp---  343 (417)
                      ..++..|.+.|+.+|++++++..+++|++||+|+.+|+.+.+|++..  +|.+|++++++|.+++++++..+....+   
T Consensus        21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~~   98 (206)
T PRK12544         21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGRA--AFKTWVFAILKNKIIDLLRQKKRHVSASSLL   98 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccccccc
Confidence            46788899999999999999999999999999999999999998653  7999999999999999999765422111   


Q ss_pred             -------------------------------ccH---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCH
Q 014852          344 -------------------------------NHL---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQ  380 (417)
Q Consensus       344 -------------------------------~~~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~  380 (417)
                                                     ...   .+....+..++..|++..|++         +++|||+.||+|+
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgis~  178 (206)
T PRK12544         99 RDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSV  178 (206)
T ss_pred             cccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence                                           000   011123566677776555543         9999999999999


Q ss_pred             HHHHHHHHHhCccc
Q 014852          381 KKVRNATEAIGKVF  394 (417)
Q Consensus       381 etVr~aL~rark~L  394 (417)
                      ++|+..++++++.+
T Consensus       179 ~tV~~~l~RAr~~L  192 (206)
T PRK12544        179 SNLNVLLYRARLRL  192 (206)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999998765

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=99.50  E-value=6.8e-14  Score=129.30  Aligned_cols=125  Identities=15%  Similarity=0.154  Sum_probs=100.5

Q ss_pred             HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC---c
Q 014852          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---N  344 (417)
Q Consensus       268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp---~  344 (417)
                      +++..|.+.|+.++.+++++..+++|++||+|+.+|+...+|++..  +|.+|++++++|.+++++++..+....+   .
T Consensus         6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~~--~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~~   83 (188)
T TIGR02943         6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRS--ALKTWLFAILKNKIIDALRAKGREVKVSDLDD   83 (188)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--HHHHHHHHHHHHHHHHHHHhhcccCCcccccc
Confidence            5678899999999999999999999999999999999999999753  8999999999999999998765432111   0


Q ss_pred             c---------------------------------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHH
Q 014852          345 H---------------------------------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKK  382 (417)
Q Consensus       345 ~---------------------------------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~et  382 (417)
                      .                                 ..+....+..++..|++..|+         .+++|||+.||+|+++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~t  163 (188)
T TIGR02943        84 ELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSN  163 (188)
T ss_pred             ccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHHH
Confidence            0                                 001123466677777654444         3999999999999999


Q ss_pred             HHHHHHHhCccc
Q 014852          383 VRNATEAIGKVF  394 (417)
Q Consensus       383 Vr~aL~rark~L  394 (417)
                      |+..+.++++.+
T Consensus       164 vk~rl~Rar~~L  175 (188)
T TIGR02943       164 CHVLLYRARLSL  175 (188)
T ss_pred             HHHHHHHHHHHH
Confidence            999999998765

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.

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.50  E-value=1.3e-13  Score=125.32  Aligned_cols=129  Identities=17%  Similarity=0.152  Sum_probs=102.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc--
Q 014852          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL--  340 (417)
Q Consensus       263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i--  340 (417)
                      ..|+..|++.|.+.++.++.++.++..++||++||.|+.+|+. ..|++..  +|.+|++++++|.+++++++..+..  
T Consensus         9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~~   85 (172)
T PRK09651          9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKAY   85 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            4799999999999999999999999999999999999999998 3565443  6999999999999999998654211  


Q ss_pred             -----cc-----Ccc--H---HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 -----RL-----PNH--L---HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 -----rl-----p~~--~---~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                           ..     +..  .   .+....+..++..|++..|++         +++|||+.||+|+++|+..++++++.+
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~  163 (172)
T PRK09651         86 LEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC  163 (172)
T ss_pred             hhHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence                 00     110  1   122345677777886655554         999999999999999999999987643

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.50  E-value=7.3e-14  Score=126.83  Aligned_cols=122  Identities=20%  Similarity=0.214  Sum_probs=97.8

Q ss_pred             HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCcc-----
Q 014852          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH-----  345 (417)
Q Consensus       271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~-----  345 (417)
                      ..|.+.++.++.++.++..++||++||+|+.+|+++++|+...  +|.+|++.+++|.+++++++..+...++..     
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~~--~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~   79 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQ--KIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD   79 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCcc--cHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence            4688999999999999999999999999999999999999743  899999999999999999987654332211     


Q ss_pred             -------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          346 -------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       346 -------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                             ..+....+..++..|++..|+         .+++|||+.||+|+.+|+..++++++.+
T Consensus        80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L  144 (170)
T TIGR02959        80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKL  144 (170)
T ss_pred             CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                   111223456666666544443         3999999999999999999999998655

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.48  E-value=1.4e-13  Score=126.91  Aligned_cols=126  Identities=18%  Similarity=0.181  Sum_probs=101.1

Q ss_pred             HHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC---
Q 014852          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP---  343 (417)
Q Consensus       267 e~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp---  343 (417)
                      +..+..+.+.|+.+|.++.++..+++|++||.|+.+|+.+.+|+...  +|.+|++++++|.++++++++.+.....   
T Consensus         7 ~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~~~~~   84 (182)
T PRK12511          7 RFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGG--NLRTWLMSILHNAFIDELRRRRVEARRADEL   84 (182)
T ss_pred             hhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHhhccccccccch
Confidence            44577889999999999999999999999999999999999998653  7999999999999999998765421100   


Q ss_pred             ---------cc--HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 ---------NH--LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ---------~~--~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                               ..  .......+..++..|++..|++         |++|||+.||||+++|+..++++++.+
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~L  155 (182)
T PRK12511         85 AVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL  155 (182)
T ss_pred             hhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence                     00  1112344677777776655553         999999999999999999999998755

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.46  E-value=2.4e-13  Score=130.77  Aligned_cols=134  Identities=13%  Similarity=0.080  Sum_probs=103.3

Q ss_pred             HHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHH
Q 014852          255 LQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALV  334 (417)
Q Consensus       255 Lr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ir  334 (417)
                      |++.+..+..+++.+++.| +.+++++.+++++..++|||+||+|+.+|+.   |+...  .|.+|++++++|.++++++
T Consensus         9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~~--~~~~WL~~IarN~~id~~R   82 (228)
T PRK06704          9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNKD--ICMTLVYKIARNRWLDQIK   82 (228)
T ss_pred             HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCccc--cHHHHHHHHHHHHHHHHHh
Confidence            3334444447888888888 7899999999999999999999999999986   55433  6999999999999999999


Q ss_pred             hhccccccCc--------c-HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          335 ENSRTLRLPN--------H-LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       335 d~~r~irlp~--------~-~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ++.+......        . ..+....+..++..|++..|.+         |++|||+.||+|+++|+..++++++.+
T Consensus        83 k~k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~L  160 (228)
T PRK06704         83 SKSVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL  160 (228)
T ss_pred             ccccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            7654322111        0 1122344677777776655554         999999999999999999999999765

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.42  E-value=6.9e-13  Score=118.46  Aligned_cols=124  Identities=15%  Similarity=0.164  Sum_probs=96.3

Q ss_pred             HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc------
Q 014852          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR------  341 (417)
Q Consensus       268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir------  341 (417)
                      .++..|.+.++.+|.++.++..++||++||+|+++|+....|++.   .|.+|++.+++|.+++++++..+...      
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~~~~~   78 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYHGDEE   78 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            357788999999999999999999999999999999988877653   58999999999999999987653211      


Q ss_pred             ----cCc---c------HHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          342 ----LPN---H------LHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       342 ----lp~---~------~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                          .+.   .      ..+....+..++..|++..|.         .+++|||+.||+|+.+|+..+.++++.+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~l  153 (163)
T PRK07037         79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHC  153 (163)
T ss_pred             cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                110   0      111223456666777554444         3999999999999999999999887654

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.40  E-value=6.9e-13  Score=118.36  Aligned_cols=121  Identities=16%  Similarity=0.085  Sum_probs=95.0

Q ss_pred             HHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc--------
Q 014852          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL--------  342 (417)
Q Consensus       271 e~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl--------  342 (417)
                      ..|.+.++..+.+++++..++||++||+|+.+|+..+.|++  + +|.||++.+++|.++++++++......        
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~~   78 (159)
T PRK12527          2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEE   78 (159)
T ss_pred             hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHhcccccchhhhhcc
Confidence            56888999999999999899999999999999999998875  3 799999999999999999865321110        


Q ss_pred             -----Cc--cH---HHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          343 -----PN--HL---HERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       343 -----p~--~~---~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                           |.  ..   .+....+..++..|++..+.         .+++|||+.||+|+++|+..+.++++.+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~L  149 (159)
T PRK12527         79 ERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC  149 (159)
T ss_pred             ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence                 00  00   11223467777777654444         3999999999999999999999988654

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.40  E-value=1e-12  Score=118.85  Aligned_cols=127  Identities=12%  Similarity=0.022  Sum_probs=99.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL---  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i---  340 (417)
                      .++..++..|.+.++.++.+++++..+++|++||.|+.+|+..+.++.  + .|.+|++++++|.+++++++.....   
T Consensus         9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~--~-~~~~wl~~Iarn~~~d~~Rr~~~~~~~~   85 (168)
T PRK12525          9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI--R-EPRALLTTIARRLMYEGWRRQDLERAYL   85 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc--c-CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999986555542  2 7999999999999999988643110   


Q ss_pred             ----c-------cCcc---HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          341 ----R-------LPNH---LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       341 ----r-------lp~~---~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                          .       .|..   ..+....+..++..|++..|.+         |++|||+.||+|+++|+..+.++.+.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~  161 (168)
T PRK12525         86 QSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKC  161 (168)
T ss_pred             HHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                0       0100   1112344667777776545443         99999999999999999999988754

>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.39  E-value=1.2e-12  Score=100.94  Aligned_cols=70  Identities=27%  Similarity=0.418  Sum_probs=66.7

Q ss_pred             HHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc
Q 014852          269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR  338 (417)
Q Consensus       269 LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r  338 (417)
                      |++.|.++|++++.+|++++.++||++||++++||+++++||+++|..|.+|++.++++.+.+.++++.+
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r   70 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR   70 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence            7899999999999999999999999999999999999999999998899999999999999999988754

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.37  E-value=1.7e-12  Score=128.01  Aligned_cols=128  Identities=17%  Similarity=0.074  Sum_probs=100.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL---  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i---  340 (417)
                      ..+..|++.|.+.++.+|++++++..++||++||+|+. |.....|+.   ..|.+|++++++|.|++++|+..+..   
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~   79 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRETY   79 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhcccccc
Confidence            45778999999999999999999999999999999999 555677752   37999999999999999998754211   


Q ss_pred             ---ccCcc----------H---HHH-HHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          341 ---RLPNH----------L---HER-LGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       341 ---rlp~~----------~---~e~-~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                         ..+..          .   .+. ...+..++..|++.+|.+         +++|||+.||+|+.+|+++++++++.+
T Consensus        80 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~L  159 (293)
T PRK09636         80 VGPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHV  159 (293)
T ss_pred             cCCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence               01110          0   111 123667777776666654         999999999999999999999998766


Q ss_pred             c
Q 014852          395 S  395 (417)
Q Consensus       395 S  395 (417)
                      .
T Consensus       160 r  160 (293)
T PRK09636        160 R  160 (293)
T ss_pred             H
Confidence            3

>PRK09191 two-component response regulator; Provisional

Probab=99.31  E-value=6.4e-12  Score=119.02  Aligned_cols=122  Identities=13%  Similarity=0.047  Sum_probs=95.9

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc
Q 014852          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN  344 (417)
Q Consensus       265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~  344 (417)
                      ++..|+..|.+.++++|.++.++..+++|++||+|+.+|+...+|++..  .|.+|+++++++........    ...+.
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~~~~~~~----~~~~~   75 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLWSSAGAN----DPEPG   75 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHhcccccc----CCCCC
Confidence            5789999999999999999999999999999999999999999998754  79999999998754322111    01011


Q ss_pred             cHHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          345 HLHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       345 ~~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .  .....+..++..|++.+|.+         |++|||+.||+|+++|+..++++++.+
T Consensus        76 ~--~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l  132 (261)
T PRK09191         76 S--PFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEI  132 (261)
T ss_pred             C--CchHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            0  11125777777776655553         999999999999999999999887654

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.30  E-value=7e-12  Score=124.36  Aligned_cols=129  Identities=11%  Similarity=-0.051  Sum_probs=101.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc---
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL---  340 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i---  340 (417)
                      ..+..+++.|.+.++.+|++++++..++||++||+|+.+|++...+   . ..|.+|++++++|.|++++++..+..   
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~---~-~~~~aWL~~Ia~n~~id~lRk~~~rr~~~   80 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD---I-DDERGWLIVVTSRLCLDHIKSASTRRERP   80 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc---c-ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence            5788999999999999999999999999999999999999986542   2 26999999999999999998743210   


Q ss_pred             -----ccC-----c-----cH---HH-HHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCc
Q 014852          341 -----RLP-----N-----HL---HE-RLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGK  392 (417)
Q Consensus       341 -----rlp-----~-----~~---~e-~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark  392 (417)
                           ..|     .     ..   .+ ....+..++..|++..|.+         +++|||+.||+|+.+|+..++++++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~  160 (290)
T PRK09635         81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR  160 (290)
T ss_pred             ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                 011     0     00   11 1234667777776656654         9999999999999999999999987


Q ss_pred             cccc
Q 014852          393 VFSL  396 (417)
Q Consensus       393 ~LSL  396 (417)
                      .+.-
T Consensus       161 ~Lr~  164 (290)
T PRK09635        161 KINE  164 (290)
T ss_pred             HHHh
Confidence            7643

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=99.30  E-value=6.1e-12  Score=123.65  Aligned_cols=124  Identities=17%  Similarity=0.099  Sum_probs=95.2

Q ss_pred             HHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccc------c
Q 014852          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL------R  341 (417)
Q Consensus       268 ~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i------r  341 (417)
                      ++++.|.+.++.+|++++++..++||++||+|+.+++.  .|+...  .|.+|++++++|.+++++++..+..      .
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~~--~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~   76 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQIE--NPKAYLTKVVTRRCIDVLRSARARREVYVGPW   76 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccccc--CHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence            37899999999999999999999999999999998775  555433  7999999999999999998754211      1


Q ss_pred             cCcc----------HH---HHH-HHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014852          342 LPNH----------LH---ERL-GLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVFS  395 (417)
Q Consensus       342 lp~~----------~~---e~~-~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~LS  395 (417)
                      +|..          ..   +.. ..+..++..|++..|.+         +++|||+.||+|+.+|+++++++++.+-
T Consensus        77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr  153 (281)
T TIGR02957        77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLD  153 (281)
T ss_pred             CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            1111          00   111 22455666676555553         9999999999999999999999987663

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.22  E-value=2.7e-11  Score=106.30  Aligned_cols=112  Identities=16%  Similarity=0.118  Sum_probs=85.2

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhh-----cCCCCCCchhhHHHHHHHhhHHHHHHhhcccc
Q 014852          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK-----FDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (417)
Q Consensus       266 re~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAier-----FD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~i  340 (417)
                      |+.|+..|.++++.+|.+|..    .+|+ ||.|+.+|+.+.+     |++.  ..|.||++++++|.++++++++.+..
T Consensus         1 f~~~~~~y~~~l~~~~~~~~~----~~~~-qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~   73 (142)
T TIGR03209         1 FEEIYMNFKNTIDIFTRKYNL----YYDY-NDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK   73 (142)
T ss_pred             ChHHHHHHHHHHHHHHHHhcc----hhhH-HHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            468999999999999999965    2344 9999999999865     5543  37999999999999999998765321


Q ss_pred             ccC-------------cc--HHHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHH
Q 014852          341 RLP-------------NH--LHERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVR  384 (417)
Q Consensus       341 rlp-------------~~--~~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr  384 (417)
                      ...             ..  ..+....+..++..|++..|++         |++|||+.||||+++|+
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        74 KIIYNSEITDIKLSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             hhhhhhhhhccccchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence            110             00  1112245777888887766654         99999999999999996

Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.20  E-value=3.2e-11  Score=107.17  Aligned_cols=106  Identities=13%  Similarity=0.101  Sum_probs=79.7

Q ss_pred             CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC----------------------
Q 014852          286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP----------------------  343 (417)
Q Consensus       286 ~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp----------------------  343 (417)
                      ++..+++|++||+|+.+|+..+.+ +  +..|.+|++++++|.+++++|++.+.....                      
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSLFSSFSDDDDDDDFDPLETLD   78 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccccccccccccccccccHHHHhc
Confidence            355679999999999999998863 3  337999999999999999998765321110                      


Q ss_pred             ------ccH------HHHHHHHHHHHHHHHHcCCCc---------cHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 ------NHL------HERLGLIRNAKLRLEEKGVTP---------SVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ------~~~------~e~~~kI~~a~~~L~e~gRep---------S~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                            ...      .+....+..++..|++..|.+         +++|||+.||||+++|+..++++++.+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L  150 (161)
T PRK09047         79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHAL  150 (161)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                  000      112244677777776655553         999999999999999999999998654

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=98.83  E-value=4.2e-08  Score=90.92  Aligned_cols=130  Identities=22%  Similarity=0.142  Sum_probs=89.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCC---CCChhh--hhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNM---GADMAD--LVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR  338 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~---g~e~ED--LIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r  338 (417)
                      .|++.|+..|.+.++.+|.++...   +.+.+|  |++|.|+.+++.....+...-..|..|+..++++.++++.|.+..
T Consensus        17 ~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~lid~~R~~~a   96 (185)
T PF07638_consen   17 AALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRKLIDHARRRQA   96 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999987632   334444  577888877774332233322379999999999999999986654


Q ss_pred             cccc------C---------ccHHHHHHHHHHHHHHHHHcC------------CCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          339 TLRL------P---------NHLHERLGLIRNAKLRLEEKG------------VTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       339 ~irl------p---------~~~~e~~~kI~~a~~~L~e~g------------RepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      ..+-      +         ....+....+.++...|....            -..|++|||+.||||+.+|+..+..++
T Consensus        97 ~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~aR  176 (185)
T PF07638_consen   97 QKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGISERTVRRRLRRAR  176 (185)
T ss_pred             HhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3221      1         011223334555555442211            123999999999999999999999887


Q ss_pred             cc
Q 014852          392 KV  393 (417)
Q Consensus       392 k~  393 (417)
                      ..
T Consensus       177 ~~  178 (185)
T PF07638_consen  177 AW  178 (185)
T ss_pred             HH
Confidence            54

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=98.53  E-value=1.6e-07  Score=74.98  Aligned_cols=67  Identities=31%  Similarity=0.316  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCCCCCCCcccc
Q 014852          348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHI  414 (417)
Q Consensus       348 e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~~~~~d~l~d  414 (417)
                      +.+++|.++...|. .+||.||.+|||+.|||+++.|+.++..++..+||+.+...+.+...++.+.|
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d   68 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIED   68 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecC
Confidence            35688999999995 68999999999999999999999999999999999998877655544444443

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=97.61  E-value=0.00087  Score=68.98  Aligned_cols=133  Identities=17%  Similarity=0.252  Sum_probs=77.2

Q ss_pred             hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhH-HHHHHH
Q 014852          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG-LIGLLR  304 (417)
Q Consensus       226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG-~IgLik  304 (417)
                      .+...|.+.+|++|+.+++|..+|++.++++..+...                   ..    ....++.+.++ -..+..
T Consensus       220 ~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~l~d  276 (367)
T PRK09210        220 RVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSHLGD  276 (367)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcchhhh
Confidence            3567788999999999999999999999877643221                   11    11111111110 011111


Q ss_pred             HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852          305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR  384 (417)
Q Consensus       305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr  384 (417)
                      .+.  |.....+........++..+..++.      .    +.++.+.|...+..|. .|...|++|||+.||||.++|+
T Consensus       277 ~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~----L~~rEr~Vl~lrygl~-~~~~~tl~EIa~~lgvs~erVr  343 (367)
T PRK09210        277 FIE--DQDATSPADHAAYELLKEQLEDVLD------T----LTDREENVLRLRFGLD-DGRTRTLEEVGKVFGVTRERIR  343 (367)
T ss_pred             hcc--CCCCCCHHHHHHHHHHHHHHHHHHH------h----CCHHHHHHHHHHhccC-CCCCccHHHHHHHHCCCHHHHH
Confidence            111  1111223444444444544444332      1    3333455555555543 2466799999999999999999


Q ss_pred             HHHHHhCccc
Q 014852          385 NATEAIGKVF  394 (417)
Q Consensus       385 ~aL~rark~L  394 (417)
                      ++...|..+|
T Consensus       344 Qi~~~Al~kL  353 (367)
T PRK09210        344 QIEAKALRKL  353 (367)
T ss_pred             HHHHHHHHHH
Confidence            9988776544

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=97.59  E-value=0.0012  Score=67.08  Aligned_cols=133  Identities=20%  Similarity=0.241  Sum_probs=75.8

Q ss_pred             hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhh-HHHHHHH
Q 014852          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG-GLIGLLR  304 (417)
Q Consensus       226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQE-G~IgLik  304 (417)
                      .+...|...+|++|+.+|+|..+|++.+++...+.                   .+..    ....++.+.+ +-..+..
T Consensus       177 ~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~-------------------~~~~----~~SLd~~~~~~~~~~l~d  233 (324)
T PRK07921        177 RIKRELHQQLGREATDEELAEESGIPEEKIADLLE-------------------HSRD----PVSLDMPVGSDEEAPLGD  233 (324)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH-------------------HcCC----CceecCCCCCCCCchHHH
Confidence            36678889999999999999999999988764321                   1111    1111111111 0011222


Q ss_pred             HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852          305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR  384 (417)
Q Consensus       305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr  384 (417)
                      .+..  .........+.....+..+..++.          .+.++...|...+..|. .+...|.+|||+.||||.++|+
T Consensus       234 ~l~d--~~~~~pe~~~~~~~~~~~l~~~L~----------~L~eREr~Vl~~rygl~-~~~~~Tl~eIa~~lgvS~eRVr  300 (324)
T PRK07921        234 FIED--SEATSAENAVIAGLLHTDIRSVLA----------TLDEREQQVIRLRFGLD-DGQPRTLDQIGKLFGLSRERVR  300 (324)
T ss_pred             HhcC--CCCCCHHHHHHHHHHHHHHHHHHH----------hCCHHHHHHHHHHHhcC-CCCCcCHHHHHHHHCCCHHHHH
Confidence            2221  111112333333333443333331          23344455666666553 1455699999999999999999


Q ss_pred             HHHHHhCccc
Q 014852          385 NATEAIGKVF  394 (417)
Q Consensus       385 ~aL~rark~L  394 (417)
                      ++..++.++|
T Consensus       301 QIe~~Al~KL  310 (324)
T PRK07921        301 QIEREVMSKL  310 (324)
T ss_pred             HHHHHHHHHH
Confidence            9988876554

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=97.58  E-value=0.0011  Score=71.22  Aligned_cols=133  Identities=18%  Similarity=0.273  Sum_probs=76.5

Q ss_pred             hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhh-HHHHHHH
Q 014852          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG-GLIGLLR  304 (417)
Q Consensus       226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQE-G~IgLik  304 (417)
                      .++..|...+|++|+.+|+|..+|++.+++...+.                       +......+++.+.+ +-..+..
T Consensus       362 ~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-----------------------~~~~~~SLD~~i~~d~~~~l~d  418 (509)
T PRK05901        362 RIERELLQELGREPTPEELAKEMGFTPEKVREIQK-----------------------YNREPISLDKTIGKEGDSQFGD  418 (509)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-----------------------hcCCCcccccccccCCcccHHH
Confidence            35677889999999999999999999988765321                       11112222222211 1111212


Q ss_pred             HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852          305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR  384 (417)
Q Consensus       305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr  384 (417)
                      .+.  |.....+.........+..+..++.          .+.++...|...++.|.. +...|.+|||+.||||.++|+
T Consensus       419 ~l~--D~~~~~p~~~~~~~~l~~~L~~aL~----------~L~eREr~VI~lRyGL~~-~e~~TL~EIa~~lGVSrERVR  485 (509)
T PRK05901        419 FIE--DSEAVSPVDAVSFTLLQDQLQEVLE----------TLSEREAGVIRMRFGLTD-GQPKTLDEIGQVYGVTRERIR  485 (509)
T ss_pred             hcc--CCCCCCHHHHHHHHHHHHHHHHHHh----------hCCHHHHHHHHHHhhccC-CCCCCHHHHHHHHCCCHHHHH
Confidence            111  1111112233333333333333321          234445666666666632 456699999999999999999


Q ss_pred             HHHHHhCccc
Q 014852          385 NATEAIGKVF  394 (417)
Q Consensus       385 ~aL~rark~L  394 (417)
                      ++..++...|
T Consensus       486 QIe~kAL~KL  495 (509)
T PRK05901        486 QIESKTLRKL  495 (509)
T ss_pred             HHHHHHHHHH
Confidence            9988776543

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=97.55  E-value=0.0014  Score=63.07  Aligned_cols=133  Identities=18%  Similarity=0.194  Sum_probs=71.1

Q ss_pred             hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHH-HHHHH
Q 014852          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL-IGLLR  304 (417)
Q Consensus       226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~-IgLik  304 (417)
                      .+...+...+|++|+.+++|..+|++.+++......                   +.    .....++.++++- ..+..
T Consensus        91 ~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~-------------------~~----~~~SLd~~~~~~~~~~l~d  147 (238)
T TIGR02393        91 KAERQLTQELGREPTDEELAERMGMPAEKVREIKKI-------------------AQ----EPISLETPIGEEEDSFLGD  147 (238)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH-------------------hc----cCCCcCCCCCCCCcccHHH
Confidence            356778889999999999999999999987643211                   11    1122222221110 01222


Q ss_pred             HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852          305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR  384 (417)
Q Consensus       305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr  384 (417)
                      .+..  +..............+..+..++.      .+|    +....|......|.. +.+.|++|||+.||||.++|+
T Consensus       148 ~l~d--~~~~~p~~~~~~~~~~~~l~~~l~------~L~----~~er~vl~l~ygl~~-~~~~t~~EIA~~lgis~~~V~  214 (238)
T TIGR02393       148 FIED--TSIESPDDYAAKELLREQLDEVLE------TLT----ERERKVLRMRYGLLD-GRPHTLEEVGKEFNVTRERIR  214 (238)
T ss_pred             HhcC--CCCCChHHHHHHHHHHHHHHHHHH------hCC----HHHHHHHHHHhCCCC-CCCccHHHHHHHHCCCHHHHH
Confidence            2221  111111222222222222222221      222    223334444333311 355699999999999999999


Q ss_pred             HHHHHhCccc
Q 014852          385 NATEAIGKVF  394 (417)
Q Consensus       385 ~aL~rark~L  394 (417)
                      ++..++.+.|
T Consensus       215 q~~~~al~kL  224 (238)
T TIGR02393       215 QIESKALRKL  224 (238)
T ss_pred             HHHHHHHHHH
Confidence            9999887655

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.

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=97.43  E-value=5.5e-05  Score=53.21  Aligned_cols=33  Identities=30%  Similarity=0.483  Sum_probs=30.7

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCc
Q 014852          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS  223 (417)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~  223 (417)
                      |.++.||++|+.+|+||++||.+|+++++.|+.
T Consensus         2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~   34 (37)
T PF00140_consen    2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE   34 (37)
T ss_dssp             HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence            689999999999999999999999999999986

2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=97.31  E-value=0.0045  Score=64.12  Aligned_cols=132  Identities=17%  Similarity=0.268  Sum_probs=71.8

Q ss_pred             HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHH
Q 014852          227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGI  306 (417)
Q Consensus       227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAi  306 (417)
                      +...|...+|++|+.+++|..+|++.++++..+..            ...+.++-..+.   .+ +|      ..+...+
T Consensus       228 a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~------------~~~~~SLd~~i~---~~-~~------~~l~d~l  285 (373)
T PRK07406        228 TTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKS------------AQLPISLETPIG---KE-ED------SRLGDFI  285 (373)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh------------cCCCcccCCCCC---CC-Cc------ccHHHhc
Confidence            56678899999999999999999999887642110            011112111110   00 01      0122222


Q ss_pred             hhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHH
Q 014852          307 EKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNA  386 (417)
Q Consensus       307 erFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~a  386 (417)
                      .  +.... ..........+..+..++.      .    +.+..+.|...+..|.. +...|.+|||+.||||.++|+++
T Consensus       286 ~--d~~~~-pee~~~~~~~~~~L~~aL~------~----L~~rEr~IL~lrygl~~-~~~~Tl~EIA~~lgiS~eRVRQi  351 (373)
T PRK07406        286 E--ADGET-PEDDVAKNLLREDLEGVLA------T----LSPRERDVLRLRYGLDD-GRMKTLEEIGQIFNVTRERIRQI  351 (373)
T ss_pred             C--CCCCC-HHHHHHHHHHHHHHHHHHH------c----CCHHHHHHHHHHHhcCC-CCCCCHHHHHHHHCcCHHHHHHH
Confidence            1  11111 2222222222222222221      1    23334555555554421 34569999999999999999999


Q ss_pred             HHHhCccc
Q 014852          387 TEAIGKVF  394 (417)
Q Consensus       387 L~rark~L  394 (417)
                      ..++.++|
T Consensus       352 e~rAL~KL  359 (373)
T PRK07406        352 EAKALRKL  359 (373)
T ss_pred             HHHHHHHH
Confidence            99887654

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=97.30  E-value=0.0043  Score=61.81  Aligned_cols=30  Identities=17%  Similarity=0.268  Sum_probs=26.5

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+.|++|||+.||||.++|+++++++.+.+
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~kL  273 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEARALEKL  273 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            455999999999999999999999887655

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=97.27  E-value=0.0015  Score=68.51  Aligned_cols=135  Identities=16%  Similarity=0.261  Sum_probs=76.0

Q ss_pred             chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHH
Q 014852          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL  303 (417)
Q Consensus       224 l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLi  303 (417)
                      +.+++..|.+.+|+.|+.+|+|+.+|++.++++..+...            +...++-.....   +-+.       .+.
T Consensus       264 lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~~~------------~~~~SLd~~vg~---~~d~-------~l~  321 (415)
T PRK07598        264 IKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRV------------PRSVSLETKVGK---DKDT-------ELG  321 (415)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHc------------cCCcccccccCC---Cccc-------cHH
Confidence            445667788899999999999999999999988653321            112222222211   1000       111


Q ss_pred             HHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHH
Q 014852          304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV  383 (417)
Q Consensus       304 kAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etV  383 (417)
                      ..+.  ++..+ .-........+..+..++.      .    +.+..+.+......|. .+...|++|||+.||+|.++|
T Consensus       322 d~l~--~~~~~-pee~~~~~~l~~~L~~~L~------~----L~~reR~VI~LRygl~-d~~~~Tl~EIA~~LGvS~erV  387 (415)
T PRK07598        322 DLLE--TDDIS-PEEMLMRESLQRDLQHLLA------D----LTSRERDVIRMRFGLA-DGHTYSLAEIGRALDLSRERV  387 (415)
T ss_pred             Hhcc--CCCCC-HHHHHHHHHHHHHHHHHHH------h----CCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCcCHHHH
Confidence            1121  11111 1111112222222222221      1    2333445555555553 256679999999999999999


Q ss_pred             HHHHHHhCccc
Q 014852          384 RNATEAIGKVF  394 (417)
Q Consensus       384 r~aL~rark~L  394 (417)
                      ++++++|.+.|
T Consensus       388 Rqie~rAl~KL  398 (415)
T PRK07598        388 RQIESKALQKL  398 (415)
T ss_pred             HHHHHHHHHHH
Confidence            99999987654

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=97.26  E-value=0.0045  Score=60.47  Aligned_cols=60  Identities=25%  Similarity=0.277  Sum_probs=40.0

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (417)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~  258 (417)
                      +...+-.|++.....|    ....+.+.++.      .+...|++.+|++|+.+++|..+|++.+++...
T Consensus        87 Ir~~i~~~lr~~~~~p----r~~~~~~~~l~------~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~  146 (257)
T PRK05911         87 IKAAIIDDLRKQDWVP----RSVHQKANKLA------DAMDSLRQSLGKEPTDGELCEYLNISQQELSGW  146 (257)
T ss_pred             HHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHH
Confidence            3345555665554422    23333444443      355678889999999999999999999987654

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=97.24  E-value=0.00091  Score=65.26  Aligned_cols=63  Identities=24%  Similarity=0.399  Sum_probs=41.1

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (417)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~  258 (417)
                      +.+.+..|++.....-.+ |....+.+++++      .+...|.+.+|++|+.+++|..+|++.+++...
T Consensus        87 Ir~~i~~~lr~~~~~vr~-pr~~~~~~~~~~------~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~  149 (256)
T PRK07408         87 IRGEIQHYLRDKSPTVRI-PRRWQELQRQAK------KVRQELRQELGRQPTDQEIAQALDISLEEWQEI  149 (256)
T ss_pred             HHHHHHHHHHHcCCeeee-CHHHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence            445566666654432112 122223444443      366788999999999999999999999987653

>PRK05949 RNA polymerase sigma factor; Validated

Probab=97.23  E-value=0.004  Score=63.29  Aligned_cols=135  Identities=19%  Similarity=0.276  Sum_probs=72.0

Q ss_pred             chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHH
Q 014852          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL  303 (417)
Q Consensus       224 l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLi  303 (417)
                      +..+...+...+|++|+.+++|..+|++.+++...+...            .-+.++-...   +.+.+.       .+.
T Consensus       180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~------------~~~~SLd~~~---~~~~~~-------~l~  237 (327)
T PRK05949        180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMA------------RQPISLDVRV---GDNQDT-------ELS  237 (327)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh------------ccccccCCCc---CCCCCc-------cHH
Confidence            344566778889999999999999999998876532111            0011211111   001000       111


Q ss_pred             HHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHH
Q 014852          304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV  383 (417)
Q Consensus       304 kAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etV  383 (417)
                      ..+..  ...+ ..........+..+..++.      .    +.+..+.|...+..|. .+...|++|||+.||||.++|
T Consensus       238 ~~l~d--~~~~-pe~~~~~~~~~~~L~~~L~------~----L~~rer~Vi~lr~gl~-~~e~~Tl~EIa~~lgiS~erV  303 (327)
T PRK05949        238 ELLED--EGPS-PDQYITQELLRQDLNNLLA------E----LTPQQREVLTLRFGLE-DGKELSLAKVGERLNLSRERV  303 (327)
T ss_pred             hhcCC--CCCC-HHHHHHHHHHHHHHHHHHH------h----CCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCcCHHHH
Confidence            11111  1111 1111111222222222221      1    2233445555555453 135569999999999999999


Q ss_pred             HHHHHHhCccc
Q 014852          384 RNATEAIGKVF  394 (417)
Q Consensus       384 r~aL~rark~L  394 (417)
                      ++++.++.+.|
T Consensus       304 rq~~~rAl~kL  314 (327)
T PRK05949        304 RQLEHQALAHL  314 (327)
T ss_pred             HHHHHHHHHHH
Confidence            99999887654

>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]

Probab=97.14  E-value=0.0075  Score=61.80  Aligned_cols=48  Identities=19%  Similarity=0.344  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       346 ~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      +.++...|...+..+. .+...|.+||++.+|||.+.|+++...+...+
T Consensus       280 Lt~rE~~Vi~~R~gl~-~~~~~TLeevg~~~~isrERvRQIE~kAl~KL  327 (342)
T COG0568         280 LTERERRVIRLRFGLD-DGEPKTLEELGEEFGISRERVRQIEAKALRKL  327 (342)
T ss_pred             CCHHHHHHHHHHhccC-CCCcchHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence            4555566777777775 24455999999999999999999988876554

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=97.13  E-value=0.01  Score=58.40  Aligned_cols=153  Identities=19%  Similarity=0.187  Sum_probs=84.0

Q ss_pred             hhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHH
Q 014852          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (417)
Q Consensus       190 ~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~L  269 (417)
                      -..+-.||++..  +.--|.-..++.+++.      .+..+|+..+|++|+.+|+|..+|++.+++...+.....     
T Consensus        86 ~Gei~d~LR~~~--~v~vpR~~~~~~~~i~------~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~-----  152 (247)
T COG1191          86 RGEILDYLRKND--SVKVPRSLRELGRRIE------EAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAING-----  152 (247)
T ss_pred             HHHHHHHHHhCC--CccCcHHHHHHHHHHH------HHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhcc-----
Confidence            346667787776  2222333344444444      366789999999999999999999999987654433211     


Q ss_pred             HHHhHHHHHHHHHHccCCCCC-hhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHH
Q 014852          270 VMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE  348 (417)
Q Consensus       270 Ie~yl~LV~sIA~Ry~~~g~e-~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e  348 (417)
                           ..+.++.......+.. ..|.                  .+.++..+-.+...+.+..++.      .    +.+
T Consensus       153 -----~~~~sld~~~~~~~d~~~~~~------------------~~~~~~~~~~~~~~~~l~~ai~------~----L~E  199 (247)
T COG1191         153 -----SQLLSLDEDVLKDDDDDVDDQ------------------IENPDDGVEKEELLEILKEAIE------P----LPE  199 (247)
T ss_pred             -----ccccchhhhhccccccchhhc------------------cccchhHHHHHHHHHHHHHHHH------c----cCH
Confidence                 1122222111111000 0111                  1113333334444443333332      1    222


Q ss_pred             HHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          349 RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       349 ~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                      +.+.|.....     ..+.|..|||+.||||+.+|.++..++.+.
T Consensus       200 REk~Vl~l~y-----~eelt~kEI~~~LgISes~VSql~kkai~k  239 (247)
T COG1191         200 REKLVLVLRY-----KEELTQKEIAEVLGISESRVSRLHKKAIKK  239 (247)
T ss_pred             HHHHHHHHHH-----HhccCHHHHHHHhCccHHHHHHHHHHHHHH
Confidence            2233333322     234589999999999999998887776543

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=96.98  E-value=0.0042  Score=62.77  Aligned_cols=135  Identities=20%  Similarity=0.280  Sum_probs=71.5

Q ss_pred             chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHH
Q 014852          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL  303 (417)
Q Consensus       224 l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLi  303 (417)
                      +..++..+...+|++|+.+++|..+|++.+++...+...            .-..++-...   +.+. |      ..+.
T Consensus       170 l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~------------~~~~SLd~~~---~~~~-~------~~l~  227 (317)
T PRK07405        170 IKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERA------------RQPLSLDLRV---GDNQ-D------TELG  227 (317)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHc------------CCCeeecCCC---CCCC-C------ccHH
Confidence            444666778899999999999999999988766431100            0011111110   0000 0      0111


Q ss_pred             HHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHH
Q 014852          304 RGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV  383 (417)
Q Consensus       304 kAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etV  383 (417)
                      ..+.  |... .........-.+..+..++.      .    +.+..+.|......|. .+...|++|||+.||||.++|
T Consensus       228 ~~~~--d~~~-~pe~~~~~~~~~~~l~~al~------~----L~~rer~Vi~lr~gl~-~~~~~Tl~EIa~~lgiS~erV  293 (317)
T PRK07405        228 ELLE--DTGA-SPEDFATQSSLQLDLERLME------D----LTPQQKEVIALRFGLE-DGQPLTLAKIGERLNISRERV  293 (317)
T ss_pred             Hhhc--CCCC-CHHHHHHHHHHHHHHHHHHH------c----CCHHHHHHHHHHhhcC-CCCCcCHHHHHHHHCcCHHHH
Confidence            1111  1111 01222221222222222221      1    2333455555555553 135569999999999999999


Q ss_pred             HHHHHHhCccc
Q 014852          384 RNATEAIGKVF  394 (417)
Q Consensus       384 r~aL~rark~L  394 (417)
                      ++++.+|.+.|
T Consensus       294 Rqi~~rAl~kL  304 (317)
T PRK07405        294 RQIEREALSKL  304 (317)
T ss_pred             HHHHHHHHHHH
Confidence            99999887654

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family

Probab=96.96  E-value=0.006  Score=60.83  Aligned_cols=132  Identities=19%  Similarity=0.229  Sum_probs=70.6

Q ss_pred             hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhh-HHHHHHH
Q 014852          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG-GLIGLLR  304 (417)
Q Consensus       226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQE-G~IgLik  304 (417)
                      .....+...+|++|+.+++|..+|++.+++...+..                   +.+..    ..+..+.+ +-..+..
T Consensus       165 k~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~-------------------~~~~~----SLd~~~~~~~~~~~~~  221 (298)
T TIGR02997       165 KVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQR-------------------ARQPV----SLDAPVGDEEDTELGD  221 (298)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH-------------------cccCc----ccCCCcCCCCcchHHH
Confidence            345667788999999999999999999987753211                   11111    11111110 0001111


Q ss_pred             HHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHH
Q 014852          305 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVR  384 (417)
Q Consensus       305 AierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr  384 (417)
                      .+..  ... ...........+..+..++.      .+|    +..+.|......|. .+...|++|||+.||||.++|+
T Consensus       222 ~~~~--~~~-~pe~~~~~~~~~~~L~~~L~------~L~----~rer~Vi~lr~gl~-~~~~~Tl~EIa~~lgiS~erVr  287 (298)
T TIGR02997       222 LLED--DGE-SPEEQVERESLRQDLESLLA------ELT----PRERQVLRLRFGLD-GGEPLTLAEIGRRLNLSRERVR  287 (298)
T ss_pred             hccC--CCC-CHHHHHHHHHHHHHHHHHHH------cCC----HHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHH
Confidence            1111  111 12222322223332222221      122    33344444444442 1344599999999999999999


Q ss_pred             HHHHHhCccc
Q 014852          385 NATEAIGKVF  394 (417)
Q Consensus       385 ~aL~rark~L  394 (417)
                      ++++++.+.+
T Consensus       288 q~~~rAl~kL  297 (298)
T TIGR02997       288 QIEAKALRKL  297 (298)
T ss_pred             HHHHHHHHHc
Confidence            9999987654

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).

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=96.89  E-value=0.0083  Score=58.12  Aligned_cols=33  Identities=18%  Similarity=0.285  Sum_probs=27.9

Q ss_pred             HHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 014852          227 HKLRLKERLGCEPSMEQLAASLRISRPELQSIL  259 (417)
Q Consensus       227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l  259 (417)
                      +...+.+.+|++|+.+++|..+|++.++++..+
T Consensus       114 ~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~  146 (251)
T PRK07670        114 AIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM  146 (251)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHH
Confidence            455677889999999999999999999877543

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=96.87  E-value=0.018  Score=56.61  Aligned_cols=63  Identities=21%  Similarity=0.272  Sum_probs=41.9

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (417)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~  258 (417)
                      +...+..||.+....-.+ |....+++.+++.      +..++.+.+|++|+.+++|..+|++.+++...
T Consensus       101 Irg~I~~~lr~~~~~ir~-Pr~~~~~~~~i~~------~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~  163 (264)
T PRK07122        101 IMGEVRRHFRDNSWSVKV-PRRLKELHLRLGR------ATAELSQRLGRAPTASELAAELGMDREEVVEG  163 (264)
T ss_pred             HHHHHHHHHHHcCCcccc-CHHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            445566666664432112 1223345555543      56678889999999999999999999987653

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=96.86  E-value=0.011  Score=57.81  Aligned_cols=34  Identities=38%  Similarity=0.470  Sum_probs=29.0

Q ss_pred             chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQS  257 (417)
Q Consensus       224 l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~  257 (417)
                      +..+...|+..+|++|+.+++|..+|++.+++..
T Consensus       120 i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~  153 (268)
T PRK06288        120 IERAIAMLEARLGRTPSDEEIADELGISLEEYNS  153 (268)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence            3346678899999999999999999999988664

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=96.74  E-value=0.0099  Score=57.27  Aligned_cols=60  Identities=22%  Similarity=0.354  Sum_probs=40.3

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (417)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~  258 (417)
                      +.+.+-.|++.....|    ........+++      .+...+...+|++|+.+++|+.+|++.+++...
T Consensus        78 Ir~~il~~lr~~~~~~----r~vr~~~~~i~------~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~  137 (231)
T PRK12427         78 IRGAILDELRELDWRP----RRLRQKTHKTN------DAIREIAKRLGHEPNFEEISAELNLTAEEYQEY  137 (231)
T ss_pred             HHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHH
Confidence            3345555666554333    22233344443      356788899999999999999999999987653

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=96.69  E-value=0.016  Score=63.58  Aligned_cols=131  Identities=15%  Similarity=0.266  Sum_probs=73.5

Q ss_pred             hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhH-HHHHHH
Q 014852          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG-LIGLLR  304 (417)
Q Consensus       226 ~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG-~IgLik  304 (417)
                      .+...+.+.+|++|+.+++|..+|++.++++..+.                   ++..    ....++-+.+. -..+. 
T Consensus       471 ~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~-------------------~~~~----~~Sld~~i~~~~~~~l~-  526 (619)
T PRK05658        471 RISRQMLQEIGREPTPEELAERLGMPEDKVRKVLK-------------------IAKE----PISLETPIGDDEDSHLG-  526 (619)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-------------------hcCC----CCcCCCCCCCCCCCchh-
Confidence            35667889999999999999999999998775322                   2221    12222211110 00111 


Q ss_pred             HHhhcCCCC--CCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHH
Q 014852          305 GIEKFDSSK--GFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKK  382 (417)
Q Consensus       305 AierFD~~r--G~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~et  382 (417)
                         .|-++.  ..++........+..+...+          ..+.++...|...+..|. .+...|.+|||+.||||.++
T Consensus       527 ---d~i~d~~~~~p~~~~~~~~~~~~l~~~l----------~~L~~rE~~Vl~~r~g~~-~~~~~tl~ei~~~lgvs~eR  592 (619)
T PRK05658        527 ---DFIEDKNAELPIDAAIQESLREATTDVL----------ASLTPREAKVLRMRFGID-MNTDHTLEEVGKQFDVTRER  592 (619)
T ss_pred             ---hhcCCCCCCChHHHHHHHHHHHHHHHHH----------HcCCHHHHHHHHHhcCCC-CCCCccHHHHHHHhCCCHHH
Confidence               121221  11233333333333222222          123334455555555442 13456999999999999999


Q ss_pred             HHHHHHHhCccc
Q 014852          383 VRNATEAIGKVF  394 (417)
Q Consensus       383 Vr~aL~rark~L  394 (417)
                      |+++...+.+.|
T Consensus       593 VrQie~~al~kL  604 (619)
T PRK05658        593 IRQIEAKALRKL  604 (619)
T ss_pred             HHHHHHHHHHHH
Confidence            999988776543

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=96.48  E-value=0.036  Score=53.88  Aligned_cols=62  Identities=15%  Similarity=0.232  Sum_probs=39.7

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (417)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~  258 (417)
                      +.+.+..|++..... .+ |....+++.++..      +..++...+|++|+.+++|+.+|++.+++...
T Consensus        95 irn~~~~~lr~~~~i-r~-p~~~~~~~~~~~~------~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~  156 (254)
T TIGR02850        95 IIGEIRRYLRDNNPI-RV-SRSLRDIAYKALQ------VRDKLISENSKEPTVSEIAKELKVPQEEVVFA  156 (254)
T ss_pred             HHHHHHHHHHhCCCc-cC-chHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            334555566554321 12 2223334444432      45678888999999999999999999987654

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.

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family

Probab=96.44  E-value=0.036  Score=52.57  Aligned_cols=34  Identities=29%  Similarity=0.443  Sum_probs=28.6

Q ss_pred             hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852          225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (417)
Q Consensus       225 ~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~  258 (417)
                      ..+...|+..+|++|+.+++|+.+|++.++++..
T Consensus        86 ~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~  119 (224)
T TIGR02479        86 ERAIRELEARLGREPTEEEIAEELGMDLKEYRQA  119 (224)
T ss_pred             HHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHH
Confidence            3456678889999999999999999999887653

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.

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=96.17  E-value=0.011  Score=55.98  Aligned_cols=31  Identities=29%  Similarity=0.506  Sum_probs=26.7

Q ss_pred             HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852          227 HKLRLKERLGCEPSMEQLAASLRISRPELQS  257 (417)
Q Consensus       227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~  257 (417)
                      +...++..+|++|+.+++|..+|++.+++..
T Consensus        95 ~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~  125 (227)
T TIGR02980        95 ATEELTQRLGRSPTIAEIAEELGVSEEEVVE  125 (227)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence            4567888899999999999999999988653

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.

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=96.16  E-value=0.0096  Score=57.66  Aligned_cols=31  Identities=23%  Similarity=0.299  Sum_probs=26.7

Q ss_pred             HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852          227 HKLRLKERLGCEPSMEQLAASLRISRPELQS  257 (417)
Q Consensus       227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~  257 (417)
                      +...++..+|++|+.+++|..++++.+++..
T Consensus       121 ~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~  151 (255)
T TIGR02941       121 AIDELTDHLQRSPKIIEIADHLGLSEEEVLE  151 (255)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            4557888899999999999999999988664

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=96.15  E-value=0.013  Score=46.61  Aligned_cols=35  Identities=34%  Similarity=0.564  Sum_probs=27.9

Q ss_pred             hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHh
Q 014852          225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL  259 (417)
Q Consensus       225 ~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l  259 (417)
                      .+++..|.+.+||+|+.+|+|..+|++.++++..+
T Consensus         7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l   41 (78)
T PF04539_consen    7 ERARRELEQELGREPTDEEIAEELGISVEEVRELL   41 (78)
T ss_dssp             HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence            34778899999999999999999999999987643

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....

>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein

Probab=96.08  E-value=0.023  Score=44.86  Aligned_cols=47  Identities=26%  Similarity=0.221  Sum_probs=40.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcc----C--CCCChhhhhhhHHHHHHHHHhhcC
Q 014852          264 LAREKLVMSNVRLVMSIAQRYD----N--MGADMADLVQGGLIGLLRGIEKFD  310 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~----~--~g~e~EDLIQEG~IgLikAierFD  310 (417)
                      .|.++++..|.|++.+++.|-.    +  .+.--+|+-|+--..|++++-+|+
T Consensus        13 ~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen   13 EAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            9999999999999999999833    1  234458999999999999999996

Some proteins with this domain are annotated as conjugative transposon proteins.

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=96.06  E-value=0.19  Score=49.91  Aligned_cols=30  Identities=17%  Similarity=0.231  Sum_probs=26.1

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+.|++|||+.||||.++|+++...+.+.|
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kL  276 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEKNAMKKL  276 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            466999999999999999999998876543

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=95.95  E-value=0.066  Score=51.26  Aligned_cols=31  Identities=29%  Similarity=0.413  Sum_probs=26.3

Q ss_pred             HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852          227 HKLRLKERLGCEPSMEQLAASLRISRPELQS  257 (417)
Q Consensus       227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~  257 (417)
                      ....+...+|++|+.+++|..+|++.+++..
T Consensus       100 ~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~  130 (236)
T PRK06986        100 AIRQLEQELGREPTDTEVAEKLGLSLEEYRE  130 (236)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence            4456777899999999999999999988664

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=95.85  E-value=0.003  Score=46.84  Aligned_cols=27  Identities=30%  Similarity=0.287  Sum_probs=22.3

Q ss_pred             ccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          367 PSVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       367 pS~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                      .|++|||+.+|+|+.+|+..+.++++.
T Consensus        27 ~s~~eIa~~l~~s~~~v~~~l~ra~~~   53 (54)
T PF08281_consen   27 MSYAEIAEILGISESTVKRRLRRARKK   53 (54)
T ss_dssp             --HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            499999999999999999999998754

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=95.82  E-value=0.056  Score=54.87  Aligned_cols=30  Identities=10%  Similarity=0.273  Sum_probs=26.9

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||||.++|+++++++++.|
T Consensus       281 e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL  310 (325)
T PRK05657        281 EAATLEDVAREIGLTRERVRQIQVEALRRL  310 (325)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            456999999999999999999999998765

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=95.52  E-value=0.067  Score=50.87  Aligned_cols=31  Identities=35%  Similarity=0.531  Sum_probs=26.6

Q ss_pred             HHHHHHHhhCCCCchHHHHHHhcCChHHHHH
Q 014852          227 HKLRLKERLGCEPSMEQLAASLRISRPELQS  257 (417)
Q Consensus       227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~  257 (417)
                      ....+...+|++|+.+++|+.+|++.+++..
T Consensus       102 ~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~  132 (231)
T TIGR02885       102 MKEELSKELGREPTINELAEALGVSPEEIVM  132 (231)
T ss_pred             HHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence            4556788899999999999999999988654

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.

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=95.42  E-value=0.11  Score=51.46  Aligned_cols=30  Identities=13%  Similarity=0.268  Sum_probs=26.8

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||||+++|+.+++++++.+
T Consensus       241 e~~s~~EIA~~Lgis~~tVk~~l~rAlkkL  270 (285)
T TIGR02394       241 EPATLEEVAAEVGLTRERVRQIQVEALKKL  270 (285)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            445999999999999999999999998765

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).

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=95.36  E-value=0.08  Score=51.50  Aligned_cols=32  Identities=25%  Similarity=0.370  Sum_probs=27.4

Q ss_pred             HHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 014852          227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (417)
Q Consensus       227 ~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~  258 (417)
                      +..++...+|++|+.+++|..+|++.+++...
T Consensus       128 ~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~  159 (258)
T PRK08215        128 VREKLINENSKEPTVEEIAKELEVPREEVVFA  159 (258)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            45578889999999999999999999987643

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=95.22  E-value=0.6  Score=45.87  Aligned_cols=30  Identities=13%  Similarity=0.197  Sum_probs=25.4

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||||.++|+++...+.+.+
T Consensus       235 ~~~t~~eIA~~lgvS~~~V~q~~~~Al~kL  264 (270)
T TIGR02392       235 DKLTLQELAAEYGVSAERIRQIEKNAMKKL  264 (270)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            456999999999999999999888776543

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.

>PRK05572 sporulation sigma factor SigF; Validated

Probab=94.21  E-value=0.29  Score=47.46  Aligned_cols=30  Identities=23%  Similarity=0.235  Sum_probs=25.9

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||+|..+|+.+.+++.+.+
T Consensus       217 ~~~s~~eIA~~lgis~~~V~~~~~ral~kL  246 (252)
T PRK05572        217 KDKTQSEVAKRLGISQVQVSRLEKKILKQM  246 (252)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            346999999999999999999998887654

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=93.47  E-value=0.14  Score=37.41  Aligned_cols=30  Identities=27%  Similarity=0.203  Sum_probs=25.3

Q ss_pred             CCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       364 gRepS~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                      ....|+.|||+.||+|.++|+++..++.+.
T Consensus        18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~k   47 (50)
T PF04545_consen   18 FEGLTLEEIAERLGISRSTVRRILKRALKK   47 (50)
T ss_dssp             TST-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence            455699999999999999999999887643

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=91.79  E-value=0.51  Score=37.17  Aligned_cols=44  Identities=30%  Similarity=0.369  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHH-HHcCCCccHHHHHHHcCCC-HHHHHHHHHHhC
Q 014852          348 ERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMS-QKKVRNATEAIG  391 (417)
Q Consensus       348 e~~~kI~~a~~~L-~e~gRepS~eEIAe~LGIS-~etVr~aL~rar  391 (417)
                      +...+|..++... .+.|..||+.|||+.+|++ ..+|...+.+..
T Consensus         6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le   51 (65)
T PF01726_consen    6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALE   51 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence            4445555555554 6689999999999999997 999999988764

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=90.50  E-value=0.16  Score=49.17  Aligned_cols=30  Identities=23%  Similarity=0.128  Sum_probs=25.9

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+.|++|||+.||||+++|+..++++++.+
T Consensus       220 ~g~s~~eIA~~l~is~~tV~~~~~ra~~kL  249 (257)
T PRK08583        220 ENLSQKETGERLGISQMHVSRLQRQAIKKL  249 (257)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            345999999999999999999999887644

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=90.31  E-value=0.65  Score=33.47  Aligned_cols=34  Identities=29%  Similarity=0.341  Sum_probs=24.3

Q ss_pred             HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852          356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI  390 (417)
Q Consensus       356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra  390 (417)
                      .+..|...+| .++.+||+.+|+|..+|.+++.+.
T Consensus         8 Il~~Lq~d~r-~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen    8 ILRLLQEDGR-RSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             HHHHHHH-TT-S-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHcCC-ccHHHHHHHHCcCHHHHHHHHHHh
Confidence            3444555555 589999999999999999988764

...

>PRK06930 positive control sigma-like factor; Validated

Probab=90.24  E-value=0.18  Score=46.84  Aligned_cols=29  Identities=31%  Similarity=0.415  Sum_probs=25.8

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      +.|+.|||+.||+|+++|+..+.++++.+
T Consensus       130 g~s~~EIA~~lgiS~~tVk~~l~Ra~~kL  158 (170)
T PRK06930        130 GLSYSEIADYLNIKKSTVQSMIERAEKKI  158 (170)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            34999999999999999999999988654

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=89.66  E-value=1  Score=42.13  Aligned_cols=65  Identities=14%  Similarity=0.277  Sum_probs=50.7

Q ss_pred             hHHHHHHHHHHccCCCCC---hhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852          273 NVRLVMSIAQRYDNMGAD---MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (417)
Q Consensus       273 yl~LV~sIA~Ry~~~g~e---~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~  337 (417)
                      .+..+..+.++|--++..   -+|+|.+|...+++.++.||+.+...+-+|+..++-++..+.|..+.
T Consensus        46 imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk  113 (179)
T PHA02547         46 IMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK  113 (179)
T ss_pred             HHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence            344445555555433333   68999999999999999999999999999999999988888776554

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=89.33  E-value=0.27  Score=34.50  Aligned_cols=29  Identities=31%  Similarity=0.255  Sum_probs=24.9

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                      ...+..+||+.||++..+|...+.+++..
T Consensus        25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          25 EGLSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            34589999999999999999999887643

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=87.64  E-value=0.55  Score=35.75  Aligned_cols=31  Identities=16%  Similarity=0.178  Sum_probs=27.0

Q ss_pred             cCCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       363 ~gRepS~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                      .-|..+..|||+.|||+..++...++++-++
T Consensus        20 ~PR~~tl~elA~~lgis~st~~~~LRrae~k   50 (53)
T PF04967_consen   20 VPRRITLEELAEELGISKSTVSEHLRRAERK   50 (53)
T ss_pred             CCCcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            3477899999999999999999999988643

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=87.01  E-value=1.1  Score=36.40  Aligned_cols=26  Identities=27%  Similarity=0.316  Sum_probs=22.7

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAI  390 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~ra  390 (417)
                      ...|+.|||+.||+|+.+|+..+..-
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~~~   56 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLKGE   56 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence            44599999999999999999998753

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=86.76  E-value=0.65  Score=33.29  Aligned_cols=29  Identities=28%  Similarity=0.329  Sum_probs=25.7

Q ss_pred             ccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014852          367 PSVDRIAEYLNMSQKKVRNATEAIGKVFS  395 (417)
Q Consensus       367 pS~eEIAe~LGIS~etVr~aL~rark~LS  395 (417)
                      .+..|||+.||+|..+|+..+.++.+.+.
T Consensus        19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~   47 (58)
T smart00421       19 LTNKEIAERLGISEKTVKTHLSNIMRKLG   47 (58)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            48999999999999999999998876654

lux regulon (activates the bioluminescence operon

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=86.47  E-value=1.8  Score=31.85  Aligned_cols=40  Identities=18%  Similarity=0.149  Sum_probs=28.9

Q ss_pred             HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ..+..|.......|.+|||+.||||..||++.+.......
T Consensus         4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            3444563334448999999999999999999988775433

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PRK00118 putative DNA-binding protein; Validated

Probab=85.75  E-value=0.45  Score=41.06  Aligned_cols=29  Identities=28%  Similarity=0.346  Sum_probs=25.3

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      +.|+.|||+.+|+|..+|...+.++++.+
T Consensus        33 g~S~~EIAe~lGIS~~TV~r~L~RArkkL   61 (104)
T PRK00118         33 DYSLGEIAEEFNVSRQAVYDNIKRTEKLL   61 (104)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            45999999999999999999999887543

>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins

Probab=85.68  E-value=2.5  Score=31.85  Aligned_cols=46  Identities=30%  Similarity=0.421  Sum_probs=35.3

Q ss_pred             ccCccHHHHHHHHHHHHHHHHHcCCC-ccHHHHHHHcCCCHHHHHHH
Q 014852          341 RLPNHLHERLGLIRNAKLRLEEKGVT-PSVDRIAEYLNMSQKKVRNA  386 (417)
Q Consensus       341 rlp~~~~e~~~kI~~a~~~L~e~gRe-pS~eEIAe~LGIS~etVr~a  386 (417)
                      .+|....+++....+++..|...|.+ ++-.|||+.+|++..+|+.=
T Consensus         2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD   48 (50)
T PF06971_consen    2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD   48 (50)
T ss_dssp             S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence            46777777888888888899877765 58999999999999999864

These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=85.55  E-value=2.2  Score=30.68  Aligned_cols=35  Identities=20%  Similarity=0.160  Sum_probs=25.1

Q ss_pred             HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      .+..|.+.++ .|..|||+.+|+|..+|...+....
T Consensus         8 Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~   42 (48)
T PF13412_consen    8 ILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLE   42 (48)
T ss_dssp             HHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3344544444 7999999999999999999987653

...

>PHA02591 hypothetical protein; Provisional

Probab=84.89  E-value=1.9  Score=35.54  Aligned_cols=35  Identities=34%  Similarity=0.472  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852          353 IRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEA  389 (417)
Q Consensus       353 I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~r  389 (417)
                      +......|.+.|  .|+++||+.||++.++|++.++-
T Consensus        48 ~~~vA~eL~eqG--lSqeqIA~~LGVsqetVrKYL~~   82 (83)
T PHA02591         48 LISVTHELARKG--FTVEKIASLLGVSVRKVRRYLES   82 (83)
T ss_pred             HHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHhc
Confidence            445555565444  59999999999999999998753

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=84.29  E-value=0.92  Score=32.68  Aligned_cols=28  Identities=25%  Similarity=0.361  Sum_probs=25.2

Q ss_pred             ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          367 PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       367 pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+..|||+.||++..+|+..++++++.+
T Consensus        16 ~s~~eia~~l~~s~~tv~~~~~~~~~~l   43 (57)
T cd06170          16 KTNKEIADILGISEKTVKTHLRNIMRKL   43 (57)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence            4999999999999999999999887654

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=83.98  E-value=3.9  Score=31.55  Aligned_cols=41  Identities=24%  Similarity=0.214  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       351 ~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      ....+++..|.+.+..++..+||+.||++..+|-..+.+..
T Consensus         7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~   47 (60)
T PF01325_consen    7 EDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA   47 (60)
T ss_dssp             HHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence            34566777777777788999999999999999999988754

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=82.64  E-value=2.5  Score=33.12  Aligned_cols=29  Identities=24%  Similarity=0.281  Sum_probs=23.8

Q ss_pred             HHcCCCccHHHHHHHcCCCHHHHHHHHHH
Q 014852          361 EEKGVTPSVDRIAEYLNMSQKKVRNATEA  389 (417)
Q Consensus       361 ~e~gRepS~eEIAe~LGIS~etVr~aL~r  389 (417)
                      .+.+...+..+||+.|||+..||+..-..
T Consensus        17 ~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   17 KESNGKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             HHhCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence            34566789999999999999999987443

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=82.22  E-value=2.3  Score=30.66  Aligned_cols=24  Identities=25%  Similarity=0.239  Sum_probs=17.5

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHH
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEA  389 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~r  389 (417)
                      ..|+.|||+.||++..||.+.+.+
T Consensus        20 G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen   20 GMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---HHHHHHHTT--HHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCcHHHHHHHhc
Confidence            369999999999999999988765

>PRK04217 hypothetical protein; Provisional

Probab=82.15  E-value=1  Score=39.30  Aligned_cols=29  Identities=14%  Similarity=0.121  Sum_probs=25.9

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      +.|++|||+.||||..+|+..+.++++.|
T Consensus        58 GlS~~EIAk~LGIS~sTV~r~L~RArkkL   86 (110)
T PRK04217         58 GLTQEEAGKRMGVSRGTVWRALTSARKKV   86 (110)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            45999999999999999999999887655

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=81.36  E-value=0.98  Score=33.96  Aligned_cols=31  Identities=32%  Similarity=0.333  Sum_probs=25.4

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      .-+..|||+.||+++.+|+..+..+.+.+-+
T Consensus        18 G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~   48 (58)
T PF00196_consen   18 GMSNKEIAEELGISEKTVKSHRRRIMKKLGV   48 (58)
T ss_dssp             TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred             cCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence            3489999999999999999999888776644

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=81.13  E-value=7.6  Score=40.37  Aligned_cols=126  Identities=11%  Similarity=-0.010  Sum_probs=76.8

Q ss_pred             HHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccH
Q 014852          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL  346 (417)
Q Consensus       267 e~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~  346 (417)
                      +..+..-.+.+..---+|+++-.-+||.+||+|+...+.--+=-+-+  .=..|++-.-|+.-++.+|+..+....+.+.
T Consensus         8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el   85 (415)
T COG4941           8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPEL   85 (415)
T ss_pred             HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhh
Confidence            33344444555555556667666799999999865544333222323  4578999999999999998877544333321


Q ss_pred             HHHH--HH---------------HHHHHHH-----HHHcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          347 HERL--GL---------------IRNAKLR-----LEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       347 ~e~~--~k---------------I~~a~~~-----L~e~gR---------epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ....  .+               +.+.+..     |+..+|         ..|..|||...=+++.++.+++-+++..+
T Consensus        86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~ri  164 (415)
T COG4941          86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKARI  164 (415)
T ss_pred             cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence            1100  00               1111111     011111         13999999999999999999999988655

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=80.50  E-value=1.7  Score=29.80  Aligned_cols=25  Identities=20%  Similarity=0.405  Sum_probs=19.7

Q ss_pred             ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          367 PSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       367 pS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      .|.+|||..+|++.++|-..+...+
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~   27 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLE   27 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence            3789999999999999999887654

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	417
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		4e-25
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		4e-25
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		5e-24
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		1e-23
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		2e-23
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		3e-23
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		3e-23
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		3e-23
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		3e-23
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		3e-17
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		5e-17
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		2e-14

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score =  112 bits (280), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 56/154 (36%), Positives = 96/154 (62%), Gaps = 9/154 (5%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +G+K STY  WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++R++ + +RT+R+P H+ E +  L R ++  L+E G  P+ + +AE + M + K+
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHIHCG 417
           R       KV  + +E   S+    G+    H G
Sbjct: 495 R-------KVLKIAKEPI-SMETPIGDDEDSHLG 520

>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613

Iteration: 1
 Score =  112 bits (280), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 56/154 (36%), Positives = 96/154 (62%), Gaps = 9/154 (5%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +G+K STY  WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++R++ + +RT+R+P H+ E +  L R ++  L+E G  P+ + +AE + M + K+
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHIHCG 417
           R       KV  + +E   S+    G+    H G
Sbjct: 495 R-------KVLKIAKEPI-SMETPIGDDEDSHLG 520

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score =  108 bits (270), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 67/201 (33%), Positives = 112/201 (55%), Gaps = 16/201 (7%)
Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLS----------LDDHKLR--LKERLGCEPS 240
           ++ Y+  +    LLT  E + L++K++ G+           LD   +R  ++ ++     
Sbjct: 5   VRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTAR 64
Query: 241 MEQLAASLRISRPELQSILM---ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 297
           +E++   L+    EL+  L    E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q 
Sbjct: 65  VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQE 124
Query: 298 GLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNA 356
           G  GL+R +EKF+  + FK STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A
Sbjct: 125 GNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTA 184
Query: 357 KLRLEEKGVTPSVDRIAEYLN 377
           +   +E G  PS + IAE + 
Sbjct: 185 RQLQQELGREPSYEEIAEAMG 205

>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2 Complexed With -10 Promoter Element Ssdna Oligo (Tacaat) Length = 245

Iteration: 1
 Score =  107 bits (266), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 118/226 (52%), Gaps = 35/226 (15%)
Query: 185 SPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS----------LDDHKLR---- 230
            P +  + ++ Y+  +    LLT  E + L++K++ G+           LD   +R    
Sbjct: 1   GPHMTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVR 60
Query: 231 --------------LKERLGCEP-SMEQLAASLRISRPELQSILM---ECSLAREKLVMS 272
                         LKE+   +P ++E++   L+    EL+  L    E   AR+ L+ +
Sbjct: 61  AKILGTARIQKIPGLKEK--PDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEA 118
Query: 273 NVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRA 332
           N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ ++RA
Sbjct: 119 NLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRA 178
Query: 333 LVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLN 377
           + + +RT+R+P H+ E +  L R A+   +E G  PS + IAE + 
Sbjct: 179 IADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMG 224

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score =  107 bits (266), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 52/121 (42%), Positives = 77/121 (63%), Gaps = 1/121 (0%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 191 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 250
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  PS + IAE +
Sbjct: 251 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 310
Query: 377 N 377
Sbjct: 311 G 311

>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423

Iteration: 1
 Score =  106 bits (264), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/121 (42%), Positives = 77/121 (63%), Gaps = 1/121 (0%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 235
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  P+ + IAE +
Sbjct: 236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 295
Query: 377 N 377
Sbjct: 296 G 296

>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423

Iteration: 1
 Score =  106 bits (264), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/121 (42%), Positives = 77/121 (63%), Gaps = 1/121 (0%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 235
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  P+ + IAE +
Sbjct: 236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 295
Query: 377 N 377
Sbjct: 296 G 296

>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase Sigma Subunit Fragment Containing Regions 1.2 To 3.1 Length = 241

Iteration: 1
 Score =  106 bits (264), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/121 (42%), Positives = 77/121 (63%), Gaps = 1/121 (0%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 100 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 159
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  PS + IAE +
Sbjct: 160 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 219
Query: 377 N 377
Sbjct: 220 G 220

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score =  106 bits (264), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/121 (42%), Positives = 77/121 (63%), Gaps = 1/121 (0%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 196 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 255
Query: 318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  P+ + IAE +
Sbjct: 256 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 315
Query: 377 N 377
Sbjct: 316 G 316

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 86.3 bits (212), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 33/74 (44%), Positives = 56/74 (75%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +G+K STY  WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 325 IRQGVSRALVENSR 338
           IRQ ++R++ + +R
Sbjct: 326 IRQAITRSIADQAR 339

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 85.5 bits (210), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 37/81 (45%), Positives = 54/81 (66%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  +GF  
Sbjct: 99  IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAF 158
Query: 318 STYVYWWIRQGVSRALVENSR 338
           STY  WWIRQ ++RA+ + +R
Sbjct: 159 STYATWWIRQAINRAIADQAR 179

>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti- Sigma Factor Spoiiab With The Sporulation Sigma Factor Sigmaf Length = 243

Iteration: 1
 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 49/127 (38%), Positives = 74/127 (58%), Gaps = 2/127 (1%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AR++++  N+RLV S+ QR+ N G +  DL Q G IGLL+ ++KFD S   K STY    
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEE-KGVTPSVDRIAEYLNMSQKKV 383
           I   + R L ++  T+++   L E    IR AK  L + +G  P+V  IA++L +S + V
Sbjct: 89  IIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 384 RNATEAI 390
             A EA+
Sbjct: 148 VLAQEAV 154

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	417
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	7e-35
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	3e-34
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	9e-33
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	1e-31
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	5e-31
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	7e-27
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	4e-21
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-13
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	8e-07

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2 Length = 243

 Score =  128 bits (324), Expect = 7e-35
 Identities = 50/134 (37%), Positives = 76/134 (56%), Gaps = 2/134 (1%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AR++++  N+RLV S+ QR+ N G +  DL Q G IGLL+ ++KFD S   K STY    
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKV 383
           I   + R L ++  T+++   L E    IR AK  L + +G  P+V  IA++L +S + V
Sbjct: 89  IIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147

Query: 384 RNATEAIGKVFSLD 397
             A EA+    S+ 
Sbjct: 148 VLAQEAVRLPTSIH 161

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 1ku2_A 3lev_A* 3les_A* Length = 245

 Score =  126 bits (318), Expect = 3e-34
 Identities = 66/221 (29%), Positives = 114/221 (51%), Gaps = 8/221 (3%)

Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGV--VSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           L + G   L ++     +  +++  ++ +  +SE      E++R   + K   +    K+
Sbjct: 13  LHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKI 72

Query: 230 RLKERLGCEPSMEQLAASLRISRPE---LQSILMECSLAREKLVMSNVRLVMSIAQRYDN 286
              +      ++E++   L+    E      I  E   AR+ L+ +N+RLV+SIA++Y  
Sbjct: 73  PGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 132

Query: 287 MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346
            G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ ++RA+ + +RT+R+P H+
Sbjct: 133 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 192

Query: 347 HERLG-LIRNAKLRLEEKGVTPSVDRIAEYL--NMSQKKVR 384
            E +  L R A+   +E G  PS + IAE +      K+V 
Sbjct: 193 VETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVE 233

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Length = 423

 Score =  126 bits (319), Expect = 9e-33
 Identities = 63/222 (28%), Positives = 103/222 (46%), Gaps = 33/222 (14%)

Query: 196 YVKGVVSEELLTHAEVVRLSKKIKTGL---------SLDDHKLRLKERLGCEPSMEQLAA 246
           Y+  +    LLT  E V L++K++ G+         +  D  L  +          ++  
Sbjct: 84  YLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRH 143

Query: 247 SLRISRPELQSILMECSL---------------------AREKLVMSNVRLVMSIAQRYD 285
              +        + E                        AR+ L+ +N+RLV+SIA++Y 
Sbjct: 144 IPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT 203

Query: 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345
             G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ ++RA+ + +RT+R+P H
Sbjct: 204 GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVH 263

Query: 346 LHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL--NMSQKKVR 384
           + E +  L R A+   +E G  P+ + IAE +      K+V 
Sbjct: 264 MVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVE 305

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Length = 438

 Score =  124 bits (312), Expect = 1e-31
 Identities = 73/318 (22%), Positives = 119/318 (37%), Gaps = 20/318 (6%)

Query: 70  QPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFER 129
           +P+K  +   +   A   +   EP   +     EL+   + L L      +         
Sbjct: 20  EPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPLDLEGPLEADLLPEEGLLE 79

Query: 130 TVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELI 189
               +    K     PV       RQ      +  L   +  +        R +      
Sbjct: 80  EEEEELSLPKVSTSDPV-------RQYLHEIGQVPLLTLEEEIDLA-----RKVEEGMEA 127

Query: 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLR 249
             +L                  +  + +I+    L +                       
Sbjct: 128 IKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPK---- 183

Query: 250 ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKF 309
                   I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF
Sbjct: 184 -ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 242

Query: 310 DSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPS 368
           +  + FK STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  PS
Sbjct: 243 EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPS 302

Query: 369 VDRIAEYL--NMSQKKVR 384
            + IAE +      K+V 
Sbjct: 303 YEEIAEAMGPGWDAKRVE 320

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 613

 Score =  124 bits (312), Expect = 5e-31
 Identities = 49/133 (36%), Positives = 87/133 (65%), Gaps = 1/133 (0%)

Query: 254 ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSK 313
            +     +   A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +
Sbjct: 364 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 423

Query: 314 GFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRI 372
           G+K STY  WWIRQ ++R++ + +RT+R+P H+ E +  L R ++  L+E G  P+ + +
Sbjct: 424 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 483

Query: 373 AEYLNMSQKKVRN 385
           AE + M + K+R 
Sbjct: 484 AERMLMPEDKIRK 496

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Length = 239

 Score =  106 bits (267), Expect = 7e-27
 Identities = 30/140 (21%), Positives = 66/140 (47%), Gaps = 11/140 (7%)

Query: 265 AREKLVMSNVRLVMSIAQR---YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYV 321
            RE+L++  + LV +IA     +     D+ DL+  G+IGL++ ++   +    +   Y+
Sbjct: 13  EREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYI 72

Query: 322 YWWIRQGVSRALVENSRTL-RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMS 379
              I+  +   L    R+L      + E+   I+    +L+ + G  P+ + +A+ L +S
Sbjct: 73  KLRIKGAIYDYL----RSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGIS 128

Query: 380 QKKVRNATEAI--GKVFSLD 397
            +++    + I    + SL+
Sbjct: 129 TEELFKTLDKINFSYILSLE 148

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Length = 339

 Score = 92.7 bits (230), Expect = 4e-21
 Identities = 33/85 (38%), Positives = 58/85 (68%)

Query: 254 ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSK 313
            +     +   A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +
Sbjct: 255 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 314

Query: 314 GFKISTYVYWWIRQGVSRALVENSR 338
           G+K STY  WWIRQ ++R++ + +R
Sbjct: 315 GYKFSTYATWWIRQAITRSIADQAR 339

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 71.8 bits (175), Expect = 1e-13
 Identities = 70/443 (15%), Positives = 126/443 (28%), Gaps = 172/443 (38%)

Query: 44  GSTKNVVAAKKSSNYN--PSFP------------SSNRQTQPIKALKEHVDTNFASTAEP 89
           GS K  VA     +Y                   S     + ++ L   +D N+ S ++ 
Sbjct: 160 GSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH 219

Query: 90  WAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERT--VLTDSPSKKTHKKVPVT 147
            +     I    +EL       LL  K          +E    VL +  + K      ++
Sbjct: 220 SSNIKLRIHSIQAELRR-----LLKSK---------PYENCLLVLLNVQNAKAWNAFNLS 265

Query: 148 CSGVSARQRRLNSKKKIL--SQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEE- 204
           C              KIL  ++ K +                   + L       +S + 
Sbjct: 266 C--------------KILLTTRFKQVT------------------DFLSAATTTHISLDH 293

Query: 205 ---LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP---SMEQLAASLR--ISRPE-- 254
               LT  EV  L  K    L      L  +E L   P   S+  +A S+R  ++  +  
Sbjct: 294 HSMTLTPDEVKSLLLKY---LDCRPQDLP-REVLTTNPRRLSI--IAESIRDGLATWDNW 347

Query: 255 -------LQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIE 307
                  L +I +E SL    L  +  R      + +D +            +       
Sbjct: 348 KHVNCDKLTTI-IESSL--NVLEPAEYR------KMFDRLS-----------V------- 380

Query: 308 KFDSSKGFKISTYV---YWW----------IRQGVSRALVE---NSRTLRLPNH------ 345
            F       I T +    W+          + +    +LVE      T+ +P+       
Sbjct: 381 -FP--PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKV 437

Query: 346 -------LHERLGLIRNAKLRLEEKGVTPSV-------------------DRIAE----Y 375
                  LH  +    N     +   + P                     +R+      +
Sbjct: 438 KLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF 497

Query: 376 LNMS--QKKVRNATEAIGKVFSL 396
           L+    ++K+R+ + A     S+
Sbjct: 498 LDFRFLEQKIRHDSTAWNASGSI 520

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Length = 164

 Score = 47.9 bits (114), Expect = 8e-07
 Identities = 23/117 (19%), Positives = 52/117 (44%), Gaps = 5/117 (4%)

Query: 288 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347
           GA+  DLVQ G++GLL+ I+ +D +K    S++ +  IR+ +  A+ + +    +  +  
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMVLNEA 59

Query: 348 ERLGLIRNAKLRLEEKGVT----PSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREA 400
            +   I       +++G       S +   E   + ++++    +     FS   + 
Sbjct: 60  LKTNAILEDSAYFDDEGHNINNYKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKE 116

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	417
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	99.89
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.78
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.74
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.72
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.71
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.69
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.52
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.51
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.43
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	99.28
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	99.15
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	97.76
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	96.63
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	95.69
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	95.35
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	95.2
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	94.59
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	94.15
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	93.3
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	93.29
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	93.01
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	92.37
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	92.31
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	92.04
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	91.98
3c57_A	95	Two component transcriptional regulatory protein;	91.66
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	90.6
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	90.36
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	90.16
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	88.75
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	87.96
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	87.3
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	86.79
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	86.23
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	85.25
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	85.03
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	84.27
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	81.73
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	80.77

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*

Probab=100.00  E-value=8.2e-35  Score=279.54  Aligned_cols=207  Identities=31%  Similarity=0.510  Sum_probs=130.5

Q ss_pred             hhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHH---HHh-----------------------hCCCCchHH
Q 014852          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL---KER-----------------------LGCEPSMEQ  243 (417)
Q Consensus       190 ~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l---~~~-----------------------lg~eps~~e  243 (417)
                      .|.+++||++|+++|+||+++|++|.++|+.|..+.+....-   ...                       .+.+|+..+
T Consensus         6 ~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~~   85 (245)
T 3ugo_A            6 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE   85 (245)
T ss_dssp             CHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHHH
T ss_pred             CCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhHH
Confidence            489999999999999999999999999999997633222110   000                       146888999


Q ss_pred             HHHHhcCCh----HHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhh
Q 014852          244 LAASLRISR----PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKIST  319 (417)
Q Consensus       244 ~A~~~~~s~----~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsT  319 (417)
                      ||.+.+++.    .+|...+.++..|++.||+.|.++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+|
T Consensus        86 ~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~t  165 (245)
T 3ugo_A           86 EVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST  165 (245)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHH
T ss_pred             HHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHHH
Confidence            999988865    3455667789999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcC--CCHHHHHHHHHHhCccccc
Q 014852          320 YVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLN--MSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       320 YA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LG--IS~etVr~aL~rark~LSL  396 (417)
                      |++||||+.+.++++++.+.+++|.++.+...++..+...|. .+++.||++|||+.||  ||+++|++++.++++.+||
T Consensus       166 ya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~lsl  245 (245)
T 3ugo_A          166 YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL  245 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHTC-------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccCC
Confidence            999999999999999999999999999999999999988885 5789999999999999  9999999999999999886

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=100.00  E-value=2.7e-32  Score=281.69  Aligned_cols=213  Identities=31%  Similarity=0.507  Sum_probs=187.8

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHH------------------HHHHhhCCCCchHHHHH------
Q 014852          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL------------------RLKERLGCEPSMEQLAA------  246 (417)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~------------------~l~~~lg~eps~~e~A~------  246 (417)
                      |.++.||++|+..|+||++||++|+++++.|..+.+...                  .....+++.|+.++|+.      
T Consensus        94 d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (438)
T 1l9z_H           94 DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEE  173 (438)
T ss_pred             ChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchhhhh
Confidence            678899999999999999999999999999975433221                  11223567788777632      


Q ss_pred             ------HhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhH
Q 014852          247 ------SLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY  320 (417)
Q Consensus       247 ------~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTY  320 (417)
                            .++++..+|...+.++..|++.||.+|+++|+++|++|.+++.+++|||||||||||+|+++||+.+|++|+||
T Consensus       174 ~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rFsTY  253 (438)
T 1l9z_H          174 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  253 (438)
T ss_pred             hhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHH
Confidence                  23566788888888899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcC--CCHHHHHHHHHHhCcccccc
Q 014852          321 VYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLN--MSQKKVRNATEAIGKVFSLD  397 (417)
Q Consensus       321 A~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LG--IS~etVr~aL~rark~LSLD  397 (417)
                      |+||||+.|.++++++.+.+++|.++.+.+++++++...|. .+||.|+.+|||+.||  ++.++|..++..+...+|||
T Consensus       254 A~~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~~~~~SLd  333 (438)
T 1l9z_H          254 ATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLE  333 (438)
T ss_pred             HHHHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhcccccccc
Confidence            99999999999999999999999999999999999988884 6899999999999999  99999999998888899999


Q ss_pred             cccCCC
Q 014852          398 REAFPS  403 (417)
Q Consensus       398 ~~~~~s  403 (417)
                      .++..+
T Consensus       334 ~~~~~d  339 (438)
T 1l9z_H          334 TPIGDE  339 (438)
T ss_pred             cccccc
Confidence            877543

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H

Probab=100.00  E-value=7e-32  Score=277.43  Aligned_cols=210  Identities=32%  Similarity=0.548  Sum_probs=185.2

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHh---------------------hCCCCchHH------
Q 014852          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKER---------------------LGCEPSMEQ------  243 (417)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~---------------------lg~eps~~e------  243 (417)
                      +.+++||++|+..|+||++||.+|+++++.|+.+.+   .|.+.                     +++.|+.++      
T Consensus        79 d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~---~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (423)
T 2a6h_F           79 DPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIK---KLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKT  155 (423)
T ss_dssp             HHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHH---HHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHH
T ss_pred             cHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHH---HHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhh
Confidence            789999999999999999999999999999865332   23322                     334555332      


Q ss_pred             ---HH---HHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCch
Q 014852          244 ---LA---ASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI  317 (417)
Q Consensus       244 ---~A---~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rF  317 (417)
                         |+   .+++.+..+|...+..+..|++.||.+|+++|+++|++|.+++.+++||+||||||||+|+++|||.+|++|
T Consensus       156 ~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~F  235 (423)
T 2a6h_F          156 VEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  235 (423)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCH
T ss_pred             hhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCH
Confidence               22   234667888888898899999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcC--CCHHHHHHHHHHhCccc
Q 014852          318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLN--MSQKKVRNATEAIGKVF  394 (417)
Q Consensus       318 sTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LG--IS~etVr~aL~rark~L  394 (417)
                      +|||+||||+.|.++++++.+.+++|.++.+.+++++++...|. ..||.|+.+|||+.||  +++++|..++..+...+
T Consensus       236 stYa~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~~~  315 (423)
T 2a6h_F          236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPV  315 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSCCE
T ss_pred             HHHHHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccCCc
Confidence            99999999999999999999999999999999999999988884 6899999999999999  99999999999998999


Q ss_pred             ccccccCCC
Q 014852          395 SLDREAFPS  403 (417)
Q Consensus       395 SLD~~~~~s  403 (417)
                      |||.+...+
T Consensus       316 Sld~~~~~~  324 (423)
T 2a6h_F          316 SLETPIGDE  324 (423)
T ss_dssp             ESSCBCSSS
T ss_pred             ccccccCCC
Confidence            999887543

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=99.89  E-value=3.9e-25  Score=236.51  Aligned_cols=141  Identities=33%  Similarity=0.675  Sum_probs=133.0

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCc
Q 014852          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN  344 (417)
Q Consensus       265 Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~  344 (417)
                      |++.||.+|.++|+++|++|++++.+++||+||||||||+++++|++.+|++|+||++|||||.|.++++++.+.+++|.
T Consensus       375 A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn~i~~~lr~~~r~~rip~  454 (613)
T 3iyd_F          375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV  454 (613)
T ss_dssp             HHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHHHHHHHTTTSCSSSCCCS
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHHHHHHHHHhcCcceeCcH
Confidence            39999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHHH-HHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccccccccCCCCC
Q 014852          345 HLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN  405 (417)
Q Consensus       345 ~~~e~~~kI~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~~~s~~  405 (417)
                      ++.+..+++.++...| .+.||+||.+|||+.||+++++|+.++..++..+||+.+...+.+
T Consensus       455 ~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~~~~~~  516 (613)
T 3iyd_F          455 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDED  516 (613)
T ss_dssp             HHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCCSSSSS
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCCCCCCC
Confidence            9999999999988888 468999999999999999999999999999999999988765433

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=99.78  E-value=7.5e-20  Score=168.08  Aligned_cols=160  Identities=33%  Similarity=0.450  Sum_probs=49.1

Q ss_pred             hcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHHHHHHhHHHHHH
Q 014852          200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS  279 (417)
Q Consensus       200 i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~LIe~yl~LV~s  279 (417)
                      +...+.++++++.+|+.+++.||.                                        .|++.|+..|.++|++
T Consensus         4 ~~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~   43 (243)
T 1l0o_C            4 MQGQSPIKDQEMKELIRRSQEGDQ----------------------------------------EARDEIIEKNMRLVWS   43 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHH
Confidence            445667888888999999999987                                        8999999999999999


Q ss_pred             HHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCccHHHHHHHHHHHHHH
Q 014852          280 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR  359 (417)
Q Consensus       280 IA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~~~e~~~kI~~a~~~  359 (417)
                      +|.+|+++..+++||+||||+++|+++++|++.+|.+|.||+++++++.+.+++++.. .+++|..+.....++..+...
T Consensus        44 ~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~~d~~r~~~-~~~~~~~~~~~~~~~~~~~~~  122 (243)
T 1l0o_C           44 VVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDE  122 (243)
T ss_dssp             --------------------------------------------------------CC-CCTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-CccCcHHHHHHHHHHHHHHHH
Confidence            9999999989999999999999999999999998889999999999999999999877 678899988888899999888


Q ss_pred             HH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhCccccccccc
Q 014852          360 LE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREA  400 (417)
Q Consensus       360 L~-e~gRepS~eEIAe~LGIS~etVr~aL~rark~LSLD~~~  400 (417)
                      +. ..++.++..++++.+|++.+.+...+.......|++.+.
T Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~  164 (243)
T 1l0o_C          123 LSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETV  164 (243)
T ss_dssp             HHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC--------
T ss_pred             HHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccc
Confidence            85 468899999999999999999998888777777887664

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=99.74  E-value=1e-17  Score=150.28  Aligned_cols=128  Identities=22%  Similarity=0.238  Sum_probs=104.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcccccc-
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL-  342 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irl-  342 (417)
                      .|++.|+..|.+.|+.+|.++++ ..+++|++||+|+++|+++++|++..  .|.+|++++++|.+.+++++..+.... 
T Consensus        23 ~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~d~~R~~~~~~~~~   99 (194)
T 1or7_A           23 KAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAKNYLVAQGRRPPSS   99 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHHHHHHHHTTCCTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHHHhccCccc
Confidence            89999999999999999999999 99999999999999999999999875  699999999999999999876543210 


Q ss_pred             ---------------------Ccc---HHHHHHHHHHHHHHHHHcC---------CCccHHHHHHHcCCCHHHHHHHHHH
Q 014852          343 ---------------------PNH---LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEA  389 (417)
Q Consensus       343 ---------------------p~~---~~e~~~kI~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~aL~r  389 (417)
                                           |..   ..+....+..++..|++..         ...|++|||+.||||+++|++.+.+
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~r  179 (194)
T 1or7_A          100 DVDAIEAENFESGGALKEISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFR  179 (194)
T ss_dssp             HHHHHHHHSCCSSCC--------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             cccccccccccccccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence                                 000   1123344567777775433         3359999999999999999999999


Q ss_pred             hCccc
Q 014852          390 IGKVF  394 (417)
Q Consensus       390 ark~L  394 (417)
                      +++.+
T Consensus       180 a~~~L  184 (194)
T 1or7_A          180 AREAI  184 (194)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98654

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=99.72  E-value=9.4e-17  Score=147.63  Aligned_cols=135  Identities=21%  Similarity=0.366  Sum_probs=117.7

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcc---CCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhcc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR  338 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~---~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r  338 (417)
                      +..|++.|+..|.++|+++|.+|+   +++.+++||+||||++||+++++|++.+|.+|.||+++|+++.+.+++++.. 
T Consensus        10 ~~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~-   88 (239)
T 1rp3_A           10 NQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD-   88 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS-
T ss_pred             cchHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-
Confidence            346899999999999999999998   6789999999999999999999999999889999999999999999998865 


Q ss_pred             ccccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccc
Q 014852          339 TLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDRE  399 (417)
Q Consensus       339 ~irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~  399 (417)
                        +.|.........+.++...+. ..++.|+..|||+.+|++++++..++....  ..+|+|.+
T Consensus        89 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~  150 (239)
T 1rp3_A           89 --FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEV  150 (239)
T ss_dssp             --TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCcccccc
Confidence              456667777788888888885 579999999999999999999998876553  34556544

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.69  E-value=5.9e-17  Score=160.96  Aligned_cols=74  Identities=43%  Similarity=0.910  Sum_probs=71.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~  337 (417)
                      .|++.||..|.++|+++|++|++++.+++||+|||||+||+++++|++.+|.+|+||++|||+|.|+++++++.
T Consensus       265 ~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~~~~~lr~~~  338 (339)
T 1sig_A          265 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA  338 (339)
T ss_dssp             HHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC-
T ss_pred             hhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            79999999999999999999999999999999999999999999999999889999999999999999999865

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=99.52  E-value=1.1e-14  Score=126.13  Aligned_cols=106  Identities=25%  Similarity=0.376  Sum_probs=78.6

Q ss_pred             CCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccC------------------------
Q 014852          288 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP------------------------  343 (417)
Q Consensus       288 g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp------------------------  343 (417)
                      |.++||++||+|+++|+++.+|++.+ .+|.||++++++|.+.+++++..+..+.+                        
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLNEALKTNAILEDSAYFDDEGHNI   79 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhHHHhhhhhhhccCCCCCcccchh
Confidence            57899999999999999999999987 59999999999999999999865432211                        


Q ss_pred             ----------cc---HHHHHHHHHHHHH-HHHHcC--------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          344 ----------NH---LHERLGLIRNAKL-RLEEKG--------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       344 ----------~~---~~e~~~kI~~a~~-~L~e~g--------RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                                ..   ..+....+..++. .|++..        ...|++|||+.||||.++|+..++++++.+
T Consensus        80 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~~L~~~~r~v~~~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~L  152 (164)
T 3mzy_A           80 NNYKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRIRKKS  152 (164)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             hhhcccCCCHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                      00   1112334566666 564333        334999999999999999999999988654

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.51  E-value=9.6e-17  Score=142.08  Aligned_cols=126  Identities=8%  Similarity=0.037  Sum_probs=98.0

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccccCcc
Q 014852          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH  345 (417)
Q Consensus       266 re~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~irlp~~  345 (417)
                      |+.|+..|.+.|+.+|.+++++..++||++||+|+++|+++++|++..  .|.+|++++++|.+++++++.......+. 
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~~~~~~e-   79 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGEAQTSQSD-   79 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTSCCCCCCS-
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccCcccCCcc-
Confidence            667899999999999999999999999999999999999999999764  79999999999999999886532111011 


Q ss_pred             HHHHHHHHHHHHHHHHHcC---------CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          346 LHERLGLIRNAKLRLEEKG---------VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       346 ~~e~~~kI~~a~~~L~e~g---------RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ..+....+..++..|++..         .+.|++|||+.||||+++|+..+.++++.+
T Consensus        80 ~~~~~~~l~~~l~~Lp~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~rar~~L  137 (157)
T 2lfw_A           80 AEGTEAVARARLARMTPLSRQALLLTAMEGFSPEDAAYLIEVDTSEVETLVTEALAEI  137 (157)
T ss_dssp             CSSSSSTTTTTTTTSCTTHHHHHTTTSSSCCCHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            1111122344444443322         335999999999999999999999998765

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.43  E-value=1.1e-14  Score=141.37  Aligned_cols=127  Identities=9%  Similarity=-0.035  Sum_probs=100.7

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccccc
Q 014852          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (417)
Q Consensus       262 ~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~ir  341 (417)
                      +..+|+.|+..|.+.++.+|.+++++..++||++||.|+.+|+...+|++..  .|.||++++++|.+++++|.......
T Consensus        19 ~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~~--~~~~wL~~ia~n~~~d~~r~~~~~~~   96 (286)
T 3n0r_A           19 SEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANL--SPRVALYRVFHAIWLSSGAQLEVGHD   96 (286)
T ss_dssp             -CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSSS--CHHHHHHHHHHHHHSCTTC----CCC
T ss_pred             CcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCCc--ChHHHHHHHHHHHHHhhccccccCCC
Confidence            3368999999999999999999999999999999999999999999999764  79999999999998888775332111


Q ss_pred             cCccHHHHHHHHHHHHHHHHHcCCC---------ccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          342 LPNHLHERLGLIRNAKLRLEEKGVT---------PSVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       342 lp~~~~e~~~kI~~a~~~L~e~gRe---------pS~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                      ..   .+....+..++..|++..|+         .+++|||+.||+++++|+..+.++++.
T Consensus        97 ~~---~~~~~~l~~al~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~rA~~~  154 (286)
T 3n0r_A           97 QG---LHAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAE  154 (286)
T ss_dssp             CC---CCTTSHHHHHHHHHSCHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cc---cchHHHHHHHHHhCCHHHeeEEEEEeeCCCCHHHHHHHhCcCHHHHHHHHHHHHhh
Confidence            11   11123467777777654444         499999999999999999998887643

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=99.28  E-value=7.6e-12  Score=104.01  Aligned_cols=73  Identities=15%  Similarity=0.154  Sum_probs=64.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhccc
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT  339 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~r~  339 (417)
                      .|++.|+..|.+.|+.+|.++ ++..++||++||+|+.+|+.+.+|++..  .|.+|++++++|.+++++|+..+.
T Consensus        24 ~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~   96 (112)
T 2o7g_A           24 RALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSARS--SARTWLLAIARHVVADHIRHVRSR   96 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCSS--CHHHHHHHHHHHHHHHHTC-----
T ss_pred             HHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHHHHHHHHHHhhcc
Confidence            899999999999999999999 8889999999999999999999999753  799999999999999998876643

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=99.15  E-value=3.6e-11  Score=95.54  Aligned_cols=75  Identities=19%  Similarity=0.217  Sum_probs=67.2

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhhc
Q 014852          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (417)
Q Consensus       261 ~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~~  337 (417)
                      ++..+++.|+..|.+.++.+|.+++++..++||++||+|+.+|+.+++|++..  .|.+|++.+++|.++++++++.
T Consensus         9 g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~   83 (87)
T 1h3l_A            9 ERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREGT--NLKAWLYRILTNTFINSYRKKQ   83 (87)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHHHTCC---
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--cHHHHHHHHHHHHHHHHHHHhc
Confidence            45689999999999999999999999999999999999999999999999763  8999999999999998887654

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=97.76  E-value=2.5e-09  Score=101.78  Aligned_cols=136  Identities=10%  Similarity=-0.017  Sum_probs=94.9

Q ss_pred             HHHHhh-hhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhh----hhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhH
Q 014852          255 LQSILM-ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLV----QGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV  329 (417)
Q Consensus       255 Lr~~l~-~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLI----QEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i  329 (417)
                      |..++. .+..+++.+...|.++++.+............|+.    ||.|+.+|+.+..|++..  .|.+|++++++|.+
T Consensus        87 ll~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~~--~~~~WL~~ia~n~~  164 (258)
T 3clo_A           87 IYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTP--AGNVWLIFCLYSLS  164 (258)
T ss_dssp             HHTTBCHHHHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECT--TSCEEEEEEEEEEC
T ss_pred             HHHhCChHHHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHH
Confidence            444444 34567999999999999999888777778889997    999999999999998754  79999999999877


Q ss_pred             HHHHHhhcccccc----------CccHHHHH----HHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014852          330 SRALVENSRTLRL----------PNHLHERL----GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFS  395 (417)
Q Consensus       330 ~~~Ird~~r~irl----------p~~~~e~~----~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~LS  395 (417)
                      .++.+.......+          +.......    .+-+.++. |-  ....|++|||+.||+|++||+..++++++.+-
T Consensus       165 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~erevl~-L~--~~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL~  241 (258)
T 3clo_A          165 ADQRPEQGIYATITQMERGEVETLSLSEEHRNILSEREKEILR-CI--RKGLSSKEIAATLYISVNTVNRHRQNILEKLS  241 (258)
T ss_dssp             SCCCCCSSCCCEEEETTTTEEEECCCHHHHTTSSCHHHHHHHH-HH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             cchhhhhHHHHHHHhhcccccccchhhHHHHccCCHHHHHHHH-HH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHc
Confidence            6654321100000          00111111    11111111 11  23459999999999999999999999987663

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=96.63  E-value=0.027  Score=58.16  Aligned_cols=44  Identities=9%  Similarity=0.324  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       350 ~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+.|...+..|.. +...|++|||+.||||.++|++++.++.+.|
T Consensus       380 eR~VI~LRygL~~-~e~~TleEIAe~LgIS~erVRqi~~RAlkKL  423 (438)
T 1l9z_H          380 EAMVLKLRKGLID-GREHTLEEVGAYFGVTRERIRQIENKALRKL  423 (438)
T ss_pred             HHHHHHHHHhccC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            3445554444431 3567999999999999999999999987665

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=95.69  E-value=0.0026  Score=50.87  Aligned_cols=30  Identities=17%  Similarity=0.130  Sum_probs=26.5

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.|||+..+|+..++++++.+
T Consensus        52 ~g~s~~eIA~~lgis~~tV~~~l~ra~~~L   81 (92)
T 3hug_A           52 RGWSTAQIATDLGIAEGTVKSRLHYAVRAL   81 (92)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            345999999999999999999999998654

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H

Probab=95.35  E-value=0.095  Score=53.54  Aligned_cols=44  Identities=7%  Similarity=0.287  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       350 ~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+.|......|. .+...|++|||+.||||.++|++++.+|.+.|
T Consensus       365 er~Vl~lr~~L~-~~e~~Tl~EIA~~lgiS~erVrqi~~rAl~kL  408 (423)
T 2a6h_F          365 EAMVLKLRKGLI-DGREHTLEEVGAFFGVTRERIRQIENKALRKL  408 (423)
T ss_dssp             HHHHHHHHHHTT-CC-----CHHHHSSSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccC-CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            344445444443 13456999999999999999999999887665

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=95.20  E-value=0.25  Score=44.27  Aligned_cols=30  Identities=13%  Similarity=0.106  Sum_probs=26.5

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||||.++|+.+++++++.|
T Consensus       202 ~g~s~~EIA~~lgis~~~V~~~~~ra~~~L  231 (239)
T 1rp3_A          202 EELPAKEVAKILETSVSRVSQLKAKALERL  231 (239)
T ss_dssp             SCCCHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            456999999999999999999999987654

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=94.59  E-value=0.013  Score=48.48  Aligned_cols=30  Identities=3%  Similarity=0.269  Sum_probs=26.4

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||||.++|++.+.++.+.+
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~rAlkkL   67 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAKALRKL   67 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            456999999999999999999999887654

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=94.15  E-value=0.0051  Score=45.87  Aligned_cols=30  Identities=10%  Similarity=0.042  Sum_probs=26.6

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||+|..+|+..++++++.+
T Consensus        30 ~g~s~~eIA~~lgis~~tv~~~~~ra~~~l   59 (70)
T 2o8x_A           30 LGLSYADAAAVCGCPVGTIRSRVARARDAL   59 (70)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            346999999999999999999999998665

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=93.30  E-value=0.033  Score=42.52  Aligned_cols=33  Identities=15%  Similarity=0.049  Sum_probs=28.1

Q ss_pred             CCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       364 gRepS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      ....|++|||+.||++..+|+..+.++.+.+-.
T Consensus        29 ~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~   61 (79)
T 1x3u_A           29 VAGLPNKSIAYDLDISPRTVEVHRANVMAKMKA   61 (79)
T ss_dssp             TTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            345699999999999999999999998876643

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=93.29  E-value=0.059  Score=40.38  Aligned_cols=30  Identities=3%  Similarity=0.269  Sum_probs=27.1

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||+|..+|+..+.++.+.+
T Consensus        24 ~g~s~~eIA~~lgis~~tV~~~~~ra~~kL   53 (68)
T 2p7v_B           24 TDYTLEEVGKQFDVTRERIRQIEAKALRKL   53 (68)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHGG
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            457999999999999999999999988765

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=93.01  E-value=0.024  Score=47.57  Aligned_cols=30  Identities=23%  Similarity=0.339  Sum_probs=26.1

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||+|+.+|+..++++++.+
T Consensus        40 ~g~s~~EIA~~lgiS~~tV~~~l~ra~~kL   69 (113)
T 1xsv_A           40 EDYSLSEIADTFNVSRQAVYDNIRRTGDLV   69 (113)
T ss_dssp             SCCCHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            345999999999999999999999887644

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=92.37  E-value=0.024  Score=51.01  Aligned_cols=28  Identities=18%  Similarity=0.210  Sum_probs=0.0

Q ss_pred             ccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          367 PSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       367 pS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .|++|||+.||||+.+|+..+.++++.+
T Consensus       215 ~s~~EIA~~lgis~~tV~~~~~ra~~~L  242 (243)
T 1l0o_C          215 QTQSEVASRLGISQVQMSRLEKKILQHI  242 (243)
T ss_dssp             ----------------------------
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence            4899999999999999999999998754

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=92.31  E-value=0.073  Score=42.05  Aligned_cols=30  Identities=10%  Similarity=0.387  Sum_probs=26.9

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||||.++|+..+.++.+.+
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~ra~~kL   66 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEVKALRKL   66 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            567999999999999999999999987655

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=92.04  E-value=0.086  Score=40.05  Aligned_cols=30  Identities=7%  Similarity=0.350  Sum_probs=26.5

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|++|||+.||+|.++|+..+.++.+.+
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~ra~~kL   58 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIENKALRKL   58 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            456999999999999999999998887655

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=91.98  E-value=0.026  Score=60.21  Aligned_cols=59  Identities=22%  Similarity=0.341  Sum_probs=33.1

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhhHHHHHH
Q 014852          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK  268 (417)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~~~Are~  268 (417)
                      ..|.++|||++++..|+||+++|++|+++|..|..                              ++...+.+++.+.+.
T Consensus        94 ~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~~------------------------------~~~~~~~~~P~ti~~  143 (613)
T 3iyd_F           94 TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGIN------------------------------QVQCSVAEYPEAITY  143 (613)
T ss_dssp             -----------C--------CSSSTTTHHHHHHHH------------------------------HHHHHHHSCHHHHHH
T ss_pred             CCCcHHHHHHHhcccccCCchhHHHHHHHHHHhHH------------------------------HHHHHHccCHHHHHH
Confidence            34899999999999999999999999999999985                              566777777788888


Q ss_pred             HHHHhHHHH
Q 014852          269 LVMSNVRLV  277 (417)
Q Consensus       269 LIe~yl~LV  277 (417)
                      |+.-|-.+.
T Consensus       144 il~~~~~l~  152 (613)
T 3iyd_F          144 LLEQYNRVE  152 (613)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888777654

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=91.66  E-value=0.02  Score=46.33  Aligned_cols=31  Identities=16%  Similarity=0.245  Sum_probs=26.8

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      ..|++|||+.|||+..+|+..+.++++.+..
T Consensus        42 g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   72 (95)
T 3c57_A           42 GLTNKQIADRMFLAEKTVKNYVSRLLAKLGM   72 (95)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            3489999999999999999999998876543

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=90.60  E-value=0.058  Score=45.32  Aligned_cols=29  Identities=21%  Similarity=0.307  Sum_probs=25.4

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ..|+.|||+.||+|..+|+..++++++.+
T Consensus        38 g~s~~EIA~~lgiS~~tV~~~l~ra~~kL   66 (113)
T 1s7o_A           38 DYSLAEIADEFGVSRQAVYDNIKRTEKIL   66 (113)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            35999999999999999999999887543

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=90.36  E-value=0.12  Score=37.34  Aligned_cols=31  Identities=19%  Similarity=0.189  Sum_probs=26.9

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      ..|.+|||+.||+|+.+|+..+.++.+.+..
T Consensus        13 g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   43 (61)
T 2jpc_A           13 GYTNHGISEKLHISIKTVETHRMNMMRKLQV   43 (61)
T ss_dssp             SCCSHHHHHHTCSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHCC
Confidence            3589999999999999999999998876644

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=90.16  E-value=0.15  Score=39.81  Aligned_cols=31  Identities=16%  Similarity=0.153  Sum_probs=27.2

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCcccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFS  395 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~LS  395 (417)
                      ...|++|||+.|||+..+|+..+.++++.+.
T Consensus        35 ~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~   65 (82)
T 1je8_A           35 QGLPNKMIARRLDITESTVKVHVKHMLKKMK   65 (82)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHc
Confidence            3469999999999999999999999887664

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=88.75  E-value=0.65  Score=36.58  Aligned_cols=28  Identities=25%  Similarity=0.234  Sum_probs=25.4

Q ss_pred             CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          364 GVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       364 gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      |..||+.|||+.+|+|..+|+.-+....
T Consensus        22 g~~psv~EIa~~lgvS~~TVrr~L~~Le   49 (77)
T 2jt1_A           22 GAPVKTRDIADAAGLSIYQVRLYLEQLH   49 (77)
T ss_dssp             TSCEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            7889999999999999999999887654

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=87.96  E-value=0.18  Score=39.87  Aligned_cols=31  Identities=19%  Similarity=0.149  Sum_probs=27.2

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      ..|++|||+.|||+..+|+..+.++++.+..
T Consensus        44 g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   74 (91)
T 2rnj_A           44 GYSNQEIASASHITIKTVKTHVSNILSKLEV   74 (91)
T ss_dssp             TCCTTHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            3589999999999999999999999877643

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=87.30  E-value=0.36  Score=38.65  Aligned_cols=31  Identities=16%  Similarity=0.245  Sum_probs=27.4

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      ..|.+|||+.|||++.||+..+.++.+++.+
T Consensus        44 G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv   74 (90)
T 3ulq_B           44 GFTNQEIADALHLSKRSIEYSLTSIFNKLNV   74 (90)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            3599999999999999999999998877654

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=86.79  E-value=0.32  Score=36.17  Aligned_cols=31  Identities=26%  Similarity=0.285  Sum_probs=26.6

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      ..|+.|||+.||+|..+|+..+.++.+.+..
T Consensus        26 g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   56 (74)
T 1fse_A           26 DKTTKEIASELFISEKTVRNHISNAMQKLGV   56 (74)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            3499999999999999999999988766543

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=86.23  E-value=0.38  Score=39.34  Aligned_cols=31  Identities=26%  Similarity=0.223  Sum_probs=27.1

Q ss_pred             ccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014852          367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSLD  397 (417)
Q Consensus       367 pS~eEIAe~LGIS~etVr~aL~rark~LSLD  397 (417)
                      .+.+|||+.|||++.+|+..+.++.+.+.+.
T Consensus        50 ~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv~   80 (99)
T 1p4w_A           50 FLVTEIAKKLNRSIKTISSQKKSAMMKLGVD   80 (99)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            4899999999999999999999988776543

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=85.25  E-value=0.61  Score=31.17  Aligned_cols=25  Identities=12%  Similarity=0.076  Sum_probs=22.0

Q ss_pred             ccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          367 PSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       367 pS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      .++.|||+.|||+..+|...+...+
T Consensus        22 ~s~~~IA~~lgis~~Tv~~~~~~~~   46 (51)
T 1tc3_C           22 VSLHEMSRKISRSRHCIRVYLKDPV   46 (51)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHCST
T ss_pred             CCHHHHHHHHCcCHHHHHHHHhhHH
Confidence            5899999999999999999886543

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=85.03  E-value=1  Score=33.93  Aligned_cols=35  Identities=9%  Similarity=0.121  Sum_probs=28.0

Q ss_pred             HHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       357 ~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      +..|.+.+...+..|||+.||+|..+|..++...+
T Consensus        16 L~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~   50 (67)
T 2heo_A           16 LQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLK   50 (67)
T ss_dssp             HHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            33444445668999999999999999999988765

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=84.27  E-value=1.5  Score=30.93  Aligned_cols=23  Identities=39%  Similarity=0.504  Sum_probs=20.5

Q ss_pred             ccHHHHHHHcCCCHHHHHHHHHH
Q 014852          367 PSVDRIAEYLNMSQKKVRNATEA  389 (417)
Q Consensus       367 pS~eEIAe~LGIS~etVr~aL~r  389 (417)
                      .|+.|||+.||++..+|...+..
T Consensus        32 ~s~~eIA~~lgis~~TV~~~l~~   54 (55)
T 2x48_A           32 YTVQQIANALGVSERKVRRYLES   54 (55)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHh
Confidence            49999999999999999988653

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=81.73  E-value=2.5  Score=33.19  Aligned_cols=36  Identities=14%  Similarity=0.137  Sum_probs=27.4

Q ss_pred             HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      ..++.|.+. ..+++.|||+.||+|+.||+.-+...-
T Consensus         6 ~Il~~L~~~-g~vsv~eLa~~l~VS~~TIRrdL~~Le   41 (78)
T 1xn7_A            6 QVRDLLALR-GRMEAAQISQTLNTPQPMINAMLQQLE   41 (78)
T ss_dssp             HHHHHHHHS-CSBCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence            344445543 457999999999999999999877643

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=80.77  E-value=2.9  Score=33.06  Aligned_cols=28  Identities=11%  Similarity=0.271  Sum_probs=25.1

Q ss_pred             CCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          364 GVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       364 gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      |...|..|||+.||++..+|+..+.+..
T Consensus        25 g~~~t~~eLA~~Lgvsr~tV~~~L~~Le   52 (81)
T 1qbj_A           25 GKATTAHDLSGKLGTPKKEINRVLYSLA   52 (81)
T ss_dssp             TCCBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4568999999999999999999998875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	417
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	9e-26
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	9e-24
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	5e-15
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	3e-06
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	5e-04

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 180

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score =  100 bits (250), Expect = 9e-26
 Identities = 53/177 (29%), Positives = 87/177 (49%), Gaps = 30/177 (16%)

Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDH------------------KLRLKER 234
           ++ Y+  +    LLT  E + L++K++ G+                       K+    R
Sbjct: 4   VRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTAR 63

Query: 235 LGCEPS---------MEQLAASLRISRPELQ---SILMECSLAREKLVMSNVRLVMSIAQ 282
           +   P          +E++   L+    EL+    I  E   AR+ L+ +N+RLV+SIA+
Sbjct: 64  IQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAK 123

Query: 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339
           +Y   G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ ++RA+ + +RT
Sbjct: 124 KYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 180

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

 Score = 98.8 bits (245), Expect = 9e-24
 Identities = 47/265 (17%), Positives = 105/265 (39%)

Query: 69  TQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFE 128
           T     L +    +     E   +  ++ ++ S + + + E    L+   +  +  +  +
Sbjct: 67  THVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAK 126

Query: 129 RTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPEL 188
                 +  +            +  +Q         +  ++   Q+    +L        
Sbjct: 127 GRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMP 186

Query: 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASL 248
            +N +  +     S+     A  +      K     ++    L++    E         +
Sbjct: 187 KKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQV 246

Query: 249 RISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308
           +     +     +   A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++K
Sbjct: 247 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 306

Query: 309 FDSSKGFKISTYVYWWIRQGVSRAL 333
           F+  +G+K STY  WWIRQ ++R++
Sbjct: 307 FEYRRGYKFSTYATWWIRQAITRSI 331

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 87

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 68.0 bits (166), Expect = 5e-15
 Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           + RE+L++  + LV +IA           D+ DL+  G+IGL++ ++   +    +   Y
Sbjct: 10  IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 69

Query: 321 VYWWIRQGVSRAL 333
           +   I+  +   L
Sbjct: 70  IKLRIKGAIYDYL 82

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 42.4 bits (100), Expect = 3e-06
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 338 RTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI 390
            T+++   L E    IR AK  L   +G  P+V  IA++L +S + V  A EA+
Sbjct: 2   GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV 55

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 36.3 bits (84), Expect = 5e-04
 Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 9/64 (14%)

Query: 337 SRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKV 393
           SR +R      E+   I+    +L+ + G  P+ + +A+ L +S +++    + I    +
Sbjct: 2   SRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI 55

Query: 394 FSLD 397
            SL+
Sbjct: 56  LSLE 59

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	417
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.95
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.79
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.73
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.45
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	99.02
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	98.55
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.49
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.05
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	96.94
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	96.57
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.35
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.24
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	95.43
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	93.28
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	91.66
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	91.35
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	90.72
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	90.69
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	89.18
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	87.04
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	86.65
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	86.48
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	86.47
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	86.14
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	85.72
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	85.69
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	85.09
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	84.98
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	84.2
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	82.16
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	81.28
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	80.44

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=99.95  E-value=4.5e-29  Score=225.66  Aligned_cols=149  Identities=34%  Similarity=0.590  Sum_probs=121.3

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHccCcchhHHHHHH------------------HhhCCCC---------chHH
Q 014852          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLK------------------ERLGCEP---------SMEQ  243 (417)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~eE~eLirk~k~Gd~l~~~~~~l~------------------~~lg~ep---------s~~e  243 (417)
                      |.+++||++|+.+|+||++||++|+++++.|..+........                  ......|         ...+
T Consensus         2 DpVr~YLreig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~~~   81 (180)
T d1ku2a2           2 DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEE   81 (180)
T ss_dssp             HHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTHHH
T ss_pred             CcHHHHHHHhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHHHH
Confidence            689999999999999999999999999998876444332111                  0122222         2333


Q ss_pred             HHHHhcCChH---HHHHHhhhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhH
Q 014852          244 LAASLRISRP---ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY  320 (417)
Q Consensus       244 ~A~~~~~s~~---eLr~~l~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTY  320 (417)
                      +...+....+   ++......+..|+++||..|+++|+++|++|.+.|.+++||+|||+|||++|+++|||++|++|+||
T Consensus        82 ~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f~ty  161 (180)
T d1ku2a2          82 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  161 (180)
T ss_dssp             HHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            4444444433   4455666888999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhHHHHHHhhccc
Q 014852          321 VYWWIRQGVSRALVENSRT  339 (417)
Q Consensus       321 A~~~IR~~i~~~Ird~~r~  339 (417)
                      |+|||++.|.++++++.|+
T Consensus       162 a~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         162 ATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHhCCC
Confidence            9999999999999988753

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

Probab=99.79  E-value=8.6e-20  Score=177.12  Aligned_cols=77  Identities=42%  Similarity=0.873  Sum_probs=73.5

Q ss_pred             hhhHHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhh
Q 014852          260 MECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN  336 (417)
Q Consensus       260 ~~~~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~  336 (417)
                      .+...|++.|+..|++||++||++|.++|.+++||+|+|++||++|+++||+.+|++|+|||+||||++|.++++++
T Consensus       258 ~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         258 AKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHHHHHHhCC
Confidence            34667999999999999999999999999999999999999999999999999999999999999999999999875

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.73  E-value=3.9e-18  Score=137.90  Aligned_cols=73  Identities=23%  Similarity=0.449  Sum_probs=68.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccC---CCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHHHhh
Q 014852          264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN  336 (417)
Q Consensus       264 ~Are~LIe~yl~LV~sIA~Ry~~---~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~Ird~  336 (417)
                      ..+++||..|+|+|.++|.+|.+   .+++.|||+|+|++||++|+++|||++|.+|+|||.++||++|++++|+.
T Consensus        10 ~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~   85 (87)
T d1rp3a3          10 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSL   85 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            45799999999999999999864   47899999999999999999999999999999999999999999999875

>d1h3la_ a.177.1.1 (A:) Sigma factor SigR {Streptomyces coelicolor a3(2) [TaxId: 100226]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigR
species: Streptomyces coelicolor a3(2) [TaxId: 100226]

Probab=99.02  E-value=1.4e-10  Score=89.23  Aligned_cols=69  Identities=19%  Similarity=0.228  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCChhhhhhhHHHHHHHHHhhcCCCCCCchhhHHHHHHHhhHHHHH
Q 014852          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRAL  333 (417)
Q Consensus       263 ~~Are~LIe~yl~LV~sIA~Ry~~~g~e~EDLIQEG~IgLikAierFD~~rG~rFsTYA~~~IR~~i~~~I  333 (417)
                      ..+|++++..|.+.++++|.+++++..++||++||.|+.+|+..++|++..  +|.+|++++++|.+++++
T Consensus         6 ~~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~   74 (75)
T d1h3la_           6 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREGT--NLKAWLYRILTNTFINSY   74 (75)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCCC--CHHHHHHHHHHHHHHHHh
Confidence            367999999999999999999999999999999999999999999999753  899999999999888764

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=98.55  E-value=4.5e-08  Score=73.04  Aligned_cols=57  Identities=28%  Similarity=0.445  Sum_probs=52.4

Q ss_pred             cccCccHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCC--CHHHHHHHHHHhCccccc
Q 014852          340 LRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNM--SQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       340 irlp~~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGI--S~etVr~aL~rark~LSL  396 (417)
                      +|+|.|+.+.++++.++...|. ++||+||.+|||+.||+  ++++|+.++..++.++||
T Consensus         1 IRlPvH~~e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~~~p~SL   60 (60)
T d1ku2a1           1 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL   60 (60)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGSSSCCCC
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHccCCCCC
Confidence            5899999999999999999994 68999999999999985  488999999999999987

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.49  E-value=8.1e-08  Score=70.73  Aligned_cols=53  Identities=36%  Similarity=0.463  Sum_probs=49.3

Q ss_pred             ccccCccHHHHHHHHHHHHHHH-HHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          339 TLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       339 ~irlp~~~~e~~~kI~~a~~~L-~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      .+++|.++.+..+++.++...| .++||+||.+|||+.||+|+++|..++..++
T Consensus         3 ~IrvPr~~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~r   56 (57)
T d1l0oc_           3 TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR   56 (57)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CEeCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHhc
Confidence            6789999999999999999999 4699999999999999999999999998764

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.05  E-value=1.2e-06  Score=67.46  Aligned_cols=57  Identities=19%  Similarity=0.316  Sum_probs=49.2

Q ss_pred             cHHHHHHHHHHHHHHHH-HcCCCccHHHHHHHcCCCHHHHHHHHHHhC--cccccccccC
Q 014852          345 HLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAF  401 (417)
Q Consensus       345 ~~~e~~~kI~~a~~~L~-e~gRepS~eEIAe~LGIS~etVr~aL~rar--k~LSLD~~~~  401 (417)
                      .+++..++|.++...|. ++||+||.+|||+.|||++++|+.++..+.  ..+|||+++.
T Consensus         4 s~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~   63 (77)
T d1rp3a1           4 QVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFR   63 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCcc
Confidence            45677889999999995 689999999999999999999999987654  6789998664

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.94  E-value=0.0012  Score=47.76  Aligned_cols=48  Identities=21%  Similarity=0.290  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhhhh
Q 014852          209 AEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC  262 (417)
Q Consensus       209 ~eE~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~~~  262 (417)
                      -.-.+++.+++.      +...|.+.+|++|+.+|+|..+|++.+++...+..+
T Consensus         8 r~~~e~~~ki~~------~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_           8 RSLKEMGNKIRK------AKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHHHHHHHH------HHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH------HHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            344556666654      778899999999999999999999999998776543

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=96.57  E-value=0.00032  Score=51.89  Aligned_cols=45  Identities=16%  Similarity=0.067  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHcCC---------CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          350 LGLIRNAKLRLEEKGV---------TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       350 ~~kI~~a~~~L~e~gR---------epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...+.+++..|++..|         +.|++|||+.||+|+++|+..++++++.+
T Consensus         9 ~~~l~~~l~~Lp~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~L   62 (68)
T d1or7a1           9 RQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRAREAI   62 (68)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            3445666666644333         34999999999999999999999998654

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.35  E-value=0.00034  Score=51.70  Aligned_cols=30  Identities=13%  Similarity=0.106  Sum_probs=26.2

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      .+.|++|||+.||+|+.+|+..++++++.+
T Consensus        36 ~~~s~~eIA~~lgis~~tv~~~~~ra~~~L   65 (71)
T d1rp3a2          36 EELPAKEVAKILETSVSRVSQLKAKALERL   65 (71)
T ss_dssp             SCCCHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            345999999999999999999999987643

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.24  E-value=0.0031  Score=47.64  Aligned_cols=37  Identities=41%  Similarity=0.515  Sum_probs=32.8

Q ss_pred             chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHhh
Q 014852          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (417)
Q Consensus       224 l~~~~~~l~~~lg~eps~~e~A~~~~~s~~eLr~~l~  260 (417)
                      ++++..+|++.+||+|+.+|+|..+|++.+++++.+.
T Consensus        12 i~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~   48 (77)
T d1rp3a1          12 IKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLD   48 (77)
T ss_dssp             HHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4557889999999999999999999999999887654

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=95.43  E-value=0.013  Score=42.62  Aligned_cols=44  Identities=25%  Similarity=0.401  Sum_probs=32.9

Q ss_pred             HHHHHHHHHccCcchhHHHHHHHhhCCCCchHHHHHHhcCC--hHHHHHHhh
Q 014852          211 VVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRIS--RPELQSILM  260 (417)
Q Consensus       211 E~eLirk~k~Gd~l~~~~~~l~~~lg~eps~~e~A~~~~~s--~~eLr~~l~  260 (417)
                      ..+.+.+++      .+...|.+.+||+|+.+|+|+++|++  .+.++..+.
T Consensus         7 ~~e~i~rv~------r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~   52 (60)
T d1ku2a1           7 MVETINKLS------RTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLK   52 (60)
T ss_dssp             HHHHHHHHH------HHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGG
T ss_pred             HHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHH
Confidence            344555554      37788999999999999999999855  566766544

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=93.28  E-value=0.0097  Score=48.07  Aligned_cols=29  Identities=21%  Similarity=0.307  Sum_probs=26.0

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ..|+.|||+.||||.++|+..+++|++.+
T Consensus        32 ~ls~~EIA~~lgiS~~aV~~~l~RA~~~L   60 (106)
T d1s7oa_          32 DYSLAEIADEFGVSRQAVYDNIKRTEKIL   60 (106)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            35999999999999999999999998654

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=91.66  E-value=0.18  Score=37.13  Aligned_cols=43  Identities=19%  Similarity=0.251  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHH-HHcCCCccHHHHHHHcCC-CHHHHHHHHHHhC
Q 014852          349 RLGLIRNAKLRL-EEKGVTPSVDRIAEYLNM-SQKKVRNATEAIG  391 (417)
Q Consensus       349 ~~~kI~~a~~~L-~e~gRepS~eEIAe~LGI-S~etVr~aL~rar  391 (417)
                      ...+|..++... ...|..||++|||+.+|+ |..+|...+....
T Consensus         6 rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le   50 (71)
T d1jhfa1           6 RQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALA   50 (71)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            345555555555 567999999999999999 8999999987754

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=91.35  E-value=0.074  Score=38.51  Aligned_cols=47  Identities=15%  Similarity=0.363  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCcc
Q 014852          346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKV  393 (417)
Q Consensus       346 ~~e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~  393 (417)
                      +.+....|......|. .+...|..|||+.||||.+.|+++..+|.+.
T Consensus         9 L~~rer~Ii~~ryGl~-~~~~~tl~eIa~~lgiS~erVrqi~~~al~k   55 (61)
T d1ku3a_           9 LSEREAMVLKMRKGLI-DGREHTLEEVGAYFGVTRERIRQIENKALRK   55 (61)
T ss_dssp             SCHHHHHHHHHHHTTT-TSSCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCCC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            3445556666666663 2455699999999999999999998887544

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=90.72  E-value=0.087  Score=39.00  Aligned_cols=46  Identities=4%  Similarity=0.242  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       348 e~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      +....|......|. .+...|.+|||+.||||.+.|+++..+|.+.+
T Consensus         8 ~rE~~Ii~~rfGl~-~~~~~tl~eI~~~lgiSrerVrqie~~al~kL   53 (68)
T d2p7vb1           8 AREAKVLRMRFGID-MNTDYTLEEVGKQFDVTRERIRQIEAKALRKL   53 (68)
T ss_dssp             HHHHHHHHHHTTTT-SSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGG
T ss_pred             HHHHHHHHHHcCCC-CCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            44455666665553 24556999999999999999999998887655

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=90.69  E-value=0.055  Score=43.45  Aligned_cols=30  Identities=23%  Similarity=0.339  Sum_probs=26.5

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ...|+.|||+.||||.++|+..+++|++.+
T Consensus        33 e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L   62 (106)
T d1xsva_          33 EDYSLSEIADTFNVSRQAVYDNIRRTGDLV   62 (106)
T ss_dssp             SCCCHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             hCCcHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            345999999999999999999999998654

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=89.18  E-value=0.063  Score=39.51  Aligned_cols=33  Identities=15%  Similarity=0.120  Sum_probs=28.2

Q ss_pred             CCccHHHHHHHcCCCHHHHHHHHHHhCcccccc
Q 014852          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLD  397 (417)
Q Consensus       365 RepS~eEIAe~LGIS~etVr~aL~rark~LSLD  397 (417)
                      ...+..|||+.||||+.||+..+..+..++-+.
T Consensus        26 ~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~   58 (70)
T d1yioa1          26 RGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVR   58 (70)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            345899999999999999999999888776554

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=87.04  E-value=0.49  Score=33.77  Aligned_cols=35  Identities=11%  Similarity=0.172  Sum_probs=28.0

Q ss_pred             HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      .+..|...+|. ++.|||+.+|+|+.+|..++++..
T Consensus        10 IL~~L~~n~r~-s~~~iA~~lgis~~tv~~Ri~~L~   44 (63)
T d2cfxa1          10 IIEELKKDSRL-SMRELGRKIKLSPPSVTERVRQLE   44 (63)
T ss_dssp             HHHHHHHCSCC-CHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCC-CHHHHHHHHCcCHHHHHHHHHHHH
Confidence            34456655654 899999999999999999988764

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=86.65  E-value=0.38  Score=34.41  Aligned_cols=33  Identities=21%  Similarity=0.261  Sum_probs=28.0

Q ss_pred             CCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       364 gRepS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      ....|.+|||+.||+|+.||+..+..+.+++.+
T Consensus        17 ~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   49 (65)
T d1l3la1          17 AVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV   49 (65)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            445699999999999999999999988776644

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=86.48  E-value=0.25  Score=38.14  Aligned_cols=45  Identities=13%  Similarity=0.391  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhCccc
Q 014852          349 RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVF  394 (417)
Q Consensus       349 ~~~kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rark~L  394 (417)
                      ....|......|.. +...|..|||+.||||.+.|+++..+|.+.+
T Consensus        22 rE~~Ii~~rfGl~~-~~~~tl~eI~~~lgiSrERVRQie~~al~kL   66 (87)
T d1ttya_          22 REAMVLRMRYGLLD-GKPKTLEEVGQYFNVTRERIRQIEVKALRKL   66 (87)
T ss_dssp             HHHHHHHHHHTTTT-SSCCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCC-CCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            34455555555532 3445999999999999999999988876544

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=86.47  E-value=0.54  Score=33.25  Aligned_cols=35  Identities=26%  Similarity=0.293  Sum_probs=27.7

Q ss_pred             HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      .+..|.+.+| .|+.|||+.+|+|+.+|..++.+..
T Consensus         8 Il~~L~~n~r-~s~~~lA~~~gls~~~v~~Ri~~L~   42 (60)
T d1i1ga1           8 ILEILEKDAR-TPFTEIAKKLGISETAVRKRVKALE   42 (60)
T ss_dssp             HHHHHHHCTT-CCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3444555555 4899999999999999999988765

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=86.14  E-value=0.6  Score=32.84  Aligned_cols=35  Identities=9%  Similarity=0.220  Sum_probs=27.8

Q ss_pred             HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      .+..|...+| .++.|||+.+|+|+.+|..++++..
T Consensus         8 Il~~L~~n~r-~s~~eiA~~l~ls~~~v~~Ri~~L~   42 (60)
T d2cyya1           8 IIKILQNDGK-APLREISKITGLAESTIHERIRKLR   42 (60)
T ss_dssp             HHHHHHHCTT-CCHHHHHHHHCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3445555555 3899999999999999999988764

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=85.72  E-value=0.61  Score=33.16  Aligned_cols=35  Identities=11%  Similarity=0.116  Sum_probs=28.0

Q ss_pred             HHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          356 AKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       356 a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      .+..|...+| .|+.|||+.+|+|..+|..++.+..
T Consensus        10 IL~~L~~~~r-~s~~eiA~~l~ls~~~v~~Ri~rL~   44 (63)
T d2cg4a1          10 ILEALMGNAR-TAYAELAKQFGVSPETIHVRVEKMK   44 (63)
T ss_dssp             HHHHHHHCTT-SCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3445655555 4899999999999999999988765

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=85.69  E-value=0.45  Score=34.15  Aligned_cols=33  Identities=24%  Similarity=0.220  Sum_probs=27.9

Q ss_pred             CCCccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       364 gRepS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      ....+.+|||+.||+++.||+..+..+.+++..
T Consensus        17 ~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v   49 (67)
T d1fsea_          17 VQDKTTKEIASELFISEKTVRNHISNAMQKLGV   49 (67)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             HccCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            445599999999999999999999888776644

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.09  E-value=0.99  Score=32.13  Aligned_cols=39  Identities=18%  Similarity=0.168  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          353 IRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       353 I~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      ....+..|.+....+|..|||+.||||..||++-+....
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~   47 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLR   47 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence            444555565544557999999999999999999877643

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=84.98  E-value=0.28  Score=35.40  Aligned_cols=31  Identities=19%  Similarity=0.211  Sum_probs=26.6

Q ss_pred             CccHHHHHHHcCCCHHHHHHHHHHhCccccc
Q 014852          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSL  396 (417)
Q Consensus       366 epS~eEIAe~LGIS~etVr~aL~rark~LSL  396 (417)
                      ..|..|||+.||+++.||+..+..+..++.+
T Consensus        21 G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   51 (67)
T d1a04a1          21 GLPNKMIARRLDITESTVKVHVKHMLKKMKL   51 (67)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            3589999999999999999999888766544

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.20  E-value=0.79  Score=32.97  Aligned_cols=40  Identities=35%  Similarity=0.427  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       352 kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      ...+++..|.+.+..++..+||+.||++..+|-..+++..
T Consensus         9 dYL~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mvkrL~   48 (63)
T d2isya1           9 MYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRME   48 (63)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHhCCCchhHHHHHHHHH
Confidence            3566777787777789999999999999999999988764

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=82.16  E-value=1.2  Score=31.73  Aligned_cols=40  Identities=20%  Similarity=0.116  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       352 kI~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      ...+++..|...+..++..+||+.||++..+|-+.+++..
T Consensus         7 dYLk~I~~l~~~~~~v~~~~iA~~L~vs~~SVs~mikrL~   46 (61)
T d2ev0a1           7 DYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLD   46 (61)
T ss_dssp             HHHHHHHHHHHHHSSCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCccHHHHHHHhCCCchhHHHHHHHHH
Confidence            3456666675545578999999999999999999988764

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.28  E-value=1.5  Score=31.92  Aligned_cols=38  Identities=21%  Similarity=0.058  Sum_probs=30.0

Q ss_pred             HHHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHhC
Q 014852          354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIG  391 (417)
Q Consensus       354 ~~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~rar  391 (417)
                      ...++.+...++..+..|||+.+|+|..++..++....
T Consensus         8 l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~   45 (75)
T d1mkma1           8 FEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLE   45 (75)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            33444455667778999999999999999999987653

>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor E/IIe-alpha, N-terminal domain
domain: Transcription factor E/IIe-alpha, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=80.44  E-value=1  Score=34.79  Aligned_cols=36  Identities=25%  Similarity=0.316  Sum_probs=30.2

Q ss_pred             HHHHHHHHcCCCccHHHHHHHcCCCHHHHHHHHHHh
Q 014852          355 NAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI  390 (417)
Q Consensus       355 ~a~~~L~e~gRepS~eEIAe~LGIS~etVr~aL~ra  390 (417)
                      +....|.+.+.++|.++||+.+|+...+|++++...
T Consensus        22 ~v~~~L~~~~~evtDe~iA~~tgi~in~VRk~Ly~L   57 (88)
T d1q1ha_          22 DVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLL   57 (88)
T ss_dssp             HHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHhccCcCCHHHHHHHhCCcHHHHHHHHHHH
Confidence            455566666778999999999999999999998764