Citrus Sinensis ID: 011324

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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-------420-------430-------440-------450-------460-------470-------480-------49
Protein Sequence
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSDIT
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccccccHHHHHHHHccccccccccccccHHHHHHHccccHHHHHHHcccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHcccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHccEEEEEHHccccccccHHHHHHHccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHcccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHcccccccccccccccccccccccccccccccccccccccccEccccccHHHccccccEEccccccccccHHHHcccccccccEcccccHccEEEcccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccHHHHHHHHHHcccccccccccccccccccHHHccccccccHHHHHHHcccccccccccccccccHHHHHHHHccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHcccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHcccccEEcccccccccccHHHHHccccccccccc
Coil and Loop (DISEMBL)
meagrnllssppsfpsrtrvkhslsssasssssssVLMHneqsapavasvptssvarhfptsvllqeqrdeyrpllhmfkedktsqatsdsrnIETEAFFveeknsgdlDQLVQDLEHqflhwpdlwnlsppmkrgedpsvsltmqslsndteesvdaepfDAVALARKALSASKEAAslaenpklngaeftdisltsslgypleevkqfsqprflerrskkrkvskpqvtnhetynSRKASVKKKLsegfdrndplrlflwgpetrklltaDEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRdlkselhsgnssREKLINANLRLVVHVAKQYqgrgislhdLLQEGSMGLMKSVEkfkpqagcrfasYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIqegnhspdkedlaRRVGITVEKLERLIFITrmplsmqqpvwadqdttFQVMPLLlshlpsdit
Flexible Loop (DISEMBL)
meagrnllssppsfpsrtrVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMfkedktsqatsdsrNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAslaenpklngaeFTDISLTSslgypleevkqfsqprflerrskkrkvskpqvtnhetynsrkasvkkklsegfdrndplrlfLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLqsqfgreptLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFqhsrtirlpeNIYTLLSKVLEAKRLYIqegnhspdkedlarRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLshlpsdit
Low Complexity Region (SEG)
MEAGRNLLSSPPSFPSRTRVKHslsssasssssssVLMHNEQsapavasvptssvaRHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDavalarkalsaskeaaslaeNPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSDIT
Disordered region (IsUnstruct)
**************************************************************************************************FFV******DLDQLVQDLEHQFLHWPDLWNL******************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE*********FGREPTLIEWAKAIGLSCRDL************KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG********LARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS*******
Disordered Region (DISOPRED)
**********PPSF**************************EQS***********VARHFPTSVLLQEQR********************************************QDLEHQFLHWP***********************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS*************EWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKR**********DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS*******
Disordered Region (DISEMBL)
******************************************************VARHFPTSVLLQEQRDEYRPLLHMFKED*********RNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQS**********AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLE*************TNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK********SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSDIT
Disordered Region (DISPRO)
************************************************SVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM************************AEPFDAVALARKALSASK*AASLAENPKLN***************************************************************FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHL*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFExxxxxxxxxxxxxxxxxxxxxFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSDIT
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	488	2.2.26 [Sep-21-2011]
Q9LD95	547	RNA polymerase sigma fact	yes	no	0.909	0.811	0.526	1e-128
O22056	572	RNA polymerase sigma fact	no	no	0.524	0.447	0.366	1e-46
P26683	390	RNA polymerase sigma fact	yes	no	0.522	0.653	0.365	3e-46
P38023	399	RNA polymerase sigma fact	yes	no	0.444	0.543	0.400	3e-43
Q31ME3	320	RNA polymerase sigma fact	no	no	0.450	0.687	0.404	4e-41
Q31QG5	320	RNA polymerase sigma fact	no	no	0.450	0.687	0.398	1e-37
P74565	425	RNA polymerase sigma fact	N/A	no	0.467	0.536	0.327	8e-37
Q59996	404	Probable RNA polymerase s	N/A	no	0.459	0.554	0.347	5e-36
P52322	416	RNA polymerase sigma fact	no	no	0.444	0.521	0.328	7e-36
Q03066	416	RNA polymerase sigma-C fa	no	no	0.450	0.528	0.349	3e-35

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

 Score =  457 bits (1177), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 254/482 (52%), Positives = 328/482 (68%), Gaps = 38/482 (7%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEA RNL+SS PSF ++T +K     S+ SS SS V++H++ + P V S   +S++RHFP
Sbjct: 1   MEATRNLVSSSPSFQTKTHLK-----SSYSSPSSVVMLHDQTTTPVVNSRHLNSLSRHFP 55

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
            SVL QE R+E RPL H  ++D+TSQ T + R                 D+LV     + 
Sbjct: 56  ASVLSQEPREESRPLSHALRDDRTSQLTLERRQ---------------FDELVSSREDEK 100

Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            E Q LH   LWNL  SP     + P+V   +           DAE  D VALA+KALSA
Sbjct: 101 FEQQLLHSTGLWNLLISPLTSETKLPAVVSPL----------ADAELCDVVALAQKALSA 150

Query: 174 SKEAASLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
           SK+AA L ++ + N ++   D   TSS     E+       R LERR+K R+  K    +
Sbjct: 151 SKQAALLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKRQLERRAKNRRAPKSNDVD 210

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
            E Y  +K S KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K
Sbjct: 211 DEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVK 270

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           +KL+SQ G EPT+ EWA+A+G+S   LKS++H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 271 TKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRG 330

Query: 353 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412
           ++  DLLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y 
Sbjct: 331 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYM 390

Query: 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472
           LL KV EA++  +QEGN+ P KE+LA  VG++ EKL++L++ TR PLSMQQP+W+DQDTT
Sbjct: 391 LLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTT 450

Query: 473 FQ 474
           FQ
Sbjct: 451 FQ 452

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

 Score =  187 bits (476), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 95/259 (36%), Positives = 161/259 (62%), Gaps = 3/259 (1%)

Query: 214 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 272
           R  ER++++ K  +   +   +  +  +  KK+L ++  D NDPLR       + KLLT 
Sbjct: 216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275

Query: 273 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332
            EE EL A IQDL++LE+ +++L  + GR+PT  +WA A G+  + L+  +H G   ++K
Sbjct: 276 REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDK 335

Query: 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392
           +I +N+RLV+ +AK YQG G++L DL+QEG  GL++  EKF    G +F++YA+WW++Q 
Sbjct: 336 MIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQA 395

Query: 393 IRKAIFQHSRTIRLPENIYTLLSKVLEA-KRLYIQEGNHSPDKEDLARRVGITVEKLERL 451
           +RK++   SR IRLP ++     +V EA K+LY + G H P  E++A   G+++++L  +
Sbjct: 396 VRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKH-PKNEEIAEATGLSMKRLMAV 454

Query: 452 IFITRMPLSMQQPVWADQD 470
           +   + P S+ Q +  +Q+
Sbjct: 455 LLSPKPPRSLDQKIGMNQN 473

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

 Score =  186 bits (472), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 98/268 (36%), Positives = 163/268 (60%), Gaps = 13/268 (4%)

Query: 206 EVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPE 265
           ++ +F +P+  E  +K  K +K +         R  S KK  +E     D +RL+L    
Sbjct: 44  DIDEFLEPQTDEDDAKSGKAAKSR--------RRTQSKKKHYTE-----DSIRLYLQEIG 90

Query: 266 TRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325
             +LL ADEE EL  +I DL+ LE+ + +L  +  R+P   EWA+A+ L     +  LH 
Sbjct: 91  RIRLLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQLPLPAFRYRLHI 150

Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
           G  +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF  + G +F++YA
Sbjct: 151 GRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 210

Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 445
            WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P +E++A R+ +T+
Sbjct: 211 TWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTI 270

Query: 446 EKLERLIFITRMPLSMQQPVWADQDTTF 473
           EKL  +    ++P+S++ P+  ++D+  
Sbjct: 271 EKLRFIAKSAQLPISLETPIGKEEDSRL 298

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

 Score =  176 bits (447), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 87/217 (40%), Positives = 141/217 (64%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
           D +RL+L      +LL ADEE EL  QI DL+ LE+ + +L  Q  R P+  EWA A+  
Sbjct: 89  DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148

Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 374
              + +  L  G  +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF 
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 208

Query: 375 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 434
            + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P +
Sbjct: 209 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTE 268

Query: 435 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
           E++A R+ +T+EKL  +    ++P+S++ P+  ++D+
Sbjct: 269 EEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDS 305

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)

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

 Score =  169 bits (428), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 89/220 (40%), Positives = 135/220 (61%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
           D +R +L      +LLTA+EE     Q+Q L+ L   +++L+ + G EP+  EWA A+ L
Sbjct: 11  DLVRAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDL 70

Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 374
           +  DL  ++  G  ++ K+I ANLRLVV +AK+YQ R +   DL+QEG++GL + VEKF 
Sbjct: 71  NLEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFD 130

Query: 375 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 434
           P  G +F++YAYWW+RQ I +AI Q SRTIRLP +I   L+K+ + +R   Q+   S   
Sbjct: 131 PSKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATA 190

Query: 435 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474
            +LA  + + +E++   I + R P+S+   V   QDT  Q
Sbjct: 191 SELAEVLELPLEQVREYIQMNRQPVSLDVKVGDSQDTELQ 230

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

 Score =  158 bits (399), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 88/221 (39%), Positives = 137/221 (61%), Gaps = 1/221 (0%)

Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG-REPTLIEWAKAI 312
           +D +R +L       LLT +EE  L  ++Q  ++L++ +  LQS+ G R+P+ +EWA A 
Sbjct: 9   SDLVRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAA 68

Query: 313 GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK 372
           GLS  +L+ + H G  ++ K+I ANLRLVV VAK+Y  R + L DL+QEG++G+ + VEK
Sbjct: 69  GLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEK 128

Query: 373 FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSP 432
           F P  G RF++YAYWW+RQ I +AI + +RTIRLP +I   L+K+ + +R   Q+   + 
Sbjct: 129 FDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKMQRQLSQQLGRTA 188

Query: 433 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473
              +LA  + +T  ++   +   R PLS+   V  +QDT  
Sbjct: 189 TLPELAAALDLTPAQVRDYLEKARHPLSLDLRVGDNQDTEL 229

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|P74565|RPOD_SYNY3 RNA polymerase sigma factor RpoD OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=rpoD PE=3 SV=1

 Score =  155 bits (391), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 91/278 (32%), Positives = 153/278 (55%), Gaps = 50/278 (17%)

Query: 239 RKASVKKK-LSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 297
           RK +VKKK  +E     D +R++L      +LL A+EE EL  QI DL+ LE  +  L  
Sbjct: 59  RKDAVKKKPYTE-----DSIRIYLQEIGRIRLLRAEEEIELARQIADLLELELIRDNLTL 113

Query: 298 QFGREPTLIEWAKAI----------------GLSCRDLKSELHSGNS------------- 328
           Q  R+P+ +EW K +                    +D+ S L + ++             
Sbjct: 114 QLERQPSELEWGKQVWKLETAKQRLVGDKKKEPKKKDIDSYLANPDNELSLENEWSQQPN 173

Query: 329 ---------------SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
                          +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF
Sbjct: 174 KNFAAFRRRLFLDRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKF 233

Query: 374 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 433
             + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P 
Sbjct: 234 DHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPT 293

Query: 434 KEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
           +E++A ++ +T+EKL  +    ++P+S++ P+  ++D+
Sbjct: 294 EEEIAEKMEMTIEKLRFIAKSAQLPISLETPIGKEEDS 331

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.

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

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

 Score =  152 bits (385), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 93/268 (34%), Positives = 141/268 (52%), Gaps = 44/268 (16%)

Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK------------------- 294
            D +RL+L       LL  DEE  +  Q+Q  +RL + +++                   
Sbjct: 48  TDLVRLYLQDIGRIPLLKRDEEVHIAQQVQSYLRLVEIQNRAAESDAAIDQYQTAIAVHD 107

Query: 295 -LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN----------------------SSRE 331
            L  Q G  P+   WAK +G +   LK  L SG                       +++ 
Sbjct: 108 QLLVQLGHRPSYERWAKILGQTVATLKQTLKSGKKRWAELAGLTVEELENIEKQGITAKA 167

Query: 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391
            +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF++Y+YWW+RQ
Sbjct: 168 HMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYSYWWIRQ 227

Query: 392 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 451
            I +AI   SR IRLP +I   L+K+  A+R   QE  H+P  +++A  +G+T E++  +
Sbjct: 228 GITRAIATQSRMIRLPVHITEKLNKIKRAQRKISQEKGHTPKIDEVAEELGMTPEQVREV 287

Query: 452 IFITRMPLSMQQPVWADQDTTFQVMPLL 479
             +T++P S+   +   QD   ++M LL
Sbjct: 288 --LTQVPRSVSLELKVGQDKDTELMDLL 313

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|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa GN=rpoD1 PE=3 SV=1

 Score =  152 bits (383), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 84/256 (32%), Positives = 143/256 (55%), Gaps = 39/256 (15%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEK------------------------ 290
           D +R++L      +LL A+EE EL  +I DL++LE+                        
Sbjct: 67  DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126

Query: 291 ----EKSK-------LQSQFGR----EPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335
               EKS+       +++  G+     P L EW           K  L+ G  ++EK++ 
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186

Query: 336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 395
           +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF  + G +F++YA WW+RQ I +
Sbjct: 187 SNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITR 246

Query: 396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455
           AI   SRTIRLP ++Y  +S++ +  ++  QE    P +E++A ++ +T+EKL  +    
Sbjct: 247 AIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSA 306

Query: 456 RMPLSMQQPVWADQDT 471
           ++P+S++ P+  ++D+
Sbjct: 307 QLPISLETPIGKEEDS 322

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.

Microcystis aeruginosa (taxid: 1126)

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

 Score =  150 bits (378), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 92/263 (34%), Positives = 135/263 (51%), Gaps = 43/263 (16%)

Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE---------------------KEK 292
            D +RL+L      +LL  DEE     ++Q  ++L                      + +
Sbjct: 59  TDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYLKLRIVLANAVKQGDEVATPYLHLIEVQ 118

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN----------------------SSR 330
            +L S+ G  P+L  WA   G++  DLK  L  G                        S+
Sbjct: 119 ERLASELGHRPSLERWAATAGINLCDLKPILSEGKRRWAEIAKMTVEELEKMQSQGLQSK 178

Query: 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 390
           E +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF++YAYWW+R
Sbjct: 179 EHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIR 238

Query: 391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 450
           Q I +AI   SRTIRLP +I   L+K+ +A+R   QE   +P  EDLA  + +T  ++  
Sbjct: 239 QGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLEDLAIELDMTPTQVRE 298

Query: 451 LIFITRMPLSMQQPVWADQDTTF 473
           ++      +S++  V  D+DT  
Sbjct: 299 VLLRVPRSVSLETKVGKDKDTEL 321

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)

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	488
297741628	561	unnamed protein product [Vitis vinifera]	0.942	0.819	0.620	1e-164
359481391	572	PREDICTED: RNA polymerase sigma factor r	0.961	0.819	0.616	1e-162
224068757	535	predicted protein [Populus trichocarpa]	0.901	0.822	0.605	1e-161
255556952	548	RNA polymerase sigma factor rpoD, putati	0.926	0.824	0.604	1e-158
356536959	571	PREDICTED: RNA polymerase sigma factor r	0.959	0.819	0.572	1e-141
356548319	574	PREDICTED: RNA polymerase sigma factor r	0.961	0.817	0.551	1e-140
449451030	562	PREDICTED: RNA polymerase sigma factor s	0.942	0.818	0.542	1e-132
312282671	547	unnamed protein product [Thellungiella h	0.909	0.811	0.537	1e-129
297827203	546	RNA polymerase sigma-70 factor [Arabidop	0.907	0.811	0.533	1e-128
18404292	547	RNApolymerase sigma-subunit F [Arabidops	0.909	0.811	0.526	1e-126

>gi|297741628|emb|CBI32760.3| unnamed protein product [Vitis vinifera]

 Score =  583 bits (1502), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 298/480 (62%), Positives = 363/480 (75%), Gaps = 20/480 (4%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEAG N+LSS PSFP RT  +         +SSSSVLM ++Q APAVAS+PT+ +AR FP
Sbjct: 1   MEAGTNILSSTPSFPPRTHFR---------NSSSSVLMLHDQVAPAVASIPTT-IARKFP 50

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
           TSVLLQEQRDEYRP     K+++T QAT + R +E      +E+NS D +Q + + E Q 
Sbjct: 51  TSVLLQEQRDEYRPFPQALKDERTFQATLEKRQMEI-VVSADEENSDDHNQYMVNFERQL 109

Query: 121 LHWPDLWNLSPPMKRGE-DPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAS 179
           L  P LW   P  + GE  P  S  M+S++ D E S+D +P D +ALA+KALSASK+A S
Sbjct: 110 LLQPGLWYSLPSSQTGEKSPFSSSIMKSITTDIENSMDVKPCDVLALAKKALSASKQAVS 169

Query: 180 LAENPKLNGAEFTD-----ISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHE 234
           L EN KL GA+  D     +   SS   PLEE K     R LERRSKKR+   P+V  HE
Sbjct: 170 LYENAKLLGADLEDSPSPSLGAISSPNLPLEE-KTVRSTRLLERRSKKRR--NPKVAVHE 226

Query: 235 TYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK 294
            + SR+A V++K++EG+D  DPLRLFLWGPETRKLLTA EE ELI QIQ+L+RLE+ K +
Sbjct: 227 NHGSRRAEVQRKINEGYDPKDPLRLFLWGPETRKLLTAKEESELIVQIQELMRLEEVKKR 286

Query: 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGIS 354
           LQS   REPT++EWA+A+GLSC+ L+S+LHSGN SR+KLI ANLR+VVH+AKQYQGRG++
Sbjct: 287 LQSHLKREPTVVEWAEAVGLSCQVLQSQLHSGNRSRQKLIYANLRMVVHIAKQYQGRGLN 346

Query: 355 LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 414
           L DLLQEGSMGLM SVEKFKP AGCRFASYAYWW+RQ +RKAIFQHSRTIRLPEN+Y+LL
Sbjct: 347 LQDLLQEGSMGLMNSVEKFKPNAGCRFASYAYWWIRQAVRKAIFQHSRTIRLPENMYSLL 406

Query: 415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474
            KV EAKRL+IQEG+H P KE++A RVGIT+EKL+RL+  TRMPLSMQQPVWADQDTTFQ
Sbjct: 407 GKVKEAKRLFIQEGHHDPTKEEIAERVGITIEKLQRLLLHTRMPLSMQQPVWADQDTTFQ 466

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359481391|ref|XP_002276710.2| PREDICTED: RNA polymerase sigma factor rpoD [Vitis vinifera]

 Score =  577 bits (1486), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 297/482 (61%), Positives = 363/482 (75%), Gaps = 13/482 (2%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSS--VLMHNEQSAPAVASVPTSSVARH 58
           MEAG N+LSS PSFP RT  ++S SS  +        VLM ++Q APAVAS+PT+ +AR 
Sbjct: 1   MEAGTNILSSTPSFPPRTHFRNSSSSGNAFFFYVVLFVLMLHDQVAPAVASIPTT-IARK 59

Query: 59  FPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEH 118
           FPTSVLLQEQRDEYRP     K+++T QAT + R +E      +E+NS D +Q + + E 
Sbjct: 60  FPTSVLLQEQRDEYRPFPQALKDERTFQATLEKRQMEI-VVSADEENSDDHNQYMVNFER 118

Query: 119 QFLHWPDLWNLSPPMKRGE-DPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEA 177
           Q L  P LW   P  + GE  P  S  M+S++ D E S+D +P D +ALA+KALSASK+A
Sbjct: 119 QLLLQPGLWYSLPSSQTGEKSPFSSSIMKSITTDIENSMDVKPCDVLALAKKALSASKQA 178

Query: 178 ASLAENPKLNGAEFTD-----ISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
            SL EN KL GA+  D     +   SS   PLEE K     R LERRSKKR+   P+V  
Sbjct: 179 VSLYENAKLLGADLEDSPSPSLGAISSPNLPLEE-KTVRSTRLLERRSKKRR--NPKVAV 235

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
           HE + SR+A V++K++EG+D  DPLRLFLWGPETRKLLTA EE ELI QIQ+L+RLE+ K
Sbjct: 236 HENHGSRRAEVQRKINEGYDPKDPLRLFLWGPETRKLLTAKEESELIVQIQELMRLEEVK 295

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
            +LQS   REPT++EWA+A+GLSC+ L+S+LHSGN SR+KLI ANLR+VVH+AKQYQGRG
Sbjct: 296 KRLQSHLKREPTVVEWAEAVGLSCQVLQSQLHSGNRSRQKLIYANLRMVVHIAKQYQGRG 355

Query: 353 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412
           ++L DLLQEGSMGLM SVEKFKP AGCRFASYAYWW+RQ +RKAIFQHSRTIRLPEN+Y+
Sbjct: 356 LNLQDLLQEGSMGLMNSVEKFKPNAGCRFASYAYWWIRQAVRKAIFQHSRTIRLPENMYS 415

Query: 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472
           LL KV EAKRL+IQEG+H P KE++A RVGIT+EKL+RL+  TRMPLSMQQPVWADQDTT
Sbjct: 416 LLGKVKEAKRLFIQEGHHDPTKEEIAERVGITIEKLQRLLLHTRMPLSMQQPVWADQDTT 475

Query: 473 FQ 474
           FQ
Sbjct: 476 FQ 477

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224068757|ref|XP_002326192.1| predicted protein [Populus trichocarpa] gi|222833385|gb|EEE71862.1| predicted protein [Populus trichocarpa]

 Score =  575 bits (1483), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 287/474 (60%), Positives = 357/474 (75%), Gaps = 34/474 (7%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEAGR LLSS PSFP+RT +K+SL+SS        VL+  EQ+ PAV+S+PT+S A+HFP
Sbjct: 1   MEAGRTLLSSSPSFPTRTHLKNSLTSS--------VLILREQATPAVSSIPTTSTAQHFP 52

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
           TSVLLQEQRDE+RPL ++FKED+ SQAT D R  E      E K+S +LDQLV++ E+Q 
Sbjct: 53  TSVLLQEQRDEFRPLQNIFKEDRASQATLDRRKTEIGTSGHEGKDSDELDQLVENFEYQL 112

Query: 121 LHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASL 180
            HWP  WNL                      T++ +D EP + + LA++ALSASK AA L
Sbjct: 113 HHWPAYWNL----------------------TDKLIDVEPTNVINLAKRALSASKHAAFL 150

Query: 181 AENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRK 240
           A+N      +  +++ TSS  + LEEVK     R L R+S  R+  K +    ETY+S+ 
Sbjct: 151 ADN----NTDLDNLASTSSSSFSLEEVKIVRSRRHLARQSLNRRAPKTKDLIFETYDSKS 206

Query: 241 ASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 300
           A ++K+LS+GFD NDPLRLFLWGPET++LLTA EEFELIAQIQDL+ LE  K++L+SQFG
Sbjct: 207 ADIQKRLSQGFDPNDPLRLFLWGPETKQLLTAKEEFELIAQIQDLMNLEGVKNRLESQFG 266

Query: 301 REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           REPTL+EWA+A+GLSC  LK +LHSGN SREKLINANLR+VVH+AK+YQ RG+ L DLLQ
Sbjct: 267 REPTLVEWAQAVGLSCHVLKLQLHSGNRSREKLINANLRMVVHIAKRYQNRGLGLQDLLQ 326

Query: 361 EGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA 420
           EG++GLMKS+EKFKPQAGCRFA+YAYWW+RQTI KAIFQHSRTIRLPEN+Y LL KV+EA
Sbjct: 327 EGTVGLMKSIEKFKPQAGCRFATYAYWWIRQTITKAIFQHSRTIRLPENVYGLLGKVMEA 386

Query: 421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474
           KR YIQEGNH P  E++ARRVGI ++KLE+L+  TR PLSMQQ VW+DQ+TTFQ
Sbjct: 387 KRSYIQEGNHQPTAEEIARRVGIAIDKLEKLLCFTRTPLSMQQTVWSDQNTTFQ 440

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556952|ref|XP_002519509.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223541372|gb|EEF42923.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]

 Score =  566 bits (1458), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 287/475 (60%), Positives = 352/475 (74%), Gaps = 23/475 (4%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           ME  R  LSSPP FPSRT  K+SLSSS +   +   ++H EQ+ PAV S PT+S+AR+FP
Sbjct: 1   METARTFLSSPPPFPSRTHFKNSLSSSDAYVDNFVFMLH-EQAVPAVTSAPTTSIARNFP 59

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
           TSVLLQEQRDE+RPLL++FKEDKT QAT D++ ++      E   S  LDQL+    H  
Sbjct: 60  TSVLLQEQRDEFRPLLNIFKEDKTFQATVDTKQMDPGTSDQEGICSDVLDQLIL---HSN 116

Query: 121 LHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASL 180
           L W                  SLTMQS++ +T+E +  EP + + LARKALSASKEAA L
Sbjct: 117 LSW------------------SLTMQSITTNTDELMVVEPTNVIDLARKALSASKEAALL 158

Query: 181 AEN-PKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSR 239
           A+    L+    T +  T    + LEEVK     R LER+SK R+V+K +   HE Y+SR
Sbjct: 159 AQKCANLDDTVSTGLEPTDLSNFSLEEVKTVRSTRRLERQSKNRRVTKTKEIFHEPYSSR 218

Query: 240 KASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF 299
           +A V+KK++EGFD  DPLRLFLWGPET++LLTA EE ELI Q+QDL+ LE  K K + QF
Sbjct: 219 RAGVQKKINEGFDPKDPLRLFLWGPETKQLLTAKEESELIGQVQDLMSLENVKEKFKLQF 278

Query: 300 GREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL 359
           GR+PTL+EWA A+GLS   ++S+LHSGN SREKLINANLR+VVH+AKQYQGRG+SL DLL
Sbjct: 279 GRDPTLVEWADAVGLSYSVMQSQLHSGNRSREKLINANLRMVVHIAKQYQGRGLSLQDLL 338

Query: 360 QEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLE 419
           QEGSMGLMKS+EKFKPQ GCRFA+YAYWW+RQT+RKAIFQHSRTIRLPEN+Y  L KV E
Sbjct: 339 QEGSMGLMKSIEKFKPQVGCRFATYAYWWIRQTVRKAIFQHSRTIRLPENVYHTLGKVSE 398

Query: 420 AKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474
           AKR YI EGNH+P KE+LA+R+GIT  +LERL+++ RMPLSMQQ VWADQ+TTFQ
Sbjct: 399 AKRSYIMEGNHNPTKEELAKRIGITTVRLERLLYMARMPLSMQQTVWADQETTFQ 453

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356536959|ref|XP_003536999.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  508 bits (1308), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 276/482 (57%), Positives = 351/482 (72%), Gaps = 14/482 (2%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           ME  R +  S P FP RT   H  S+  SSSS+SSVLM +EQ++P VAS  ++  A++FP
Sbjct: 1   MEFARTMFCSSPPFPPRTH--HPWSTLPSSSSTSSVLMLHEQASPTVASWSSNFSAQNFP 58

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
            SVLL EQRDEYRPLLHM KEDKTSQA   +R ++T     EE N+ + DQ+V D     
Sbjct: 59  ASVLLPEQRDEYRPLLHMSKEDKTSQAMLSTRQMDTVTVH-EENNTENADQVVLDFRKHL 117

Query: 121 LHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASL 180
            HWP+L   S  +  GE  + S T++ +S D E   +   F+ V+LA+KALS SK+ +S+
Sbjct: 118 HHWPNLQLTSSQI--GE-VAASSTLEHVSVDLERRPNGVQFNGVSLAKKALSTSKQESSV 174

Query: 181 AENPKLNGAEFTDISLTS-SLGYP-LEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNS 238
            E+ K   A+    SL S SL  P +   K     R LERRSK+RKV K +V + ETY +
Sbjct: 175 VEDLKSIKADDVPFSLASTSLADPSIGRNKTVRSTRLLERRSKQRKVPKSKVIDDETYLA 234

Query: 239 RKASVKKKL------SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
           RK   ++KL      +E  D++DPLRLFLWGPET++LLT ++E +LI+QIQDL+RLE+ K
Sbjct: 235 RKDDAQEKLRAEKKKNEELDQDDPLRLFLWGPETKQLLTLEQESQLISQIQDLLRLEEVK 294

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           + LQSQFGREPT+ EWA+  GL+CR L+S+LHSGN SREKLI ANLR+VVHVAK YQGRG
Sbjct: 295 TNLQSQFGREPTMAEWAEGAGLNCRLLQSQLHSGNRSREKLIQANLRMVVHVAKSYQGRG 354

Query: 353 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412
           +SL DLLQEGSMGLMKSVEKF P AG RF +YA+WW+RQ IRKA+F+HSRTIRLPE ++ 
Sbjct: 355 LSLQDLLQEGSMGLMKSVEKFNPLAGSRFGNYAFWWIRQAIRKAVFRHSRTIRLPEKVFI 414

Query: 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472
           LL KV+EAK+LYIQEGN  P KE+LARRVG+TVEK+++L+F  R+P+SMQQ VWADQ+TT
Sbjct: 415 LLGKVMEAKKLYIQEGNLHPTKEELARRVGVTVEKIDKLLFSARIPISMQQTVWADQNTT 474

Query: 473 FQ 474
           FQ
Sbjct: 475 FQ 476

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356548319|ref|XP_003542550.1| PREDICTED: RNA polymerase sigma factor rpoD [Glycine max]

 Score =  504 bits (1299), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 267/484 (55%), Positives = 344/484 (71%), Gaps = 15/484 (3%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           ME  R +  S P FP RT   H   ++   SSS+SVLM  EQ++P VAS  ++  A++FP
Sbjct: 1   MEFSRTMFCSSPPFPPRT---HHPWNTLPLSSSTSVLMLREQASPTVASWSSNFSAQNFP 57

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
            SVLLQEQRDEYRPLLHM KEDKTSQA   +R ++T     EE N+ + DQ+V D     
Sbjct: 58  ASVLLQEQRDEYRPLLHMSKEDKTSQAMLSTRQMDT-VMVHEENNTENADQVVLDFRKHL 116

Query: 121 LHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASL 180
            +WP L NL    + GE  S S T+Q +S+D +   +    + V+LA+KALS SK+ +S+
Sbjct: 117 HYWPHLQNLLASSQTGE-ISASSTLQQVSSDLDRHTNGVQCNRVSLAKKALSTSKQGSSV 175

Query: 181 AENPKLNGAEFTDISL---TSSLGYP-LEEVKQFSQPRFLERRSKKRKVSKPQVTNHETY 236
            E+ K   A+   I     ++ L  P +   K     R LERRSK+RKV K +V + ETY
Sbjct: 176 VEDLKSIKADDDSIPFGLASTGLADPSIGRNKTVRSTRLLERRSKQRKVPKSKVIDDETY 235

Query: 237 NSRKAS------VKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEK 290
            +RK        V+KK +E  D+NDPL  FL GPET++LLT ++E +LI+QIQDL+RLE+
Sbjct: 236 LARKDDAHEKLRVEKKKNEELDQNDPLCFFLRGPETKQLLTLEQESQLISQIQDLLRLEE 295

Query: 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQG 350
            K+KLQSQFGREPT+ EWA+ +GL+CR L ++L SG+ SREKLI ANLR+VVHVAK YQG
Sbjct: 296 VKTKLQSQFGREPTMAEWAEGVGLNCRMLHAQLRSGSRSREKLIQANLRMVVHVAKSYQG 355

Query: 351 RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI 410
           RG+SL DLLQEGSMGLMKSVEKF P  G RF +YA+WW+RQ IRKA+F+HSRTIRLPE +
Sbjct: 356 RGLSLQDLLQEGSMGLMKSVEKFNPLVGSRFGNYAFWWIRQAIRKAVFRHSRTIRLPEKV 415

Query: 411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 470
           + LL KV+EAK+LYIQEGN  P KE+LARRVG+TVEK+++L+F  R+P+SMQQ VWADQ+
Sbjct: 416 FILLGKVMEAKKLYIQEGNLHPTKEELARRVGVTVEKIDKLLFSARIPISMQQTVWADQN 475

Query: 471 TTFQ 474
           TTFQ
Sbjct: 476 TTFQ 479

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449451030|ref|XP_004143265.1| PREDICTED: RNA polymerase sigma factor sigF, chloroplastic-like [Cucumis sativus] gi|449482444|ref|XP_004156283.1| PREDICTED: RNA polymerase sigma factor sigF, chloroplastic-like [Cucumis sativus]

 Score =  478 bits (1231), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 261/481 (54%), Positives = 333/481 (69%), Gaps = 21/481 (4%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSS-------VLMHNEQSAPAVASVPTS 53
           MEAG NLLSS   F SR   +  L+ S SS++S S       V M  EQ++PA       
Sbjct: 1   MEAGLNLLSSSSPFISRCHPRSFLAPSCSSAASPSSSSSSSSVYMFPEQASPA------- 53

Query: 54  SVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV 113
              R+F TS L QEQ  E RP   + K+D++SQ T + R IE  +  ++E +  D D L+
Sbjct: 54  ---RYFSTSFLSQEQHHECRPQSQILKDDRSSQMTLERRLIE-RSVPIDEGSRDDHDHLI 109

Query: 114 QDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            +L+HQ + WP L +  PP++  E    S+  +S +   E  V  EP + +ALA+KALSA
Sbjct: 110 WELKHQAVEWPGLLSSWPPVQMEEYKISSIEKESYNAAGEMLVKDEPENVIALAKKALSA 169

Query: 174 SKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNH 233
           SK+AA L +  +L G      SL  SL    +E +     R  +RRSKKRKV K   T  
Sbjct: 170 SKQAALLVDETELVGTSLDYSSLDDSLS---KEGRTVRSTRLQDRRSKKRKVPKHVTTID 226

Query: 234 ETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS 293
           E  N R    ++K SE FD NDPLRLFLWGPET+KLLTA EE ELI QIQDL+ L+  K+
Sbjct: 227 EISNFRGKDSRRKTSEKFDPNDPLRLFLWGPETKKLLTAQEESELIVQIQDLMILDNVKA 286

Query: 294 KLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGI 353
           +LQSQF REPTL+EWA+A+G++C+ L+S+LH   +SREKLINANLR+VVH+AKQYQGRG+
Sbjct: 287 RLQSQFDREPTLVEWAEALGITCQHLQSQLHVFQTSREKLINANLRMVVHIAKQYQGRGL 346

Query: 354 SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL 413
           SLHDLLQ GS+GLMKSVEKFKPQAGCRF SYAYWW+R +I KAIFQHSRTIRLPEN+Y L
Sbjct: 347 SLHDLLQVGSLGLMKSVEKFKPQAGCRFGSYAYWWIRHSITKAIFQHSRTIRLPENVYAL 406

Query: 414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473
           L KV EAK  +++ GN+ P KE+LA RVGITVE+ ++L+F++R+P S+QQPVWADQ+TTF
Sbjct: 407 LGKVTEAKNYFVRAGNYKPSKEELAARVGITVERFDKLMFMSRIPRSLQQPVWADQETTF 466

Query: 474 Q 474
           Q
Sbjct: 467 Q 467

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312282671|dbj|BAJ34201.1| unnamed protein product [Thellungiella halophila]

 Score =  469 bits (1208), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 259/482 (53%), Positives = 326/482 (67%), Gaps = 38/482 (7%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEA RNL+SS PSF ++T +K     S  SS SS V++H + + P V S   +S++RHFP
Sbjct: 1   MEATRNLVSSSPSFQTKTHLK-----SGFSSPSSVVMLHEQTATPVVNSRHLTSLSRHFP 55

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
            SVL QE R+E +PL H  +ED+TSQ T + R                 D+LV     + 
Sbjct: 56  ASVLSQELREESKPLSHALREDRTSQLTLERRQ---------------FDELVSSREDEK 100

Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            E Q LH   LWNL  SP     + P+V             S DA+  D VALA+KALSA
Sbjct: 101 FEQQLLHSAGLWNLLISPLTTEKQLPAV----------VSPSADADLCDLVALAQKALSA 150

Query: 174 SKEAASLAENPKLNGAEF-TDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
           SK+AA L EN + +  +   D   TSS     E+       R LERR+K R+  K    +
Sbjct: 151 SKQAALLVENSEADPPDNPRDSLSTSSSMSLPEKGTIVRSKRQLERRAKNRRAPKSNNMD 210

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
            E Y  +K + KKK+ +GFD +D L+LFLWGPET++LLTA EE ELIA IQ LI+LEK K
Sbjct: 211 SEGYVPQKINAKKKMKQGFDTDDALQLFLWGPETKQLLTAKEEAELIAHIQHLIKLEKVK 270

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           +KL+SQ G EPT+ EWA+A+GLS   LKSE+H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 271 TKLESQNGCEPTIGEWAEAMGLSSPVLKSEIHRGRSSREKLITANLRLVVHIAKQYQNRG 330

Query: 353 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412
           ++  DLLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y 
Sbjct: 331 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYM 390

Query: 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472
           LL KV EA++  IQ+GN+ P KE LA  VG++ EKL++L++ TR PLSMQQP+W+DQDTT
Sbjct: 391 LLGKVSEARKTCIQDGNYRPSKEQLASHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTT 450

Query: 473 FQ 474
           FQ
Sbjct: 451 FQ 452

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297827203|ref|XP_002881484.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata] gi|297327323|gb|EFH57743.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]

 Score =  466 bits (1198), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 257/482 (53%), Positives = 330/482 (68%), Gaps = 39/482 (8%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEA RNL+SS PSF ++T +K      + SS SS V++H + + P V S   +S++RHFP
Sbjct: 1   MEATRNLVSSSPSFQTKTHLK------SYSSPSSVVMLHEQTTTPVVNSRHLNSLSRHFP 54

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
            SVL QE R+E RPL H  +ED+TSQ T + R                 D+LV     + 
Sbjct: 55  ASVLSQEPREESRPLSHALREDRTSQLTLERRQ---------------FDELVSSREDEK 99

Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            E Q LH   LWNL  SP     + P V   +           DAE  D VALA+KALSA
Sbjct: 100 FEQQLLHSAGLWNLLISPLTAETKLPPVVPPL----------ADAELCDIVALAQKALSA 149

Query: 174 SKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQP-RFLERRSKKRKVSKPQVTN 232
           SK+AA LA++ + N ++ T  SL++S    L E     +  R LERR+K R+  K    +
Sbjct: 150 SKQAALLADDTEANPSDNTRGSLSTSSSMSLPEKGAIVRSKRQLERRAKNRRAPKSNDVD 209

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
           +E Y  +K + KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K
Sbjct: 210 NEGYVPQKINAKKKFKQGVDTDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVK 269

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           +KL+SQ G EPT+ EWA+A+G+S  DLKSE+H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 270 TKLESQNGCEPTIGEWAEAMGISSPDLKSEIHRGRSSREKLITANLRLVVHIAKQYQNRG 329

Query: 353 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412
           ++  DLLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y 
Sbjct: 330 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYM 389

Query: 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472
           LL KV EA++  +QEGN+ P KE LA  VG++ EKL++L++ TR PLSMQQP+W+DQDTT
Sbjct: 390 LLGKVSEARKTCVQEGNYRPSKEQLAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTT 449

Query: 473 FQ 474
           FQ
Sbjct: 450 FQ 451

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18404292|ref|NP_565856.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana] gi|75173811|sp|Q9LD95.1|SIGF_ARATH RecName: Full=RNA polymerase sigma factor sigF, chloroplastic; Short=Sigma factor F; Short=Sigma-F; AltName: Full=Protein SINGLET OXYGEN-LINKED DEATH ACTIVATOR 8; AltName: Full=RNA polymerase sigma factor sig6; Short=Atsig6; Short=Sigma factor 6; Flags: Precursor gi|7209640|dbj|BAA92288.1| SigF [Arabidopsis thaliana] gi|7688083|emb|CAB89775.1| sigma factor-like protein [Arabidopsis thaliana] gi|16604647|gb|AAL24116.1| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana] gi|20197948|gb|AAD31584.2| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana] gi|20259557|gb|AAM14121.1| putative RNA polymerase sigma-70 factor protein [Arabidopsis thaliana] gi|330254238|gb|AEC09332.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana]

 Score =  457 bits (1177), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 254/482 (52%), Positives = 328/482 (68%), Gaps = 38/482 (7%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEA RNL+SS PSF ++T +K     S+ SS SS V++H++ + P V S   +S++RHFP
Sbjct: 1   MEATRNLVSSSPSFQTKTHLK-----SSYSSPSSVVMLHDQTTTPVVNSRHLNSLSRHFP 55

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
            SVL QE R+E RPL H  ++D+TSQ T + R                 D+LV     + 
Sbjct: 56  ASVLSQEPREESRPLSHALRDDRTSQLTLERRQ---------------FDELVSSREDEK 100

Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            E Q LH   LWNL  SP     + P+V   +           DAE  D VALA+KALSA
Sbjct: 101 FEQQLLHSTGLWNLLISPLTSETKLPAVVSPL----------ADAELCDVVALAQKALSA 150

Query: 174 SKEAASLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
           SK+AA L ++ + N ++   D   TSS     E+       R LERR+K R+  K    +
Sbjct: 151 SKQAALLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKRQLERRAKNRRAPKSNDVD 210

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
            E Y  +K S KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K
Sbjct: 211 DEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVK 270

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           +KL+SQ G EPT+ EWA+A+G+S   LKS++H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 271 TKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRG 330

Query: 353 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412
           ++  DLLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y 
Sbjct: 331 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYM 390

Query: 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472
           LL KV EA++  +QEGN+ P KE+LA  VG++ EKL++L++ TR PLSMQQP+W+DQDTT
Sbjct: 391 LLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTT 450

Query: 473 FQ 474
           FQ
Sbjct: 451 FQ 452

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	488
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.770	0.687	0.510	7.8e-94
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.532	0.454	0.479	2e-63
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.524	0.447	0.366	3e-46
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.305	0.237	0.409	2.4e-34
TIGR_CMR|GSU_1525	328	GSU_1525 "RNA polymerase sigma	0.315	0.469	0.374	3.8e-33
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.567	0.480	0.303	3.9e-32
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.395	0.521	0.358	1.4e-30
TIGR_CMR|ECH_0760	622	ECH_0760 "RNA polymerase sigma	0.448	0.352	0.353	1.2e-29
TIGR_CMR|BA_4515	373	BA_4515 "RNA polymerase sigma-	0.415	0.544	0.322	1.3e-29
UNIPROTKB|O48655	519	rsigA "Plastid RNA polymerase	0.420	0.394	0.330	1.7e-29

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

 Score = 934 (333.8 bits), Expect = 7.8e-94, P = 7.8e-94
 Identities = 202/396 (51%), Positives = 261/396 (65%)

Query:    85 SQATSDSRNIETEAFFVEEKNSGDLDQLVQD--LEHQFLHWPDLWNL--SPPMKRGEDPS 140
             S A  D R   T    +E +   +L    +D   E Q LH   LWNL  SP     + P+
Sbjct:    71 SHALRDDR---TSQLTLERRQFDELVSSREDEKFEQQLLHSTGLWNLLISPLTSETKLPA 127

Query:   141 VSLTMQSLSNDTEESVDAEPFDXXXXXXXXXXXXXXXXXXXXNPKLNGAE-FTD-ISLTS 198
             V   +  L+       DAE  D                    + + N ++   D +S +S
Sbjct:   128 V---VSPLA-------DAELCDVVALAQKALSASKQAALLVDDTEANPSDNIKDSLSTSS 177

Query:   199 SLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLR 258
             S+  P E+       R LERR+K R+  K    + E Y  +K S KKK  +G D +D L+
Sbjct:   178 SMSLP-EKGNIVRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYKQGADNDDALQ 236

Query:   259 LFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRD 318
             LFLWGPET++LLTA EE ELI+ IQ L++LEK K+KL+SQ G EPT+ EWA+A+G+S   
Sbjct:   237 LFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPV 296

Query:   319 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAG 378
             LKS++H G SSREKLI ANLRLVVH+AKQYQ RG++  DLLQEGSMGLMKSVEKFKPQ+G
Sbjct:   297 LKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSG 356

Query:   379 CRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLA 438
             CRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y LL KV EA++  +QEGN+ P KE+LA
Sbjct:   357 CRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELA 416

Query:   439 RRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474
               VG++ EKL++L++ TR PLSMQQP+W+DQDTTFQ
Sbjct:   417 GHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQ 452

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

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

 Score = 647 (232.8 bits), Expect = 2.0e-63, P = 2.0e-63
 Identities = 126/263 (47%), Positives = 179/263 (68%)

Query:   214 RFLERRSKKRKVSKPQVTNHETY--NSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLT 271
             R LERRSK+R   +  + +      NS+K    KK     + ++P +LFL   ET + LT
Sbjct:   216 RLLERRSKRRYAPRASIADVSCSADNSKKKEKSKKYGRVLEPDEPFKLFLRDRETTEFLT 275

Query:   272 ADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 331
             A EE  L ++IQ L+++E+   KL+ Q GREPTL EWA+A+G+S ++L+S + +G   RE
Sbjct:   276 AKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCRE 335

Query:   332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391
             K+  +N RLV+HVA++Y+G G+ + DL+Q+G  GLMK+ EKF P  GCRF +YAYWW+RQ
Sbjct:   336 KMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQ 395

Query:   392 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 451
             +I+K+IF++SR IRLPE++Y LL KV +A+   I EG   P   ++ARR GIT+EKL +L
Sbjct:   396 SIKKSIFKNSRLIRLPESVYALLRKVGKARMECIMEGEQ-PTNANVARRAGITIEKLAKL 454

Query:   452 IFITRMPLSMQQPVWADQDTTFQ 474
                TR P SMQ  VW+D+  TFQ
Sbjct:   455 RAKTRKPRSMQDHVWSDEGVTFQ 477

GO:0009536 "plastid" evidence=RCA

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

 Score = 485 (175.8 bits), Expect = 3.0e-46, P = 3.0e-46
 Identities = 95/259 (36%), Positives = 161/259 (62%)

Query:   214 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 272
             R  ER++++ K  +   +   +  +  +  KK+L ++  D NDPLR       + KLLT 
Sbjct:   216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275

Query:   273 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332
              EE EL A IQDL++LE+ +++L  + GR+PT  +WA A G+  + L+  +H G   ++K
Sbjct:   276 REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDK 335

Query:   333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392
             +I +N+RLV+ +AK YQG G++L DL+QEG  GL++  EKF    G +F++YA+WW++Q 
Sbjct:   336 MIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQA 395

Query:   393 IRKAIFQHSRTIRLPENIYTLLSKVLEA-KRLYIQEGNHSPDKEDLARRVGITVEKLERL 451
             +RK++   SR IRLP ++     +V EA K+LY + G H P  E++A   G+++++L  +
Sbjct:   396 VRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKH-PKNEEIAEATGLSMKRLMAV 454

Query:   452 IFITRMPLSMQQPVWADQD 470
             +   + P S+ Q +  +Q+
Sbjct:   455 LLSPKPPRSLDQKIGMNQN 473

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

TIGR_CMR|APH_0576 APH_0576 "RNA polymerase sigma factor RpoD" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 332 (121.9 bits), Expect = 2.4e-34, Sum P(3) = 2.4e-34
 Identities = 61/149 (40%), Positives = 101/149 (67%)

Query:   325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASY 384
             + N +++++I ANLRLVV +AK+Y  RG+   DL+QEG++GLMK+V+KF  + G +F++Y
Sbjct:   386 TANRAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTY 445

Query:   385 AYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT 444
             A WWVRQ I +AI   +RTIR+P ++   ++K+    R  + E    P  E+L+ R+ I 
Sbjct:   446 ATWWVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLNIN 505

Query:   445 VEKLERLIFITRMPLSMQQPVWADQDTTF 473
             VEK+ +++ I + P+S++ P+  D  +TF
Sbjct:   506 VEKIRKVMKIVKDPVSLESPIGDDDSSTF 534

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|GSU_1525 GSU_1525 "RNA polymerase sigma-70 factor family" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 311 (114.5 bits), Expect = 3.8e-33, Sum P(2) = 3.8e-33
 Identities = 58/155 (37%), Positives = 103/155 (66%)

Query:   317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 375
             ++L   +  G+ ++R+K+I +NLRLVV +AK+Y  RG+   DL++EG+MGL+K+VE+FK 
Sbjct:    79 KELAGRIAKGDKAARDKMIESNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKL 138

Query:   376 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 435
                CRF++YA WW+RQ+I +A+   SRTIRLP ++   ++K+L+  R  +Q  N  P  +
Sbjct:   139 SKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDDINKMLKITRELVQRLNREPSVK 198

Query:   436 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 470
             ++A  + +    + RL+ + +   S+++P+  + D
Sbjct:   199 EVATEMKVNSAYVRRLMVLLKKTYSIERPMGENSD 233

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 356 (130.4 bits), Expect = 3.9e-32, P = 3.9e-32
 Identities = 89/293 (30%), Positives = 163/293 (55%)

Query:   193 DISLTSSLGYPLEEVKQFSQPR---FLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSE 249
             D+ L ++L   LEE    +  R     ER+  K K+++  VT+    +   A + ++L E
Sbjct:   192 DVRL-AALNAELEEESLSASRRQELLAERQELKEKLAE-MVTSLRLKDRHIAKIAQRLKE 249

Query:   250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQ--IQDLIRLEKEKSKLQSQFGR--EPTL 305
                + D +   +   E    ++AD   E+ A   +   I+L  E ++   +  R  E  L
Sbjct:   250 LSAKVDTIMAEIAAIEKEAGVSADTLKEIAASEAVGKGIKLSLEDAQKHEKKVRSAEKKL 309

Query:   306 IEWAKAIGLSCRDLKSELHS---GNS----SREKLINANLRLVVHVAKQYQGRGISLHDL 358
              +  +  G   R+L   L +   G +    ++ +L+ ANLRLVV +AK+Y  RG+   DL
Sbjct:   310 KKVEEESGFKARELSDALRAIDRGEAKSKLAKSELVEANLRLVVSIAKKYTNRGLQFLDL 369

Query:   359 LQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVL 418
             +QEG++GLMK+V+KF+ Q G +F++YA WW+RQ I +AI   +RTIR+P ++   ++K++
Sbjct:   370 IQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLI 429

Query:   419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
                R  +QE    P  E++A R+ + ++K+ +++ I + P+S++ P+  ++D+
Sbjct:   430 RTSRQLVQEIGREPSPEEIAERMNLPLDKVRKVLKIAKEPISLETPIGEEEDS 482

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|CHY_0455 CHY_0455 "RNA polymerase sigma factor RpoD" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 71/198 (35%), Positives = 121/198 (61%)

Query:   274 EEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333
             +E +L   I + I ++        + GR P L    + I L+ R  K E      ++ KL
Sbjct:    83 DEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTP-EEEIELAKR--KEE--GDEEAKRKL 137

Query:   334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 393
               ANLRLVV +AK+Y GRG+   DL+QEG++GL+K+VEKF  + G +F++YA WW+RQ I
Sbjct:   138 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAI 197

Query:   394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 453
              +AI   +RTIR+P ++   ++K++   R  +QE    P  E++A+ +GI+ +K+  ++ 
Sbjct:   198 TRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEEIAKEMGISEDKVREIMK 257

Query:   454 ITRMPLSMQQPVWADQDT 471
             I + P+S++ P+  ++D+
Sbjct:   258 IAQEPVSLETPIGEEEDS 275

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|ECH_0760 ECH_0760 "RNA polymerase sigma factor RpoD" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 335 (123.0 bits), Expect = 1.2e-29, P = 1.2e-29
 Identities = 80/226 (35%), Positives = 131/226 (57%)

Query:   248 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIE 307
             S G  R D L  +      +K  T+ +   ++   +  I     K KL S  G E  L E
Sbjct:   311 SYGIQRKDFLDAYNTNSVLQKKGTSPQWDNMLLNEESNIVSMYSKIKLLS--G-ENNLTE 367

Query:   308 WAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLM 367
             + KA+    +  K E  + N +++++I ANLRLVV +AK+Y  RG+   DL+QEG++GLM
Sbjct:   368 F-KALVTKIQ--KHE-RAANQAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLM 423

Query:   368 KSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 427
             K+V+KF  + G +F++YA WWVRQ I +AI   +RTIR+P ++   ++K+    R  + E
Sbjct:   424 KAVDKFDYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHE 483

Query:   428 GNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473
                 P  E+L+ R+ I V+K+ +++ I + P+S++ P+  D  +TF
Sbjct:   484 MGREPTLEELSARLNINVDKIRKVMKIVKDPVSLESPIGDDDSSTF 529

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 328 (120.5 bits), Expect = 1.3e-29, P = 1.3e-29
 Identities = 68/211 (32%), Positives = 123/211 (58%)

Query:   263 GPETRKLLTADEEFELI-AQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS 321
             GP   ++   +EEF+L    +   +++         + GR   L+   + I L+ R    
Sbjct:    74 GPNNHQITKTEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVD-LLSAEEEIRLATR---- 128

Query:   322 ELHSGNS-SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
              +  G+  ++ +L  ANLRLVV +AK+Y GRG+   DL+QEG+MGL+K+VEKF  + G +
Sbjct:   129 -IEEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFK 187

Query:   381 FASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR 440
             F++YA WW+RQ I +AI   +RTIR+P ++   ++K++  +R  +Q+    P  E++   
Sbjct:   188 FSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIGEE 247

Query:   441 VGITVEKLERLIFITRMPLSMQQPVWADQDT 471
             + +  EK+  ++ I + P+S++ P+  + D+
Sbjct:   248 MDLAPEKVREILKIAQEPVSLETPIGEEDDS 278

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 330 (121.2 bits), Expect = 1.7e-29, P = 1.7e-29
 Identities = 68/206 (33%), Positives = 125/206 (60%)

Query:   258 RLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCR 317
             R++L G  +++LLT  +   L  +I+D I L++++SKL+ + G EP+  + A ++ +S  
Sbjct:   205 RIYLRGTVSKELLTHKQVVHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPP 264

Query:   318 DLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQA 377
             +L+S +H    +RE L  +NLRLV+ +A++Y   G+ L DL+Q G +GL++ +EKF    
Sbjct:   265 ELRSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASR 324

Query:   378 GCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDL 437
             G R ++Y YWW+RQ + +A+ ++S+T RLP  ++  L  +  AK   +++   +P  E++
Sbjct:   325 GFRISTYVYWWIRQGVSRALAENSKTFRLPTYLHERLIAIRGAK-YELEDQGIAPTIENI 383

Query:   438 ARRVGITVEKLERLIFITRMPLSMQQ 463
             A  + I+ +K+          LS+ Q
Sbjct:   384 AGSLNISEKKVLNATEAVNKVLSLDQ 409

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

---

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)
Q9LD95	SIGF_ARATH	No assigned EC number	0.5269	0.9098	0.8117	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	488
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	3e-67
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	2e-56
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	5e-53
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	8e-50
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	5e-49
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	2e-45
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	2e-44
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	3e-38
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	2e-37
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	3e-36
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	2e-34
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-33
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	2e-28
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	2e-19
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	4e-19
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	1e-18
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	2e-17
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	2e-17
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	6e-17
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	3e-16
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	2e-13
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	1e-12
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	6e-12
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	6e-12
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	4e-11
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	1e-10
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	3e-10
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	2e-09
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	2e-09
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	3e-09
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	9e-09
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	1e-07
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	5e-05
PRK08295	208	PRK08295, PRK08295, RNA polymerase factor sigma-70	7e-05
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	8e-05
TIGR02859	198	TIGR02859, spore_sigH, RNA polymerase sigma-H fact	9e-05
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	2e-04
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	0.001

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

 Score =  217 bits (556), Expect = 3e-67
 Identities = 93/206 (45%), Positives = 137/206 (66%)

Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328
           LLT +EE EL  Q+Q ++ LE+ + +L+ Q GREP+  EWA A GLS  +L+  L  G  
Sbjct: 15  LLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQR 74

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           ++EK+I ANLRLVV VAK+YQ RG+ L DL+QEGS+GL ++VEKF P  G +F++YAYWW
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWW 134

Query: 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
           +RQ I +AI   SRTIRLP +I   L+K+ + +R   Q+   +P + ++A  + +  E++
Sbjct: 135 IRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQV 194

Query: 449 ERLIFITRMPLSMQQPVWADQDTTFQ 474
             L+   R P+S+  PV  ++DT   
Sbjct: 195 RELLQRARQPVSLDAPVGDEEDTELG 220

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|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated

 Score =  191 bits (488), Expect = 2e-56
 Identities = 87/234 (37%), Positives = 147/234 (62%), Gaps = 5/234 (2%)

Query: 238 SRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 297
             K   KK  +E     D +R++L      +LL  DEE EL  +I DL+ LE+ + + +S
Sbjct: 51  RIKIGPKKVYTE-----DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFES 105

Query: 298 QFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHD 357
           + GREP+  EWA+ + +     +  L  G  ++EK++ +NLRLVV +AK+Y  RG+S  D
Sbjct: 106 ELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQD 165

Query: 358 LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKV 417
           L+QEGS+GL+++ EKF  + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++
Sbjct: 166 LIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRI 225

Query: 418 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
            +  ++  QE    P +E++A  + +T+EKL  +    ++P+S++ P+  ++D+
Sbjct: 226 KKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDS 279

Length = 373

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

 Score =  181 bits (460), Expect = 5e-53
 Identities = 90/217 (41%), Positives = 136/217 (62%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
           D +R +L       LLT +EE     Q+Q L+ L++ + +L  + GREPT  EWAKA  L
Sbjct: 8   DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKL 67

Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 374
           S  +L+S +  G +++ K++ ANLRLVV VAK+Y  R + L DL+QEG++G+ + VEKF 
Sbjct: 68  SEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFD 127

Query: 375 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 434
           P  G RF++YAYWW+RQ I +AI + SRTIRLP +I   L+K+ +A+R   Q+   +   
Sbjct: 128 PTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATI 187

Query: 435 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
            +LA  + +T +++   +   R PLS+   V  +QDT
Sbjct: 188 GELAEELELTPKQVREYLERARQPLSLDLRVGDNQDT 224

Length = 317

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

 Score =  173 bits (439), Expect = 8e-50
 Identities = 83/206 (40%), Positives = 129/206 (62%)

Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328
           LLT ++E     Q+Q ++ L + K  L  + GREP+L EWA+A+ LS  +LK  L  G  
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           +++K+I ANLRLVV +AK+YQ R +   DL+QEG++GL + VEKF P  G +F++YAYWW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
           +RQ I +AI Q +RTIRLP +I   L+K+ + +R   Q+   S    ++A+ + +   ++
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQI 211

Query: 449 ERLIFITRMPLSMQQPVWADQDTTFQ 474
              + + R P+S+   V  +QDT   
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELS 237

Length = 327

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

 Score =  171 bits (435), Expect = 5e-49
 Identities = 79/226 (34%), Positives = 124/226 (54%), Gaps = 20/226 (8%)

Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKL-QSQFGREPTL---------------IEWAKAI 312
           LL  + E EL  Q++D   L +    L   + GREP+                IE A  +
Sbjct: 23  LLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLL 82

Query: 313 GLS-CRDLKSELHSGNSSRE---KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK 368
                + L   L  G    +   KL+ +NLRLVV +AK+Y GRG+   DL+QEG++GLMK
Sbjct: 83  TPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMK 142

Query: 369 SVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG 428
           +VEKF P+ G +F++YA WW+RQ I +AI   +RTIR+P +   L++K+   KR  +QE 
Sbjct: 143 AVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQEL 202

Query: 429 NHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 474
              P  E++A  +G++ +K+  ++     P+S+  P+  D+D+   
Sbjct: 203 GREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELG 248

Length = 342

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

 Score =  163 bits (415), Expect = 2e-45
 Identities = 93/261 (35%), Positives = 138/261 (52%), Gaps = 46/261 (17%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKE--------------------KSK 294
           D +RL+L      +LL  DEE     ++Q  ++L                       + +
Sbjct: 60  DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRER 119

Query: 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS----------------------SREK 332
           L S+ G  P+L  WAK   +S  DLK  L  G                        ++E 
Sbjct: 120 LTSELGHRPSLERWAKTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEH 179

Query: 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392
           +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF++YAYWW+RQ 
Sbjct: 180 MIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQG 239

Query: 393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI 452
           I +AI   SRTIRLP +I   L+K+ +A+R   QE   +P  ED+A+ + +T  ++  + 
Sbjct: 240 ITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV- 298

Query: 453 FITRMP--LSMQQPVWADQDT 471
            + R+P  +S++  V  D+DT
Sbjct: 299 -LLRVPRSVSLETKVGKDKDT 318

Length = 415

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

 Score =  155 bits (395), Expect = 2e-44
 Identities = 60/144 (41%), Positives = 101/144 (70%)

Query: 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 389
           +++L+ +NLRLVV +AK+Y  RG+S  DL+QEG++GLMK+VEKF  + G +F++YA WW+
Sbjct: 2   KKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWI 61

Query: 390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 449
           RQ I +AI   +RTIR+P ++   ++K+++A+R   QE    P  E+LA R+G+  EK+ 
Sbjct: 62  RQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVR 121

Query: 450 RLIFITRMPLSMQQPVWADQDTTF 473
            +  I + P+S++ P+  ++D+  
Sbjct: 122 EIKKIAQEPISLETPIGEEEDSFL 145

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|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed

 Score =  141 bits (358), Expect = 3e-38
 Identities = 83/218 (38%), Positives = 132/218 (60%), Gaps = 17/218 (7%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
           D +R++L G     LLTA +E EL  +I+         + L ++      L+E  K +  
Sbjct: 26  DLVRVYLNGIGKTALLTAADEVELAKRIE---------AGLYAE-----HLLETRKRLSE 71

Query: 315 SC-RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
           +  RDL + +  G ++R  L+ ANLRLVV +AK+Y GRG+ L DL+QEG++GL++++EKF
Sbjct: 72  ARKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKF 131

Query: 374 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKR-LYIQEGNHSP 432
               G +F++YA WW+RQ I + +   SRTIRLP ++   ++K+   KR L+ Q G  + 
Sbjct: 132 DYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREAT 191

Query: 433 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 470
           D E+LA   GI  EK+  L+  +R P+S+  PV +D++
Sbjct: 192 D-EELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEE 228

Length = 324

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

 Score =  138 bits (349), Expect = 2e-37
 Identities = 58/140 (41%), Positives = 89/140 (63%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           +R+ +I +NLRLVV +AK Y  RG+ L DL++EG++GLM +VEKF P+ G RF++YA WW
Sbjct: 47  ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWW 106

Query: 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
           +RQTI +AI   +RTIRLP ++   L+  L A R   ++    P  E++A  +   VE +
Sbjct: 107 IRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDV 166

Query: 449 ERLIFITRMPLSMQQPVWAD 468
            R++ +     S+  P+  D
Sbjct: 167 SRVLALNERITSLDAPLDDD 186

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 =  136 bits (344), Expect = 3e-36
 Identities = 54/123 (43%), Positives = 87/123 (70%)

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 387
           ++R+++I +NLRLVV +AK+Y  RG++L DL++EG++GL+++VEKF P+ G RF++YA W
Sbjct: 86  AARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 145

Query: 388 WVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK 447
           W+RQTI +AI   +RTIRLP ++   L+  L A R    + +H P  E++A  +   V+ 
Sbjct: 146 WIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDD 205

Query: 448 LER 450
           + R
Sbjct: 206 VSR 208

Length = 325

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

 Score =  132 bits (334), Expect = 2e-34
 Identities = 79/237 (33%), Positives = 123/237 (51%), Gaps = 52/237 (21%)

Query: 248 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIE 307
             G   NDP+R++L       LLTA+EE EL                             
Sbjct: 89  PPGVKINDPVRMYLKEIGRVPLLTAEEEIEL----------------------------- 119

Query: 308 WAKAIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGL 366
            AK I             G+  ++++L  ANLRLVV +AK+Y GRG+   DL+QEG+MGL
Sbjct: 120 -AKRIE-----------EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGL 167

Query: 367 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQ 426
           MK+VEKF  + G +F++YA WW+RQ I +AI   +RTIR+P ++   ++K++  +R  +Q
Sbjct: 168 MKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQ 227

Query: 427 EGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHL 483
           E    P  E++A  + +  EK+  ++ I + P+S++ P+  + D          SHL
Sbjct: 228 ELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDD----------SHL 274

Length = 367

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

 Score =  130 bits (330), Expect = 5e-33
 Identities = 78/210 (37%), Positives = 116/210 (55%), Gaps = 21/210 (10%)

Query: 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 327
           KLL A+EE EL        R+E         +  E  L E  K      RDL+     G 
Sbjct: 224 KLLNAEEEVELA------KRIEAG------LYAEE-LLAEGEKLDPELRRDLQWIGRDGK 270

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 387
            ++  L+ ANLRLVV +AK+Y  RG+S  DL+QEG++GL+K+VEKF    G +F++YA W
Sbjct: 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATW 330

Query: 388 WVRQTIRKAIFQHSRTIRLP----ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI 443
           W+RQ I +A+   +RTIR+P    E I    +K+   +R  +QE    P  E+LA+ +G 
Sbjct: 331 WIRQAITRAMADQARTIRIPVHMVETI----NKLGRIERELLQELGREPTPEELAKEMGF 386

Query: 444 TVEKLERLIFITRMPLSMQQPVWADQDTTF 473
           T EK+  +    R P+S+ + +  + D+ F
Sbjct: 387 TPEKVREIQKYNREPISLDKTIGKEGDSQF 416

Length = 509

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

 Score =  118 bits (298), Expect = 2e-28
 Identities = 69/208 (33%), Positives = 119/208 (57%), Gaps = 26/208 (12%)

Query: 281 QIQDLIRLEKEKSKLQSQFGREPT-LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLR 339
              ++ +L++E   ++ + G     L E  + I       K E  +  + +E ++ ANLR
Sbjct: 339 VYDEIKKLQQELEAIEEETGLTIEELKEINRQI------SKGEAKARRAKKE-MVEANLR 391

Query: 340 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399
           LV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I  
Sbjct: 392 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 451

Query: 400 HSRTIRLP----ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 455
            +RTIR+P    E I    +K+    R  +QE    P  E+LA R+G+  +K+ +++ I 
Sbjct: 452 QARTIRIPVHMIETI----NKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIA 507

Query: 456 RMPLSMQQPVWADQDTTFQVMPLLLSHL 483
           + P+S++ P+  D+D          SHL
Sbjct: 508 KEPISLETPIGDDED----------SHL 525

Length = 619

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

 Score = 81.8 bits (203), Expect = 2e-19
 Identities = 27/71 (38%), Positives = 44/71 (61%)

Query: 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 392
           L+   L LV  +A++Y G G    DL+QEG +GL+++VE+F P+ G  F+++ Y  +R  
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 393 IRKAIFQHSRT 403
           I  A+ +  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|224112 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription]

 Score = 86.2 bits (214), Expect = 4e-19
 Identities = 40/136 (29%), Positives = 72/136 (52%), Gaps = 8/136 (5%)

Query: 317 RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLH-DLLQEGSMGLMKSVEKFKP 375
             L      G+    +LI   L LV  +A++++ RG S + DL+Q G +GL+K++E++ P
Sbjct: 12  EKLLEYYAEGDEEARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDP 71

Query: 376 QAGCRFASYAYWWVRQTIRKAIFQHSR---TIRLPENIYTLLSKVLEAKRLYIQEGNHSP 432
             G +F++YA     + IR  I  + R   ++++P ++  L  ++ EA     QE    P
Sbjct: 72  SKGTKFSTYA----VRRIRGEILDYLRKNDSVKVPRSLRELGRRIEEAIDELEQELGREP 127

Query: 433 DKEDLARRVGITVEKL 448
             E++A  +GI  E+ 
Sbjct: 128 TDEEIAEELGIDKEEY 143

Length = 247

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

 Score = 85.0 bits (211), Expect = 1e-18
 Identities = 29/66 (43%), Positives = 47/66 (71%)

Query: 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391
           KL+ ++LR VV +A+ Y+G G+   DL+QEG++GLMK+V++F P+ G R  S+A  W++ 
Sbjct: 39  KLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKA 98

Query: 392 TIRKAI 397
            I + I
Sbjct: 99  EIHEYI 104

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 = 82.1 bits (204), Expect = 2e-17
 Identities = 28/62 (45%), Positives = 46/62 (74%)

Query: 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 391
           +L+ ++LR VVH+A+ Y+G G+   DL+QEG++GLMK+V++F P+ G R  S+A  W++ 
Sbjct: 52  QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKA 111

Query: 392 TI 393
            I
Sbjct: 112 EI 113

Length = 284

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

 Score = 80.7 bits (200), Expect = 2e-17
 Identities = 39/149 (26%), Positives = 78/149 (52%), Gaps = 2/149 (1%)

Query: 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 389
           REKL+  NL LV  +A++++ RG    DL+Q G++GL+K++++F P  G +F+++A   +
Sbjct: 5   REKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTI 64

Query: 390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 449
              I++     +  +R+P  +  L  K+ +A     Q    SP   ++A R+G++ E++ 
Sbjct: 65  MGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVV 124

Query: 450 RLIFITRM--PLSMQQPVWADQDTTFQVM 476
             +        LS+   +  D      ++
Sbjct: 125 EALEAGNAYQALSLDASIEDDDGDPIALL 153

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|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed

 Score = 80.0 bits (198), Expect = 6e-17
 Identities = 47/161 (29%), Positives = 90/161 (55%), Gaps = 2/161 (1%)

Query: 317 RDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 375
           R+L   + +G   +REKLIN NLRLV+ V +++  RG ++ DL Q G +GLMK+++ F  
Sbjct: 25  RELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDL 84

Query: 376 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 435
               +F++YA   +   IR+ +  ++  IR+  ++  +  K L+ +   I E +  P  E
Sbjct: 85  SQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVE 143

Query: 436 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVM 476
           ++A+ + +  E++   +   + P+S+ +P++ D      VM
Sbjct: 144 EIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVM 184

Length = 258

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

 Score = 77.9 bits (192), Expect = 3e-16
 Identities = 48/161 (29%), Positives = 90/161 (55%), Gaps = 2/161 (1%)

Query: 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 375
           R+L   + SG+ ++REKLIN NLRLV+ V +++  RG  + DL Q G +GLMKS++ F  
Sbjct: 22  RELFIRMQSGDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDL 81

Query: 376 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 435
               +F++YA   +   IR+ + + +  IR+  ++  +  K L+ +   I E +  P   
Sbjct: 82  SQNVKFSTYAVPMIIGEIRRYL-RDNNPIRVSRSLRDIAYKALQVRDKLISENSKEPTVS 140

Query: 436 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVM 476
           ++A+ + +  E++   +   + P+S+ +P++ D      VM
Sbjct: 141 EIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVM 181

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 = 70.4 bits (173), Expect = 2e-13
 Identities = 24/65 (36%), Positives = 49/65 (75%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           +  ++I+A++RLV+ +A +++  G+ ++DL+QEG +GL+++  +F+P    RF++YA WW
Sbjct: 41  ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWW 100

Query: 389 VRQTI 393
           +R +I
Sbjct: 101 IRASI 105

Length = 289

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

 Score = 67.6 bits (166), Expect = 1e-12
 Identities = 43/144 (29%), Positives = 78/144 (54%), Gaps = 3/144 (2%)

Query: 330 REKLINANLRLVVHVAKQY-QGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           R +L+  NL LV   A ++         DL+Q GS+GL++++E+F P  G  F+S+A  +
Sbjct: 27  RNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPY 86

Query: 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
           +R  I+  +   S T+R+P     L  +  + ++   QE    P  +++A+ + I++E+ 
Sbjct: 87  IRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEW 146

Query: 449 E--RLIFITRMPLSMQQPVWADQD 470
           +  +L    R PLS+  PV  D+D
Sbjct: 147 QEIKLALQNRTPLSLDAPVNQDED 170

Length = 256

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

 Score = 65.1 bits (159), Expect = 6e-12
 Identities = 36/126 (28%), Positives = 68/126 (53%), Gaps = 2/126 (1%)

Query: 324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
            +G+  +R+KLI  NLRLV  + K++  RG    DL Q G +GL+K+++KF      +F+
Sbjct: 6   QNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFS 65

Query: 383 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG 442
           +YA   +   I++ + +    I++  ++  L  K+   K    +E    P   +LA  +G
Sbjct: 66  TYAVPMIMGEIKRFL-RDDGIIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALG 124

Query: 443 ITVEKL 448
           ++ E++
Sbjct: 125 VSPEEI 130

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

 Score = 63.1 bits (154), Expect = 6e-12
 Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 2/100 (2%)

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 387
            + E+L    L LV   A++Y G      DL+QE  + L++++++F P+    F ++ + 
Sbjct: 1   EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFR 58

Query: 388 WVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE 427
             R  I   + +  R  R  + +  LL      +    QE
Sbjct: 59  IARNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQE 98

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|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated

 Score = 63.1 bits (154), Expect = 4e-11
 Identities = 36/126 (28%), Positives = 69/126 (54%), Gaps = 2/126 (1%)

Query: 324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
             G+  +R+ L+  NLRLV  V +++  RG    DL Q G +GL+K+V+KF      +F+
Sbjct: 27  QDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFS 86

Query: 383 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG 442
           +YA   +   I++ + +   T+++  ++    +K+ + K    +E    P  E+LA  +G
Sbjct: 87  TYAVPMIIGEIQRFL-RDDGTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLG 145

Query: 443 ITVEKL 448
           +T E++
Sbjct: 146 VTPEEV 151

Length = 252

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

 Score = 61.3 bits (149), Expect = 1e-10
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
           +R  LI  NLRLV H+ K++   G  + DL+  G++GL+K+++ F P  G R A+YA
Sbjct: 49  ARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYA 105

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|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed

 Score = 60.0 bits (146), Expect = 3e-10
 Identities = 23/57 (40%), Positives = 37/57 (64%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
           +R  LI  NLRLV H+ K+++  G  + DL+  G++GL+K++E F    G + A+YA
Sbjct: 50  ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA 106

Length = 233

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 20/62 (32%), Positives = 34/62 (54%)

Query: 413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 472
           LL+K+  A+R   QE    P  E++A  +GI+ EK+  ++   R P+S+  PV  ++D  
Sbjct: 2   LLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDGE 61

Query: 473 FQ 474
             
Sbjct: 62  LG 63

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|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed

 Score = 57.6 bits (140), Expect = 2e-09
 Identities = 27/69 (39%), Positives = 46/69 (66%), Gaps = 1/69 (1%)

Query: 318 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQ 376
            L ++L  G  + R  LI  NLRLVV++A++++  GI++ DL+  G++GL+K+V  F P+
Sbjct: 41  YLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPE 100

Query: 377 AGCRFASYA 385
              + A+YA
Sbjct: 101 KKIKLATYA 109

Length = 234

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

 Score = 57.1 bits (138), Expect = 3e-09
 Identities = 24/59 (40%), Positives = 40/59 (67%)

Query: 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
            S++  LI  NLRLVV++A++++  GI + DL+  G++GL+K+V  F P    + A+YA
Sbjct: 51  ESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYA 109

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|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed

 Score = 55.9 bits (135), Expect = 9e-09
 Identities = 29/114 (25%), Positives = 59/114 (51%)

Query: 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 389
           R++++   L L  H+A+++ GRG    DL+Q   +GL+ +V +F  + G  F S+A   +
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTI 101

Query: 390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI 443
              +R+    +S ++++P  +  L  ++  A     Q    +P   +LA  +G+
Sbjct: 102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGM 155

Length = 264

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

 Score = 51.9 bits (125), Expect = 1e-07
 Identities = 32/123 (26%), Positives = 58/123 (47%), Gaps = 8/123 (6%)

Query: 333 LINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 389
           LI   L LV  +A +        + L DL+Q G  GL+ ++E++ P  G +F +YA    
Sbjct: 1   LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYA---- 56

Query: 390 RQTIRKAIFQHSRTIR-LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
            Q IR A+    R +  +P ++     K+  A R         P +E++A  +G+ +++ 
Sbjct: 57  VQRIRGAMLDELRRLDWVPRSLRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEY 116

Query: 449 ERL 451
            + 
Sbjct: 117 RQA 119

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|235770 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed

 Score = 44.7 bits (106), Expect = 5e-05
 Identities = 38/130 (29%), Positives = 62/130 (47%), Gaps = 16/130 (12%)

Query: 330 REKLINANLRLVVHVAKQYQGR-GISLH------DLLQEGSMGLMKSVEKFKPQAGCRFA 382
           RE LI     LV +VA    GR  + +       DL+  G  GL+ ++EKF P+   +F 
Sbjct: 33  REYLILKYSPLVKYVA----GRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFK 88

Query: 383 SYAYWWVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRV 441
           +YA       IR AIF   R+I  +P ++     ++  A  +       +P  E++A  +
Sbjct: 89  TYAV----TRIRGAIFDELRSIDWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADEL 144

Query: 442 GITVEKLERL 451
           GI++E+   L
Sbjct: 145 GISLEEYNSL 154

Length = 268

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

 Score = 43.7 bits (104), Expect = 7e-05
 Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 1/96 (1%)

Query: 324 HSGNS-SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
            SG+  + E LI      V   A+ Y   G    D++QEG +GL K++  +       F 
Sbjct: 19  RSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFK 78

Query: 383 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVL 418
           S+A   + + I  AI   +R   +P N Y  L K +
Sbjct: 79  SFAELCITRQIITAIKTANRQKHIPLNSYVSLDKPI 114

Length = 208

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

 Score = 43.7 bits (104), Expect = 8e-05
 Identities = 33/130 (25%), Positives = 63/130 (48%), Gaps = 12/130 (9%)

Query: 324 HSGNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
             G   +++L+     LV  +A + + R    + L DL+Q G +GL+++  ++  + G  
Sbjct: 4   AEGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGAS 63

Query: 381 FASYAYWWVRQTIRKAIFQHSRTIRL---PENIYTLLSKVLEAKRLYIQEGNHSPDKEDL 437
           F +YA     Q IR A+    R   L   P ++     +V +A R   QE    P   ++
Sbjct: 64  FETYA----GQRIRGAMLDELR--SLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTEV 117

Query: 438 ARRVGITVEK 447
           A ++G+++E+
Sbjct: 118 AEKLGLSLEE 127

Length = 236

>gnl|CDD|131906 TIGR02859, spore_sigH, RNA polymerase sigma-H factor

 Score = 43.2 bits (102), Expect = 9e-05
 Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 1/104 (0%)

Query: 314 LSCRDLKSELHSGNS-SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK 372
           L   ++      GN+ + E LIN     V   A+ Y   G    D++QEG +GL K++  
Sbjct: 4   LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRD 63

Query: 373 FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSK 416
           F+P     F ++A   V + I  AI   +R   +P N Y  L+K
Sbjct: 64  FRPDKLSSFKAFAELCVTRQIITAIKTATRQKHIPLNSYVSLNK 107

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 in Listeria score above the noise cutoff to This model, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 198

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

 Score = 42.6 bits (100), Expect = 2e-04
 Identities = 28/119 (23%), Positives = 58/119 (48%)

Query: 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 389
           +EKL++    LV  +A +Y   G    DL+Q G +GL+ ++ ++    G  F  +A   +
Sbjct: 31  QEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTI 90

Query: 390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
              I++ +   + ++ +P  I  L  K+ +A          SP   ++A  +G++ E++
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEV 149

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

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

 Score = 40.1 bits (94), Expect = 0.001
 Identities = 41/147 (27%), Positives = 73/147 (49%), Gaps = 12/147 (8%)

Query: 331 EKLINANLRLVVHVAKQYQGRGISLH-DLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 389
           EKL+     LV  +A +Y  +G S H DL+Q G +GL+ ++ ++ P  G  F ++A   +
Sbjct: 32  EKLVKHYKNLVESLAYKYS-KGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTI 90

Query: 390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK-L 448
              I++ +   + ++ +P  I  L  K+ +A      E   SP   ++A R+G++ E+ L
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVL 150

Query: 449 ERLIFITRM-----PLSMQQPVWADQD 470
           E +     M      LS+   + AD D
Sbjct: 151 EAM----EMGKSYQALSVDHSIEADSD 173

Length = 257

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	488
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.98
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.97
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.97
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	99.97
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	99.97
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	99.97
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	99.96
PRK08215	258	sporulation sigma factor SigG; Reviewed	99.96
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	99.95
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	99.95
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	99.94
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	99.94
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	99.93
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	99.93
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	99.93
PRK05572	252	sporulation sigma factor SigF; Validated	99.92
PRK07670	251	RNA polymerase sigma factor SigD; Validated	99.91
PRK08583	257	RNA polymerase sigma factor SigB; Validated	99.91
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	99.9
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	99.89
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	99.87
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.85
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.77
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.77
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.76
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.74
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.74
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.74
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.72
PRK12513	194	RNA polymerase sigma factor; Provisional	99.7
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.69
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.69
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.68
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.68
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.67
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.67
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.67
PRK12514	179	RNA polymerase sigma factor; Provisional	99.67
PRK12537	182	RNA polymerase sigma factor; Provisional	99.67
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.66
PRK12524	196	RNA polymerase sigma factor; Provisional	99.66
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.66
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.65
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.65
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.65
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.64
PRK12534	187	RNA polymerase sigma factor; Provisional	99.63
PRK12538	233	RNA polymerase sigma factor; Provisional	99.63
PRK12526	206	RNA polymerase sigma factor; Provisional	99.63
PRK12531	194	RNA polymerase sigma factor; Provisional	99.63
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.63
PRK12519	194	RNA polymerase sigma factor; Provisional	99.63
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.62
PRK11922	231	RNA polymerase sigma factor; Provisional	99.62
PRK12536	181	RNA polymerase sigma factor; Provisional	99.61
PRK12539	184	RNA polymerase sigma factor; Provisional	99.61
PRK12515	189	RNA polymerase sigma factor; Provisional	99.6
PRK12542	185	RNA polymerase sigma factor; Provisional	99.59
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.58
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.57
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.57
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.57
PRK11924	179	RNA polymerase sigma factor; Provisional	99.57
PRK12512	184	RNA polymerase sigma factor; Provisional	99.56
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.55
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.55
PRK12543	179	RNA polymerase sigma factor; Provisional	99.54
PRK12522	173	RNA polymerase sigma factor; Provisional	99.54
PRK12520	191	RNA polymerase sigma factor; Provisional	99.54
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.53
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.52
PRK12518	175	RNA polymerase sigma factor; Provisional	99.52
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.52
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.52
PRK12516	187	RNA polymerase sigma factor; Provisional	99.52
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.51
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.51
PRK12547	164	RNA polymerase sigma factor; Provisional	99.49
PRK12529	178	RNA polymerase sigma factor; Provisional	99.49
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.49
PRK12541	161	RNA polymerase sigma factor; Provisional	99.48
PRK12535	196	RNA polymerase sigma factor; Provisional	99.47
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.47
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.47
PRK12533	216	RNA polymerase sigma factor; Provisional	99.47
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.46
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.46
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.43
PRK12545	201	RNA polymerase sigma factor; Provisional	99.43
PRK12528	161	RNA polymerase sigma factor; Provisional	99.43
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.43
PRK12540	182	RNA polymerase sigma factor; Provisional	99.43
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.42
PRK12532	195	RNA polymerase sigma factor; Provisional	99.42
PRK12517	188	RNA polymerase sigma factor; Provisional	99.4
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.4
PRK12530	189	RNA polymerase sigma factor; Provisional	99.4
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.4
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.39
PRK12544	206	RNA polymerase sigma factor; Provisional	99.39
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.39
PRK12546	188	RNA polymerase sigma factor; Provisional	99.38
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.36
PRK12511	182	RNA polymerase sigma factor; Provisional	99.33
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.32
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.28
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.27
PRK12525	168	RNA polymerase sigma factor; Provisional	99.26
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.26
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.21
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.13
PRK09191	261	two-component response regulator; Provisional	99.12
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.12
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	99.1
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.06
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.01
PF07638	185	Sigma70_ECF: ECF sigma factor	98.76
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	97.92
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	97.13
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	96.48
PRK07670	251	RNA polymerase sigma factor SigD; Validated	96.25
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	96.17
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	96.14
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	96.11
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	96.02
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	96.01
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	96.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	95.97
PRK05949	327	RNA polymerase sigma factor; Validated	95.82
PRK05901	509	RNA polymerase sigma factor; Provisional	95.75
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	95.69
PRK07598	415	RNA polymerase sigma factor SigC; Validated	95.57
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	95.41
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	95.38
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	95.26
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	94.85
PRK07405	317	RNA polymerase sigma factor SigD; Validated	94.82
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	94.79
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	94.73
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	94.61
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	94.52
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	93.81
PRK05572	252	sporulation sigma factor SigF; Validated	93.56
PRK08215	258	sporulation sigma factor SigG; Reviewed	93.28
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	93.18
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	92.53
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	92.43
PRK08583	257	RNA polymerase sigma factor SigB; Validated	92.36
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	91.88
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	91.85
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	91.69
PHA02547	179	55 RNA polymerase sigma factor; Provisional	91.39
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	89.48
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	87.84
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	85.22
PF06971	50	Put_DNA-bind_N: Putative DNA-binding protein N-ter	84.13
COG4941	415	Predicted RNA polymerase sigma factor containing a	82.91
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	82.86
PRK06930	170	positive control sigma-like factor; Validated	82.54

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=7e-49  Score=411.27  Aligned_cols=234  Identities=38%  Similarity=0.627  Sum_probs=223.2

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhhCCCCcHHHHHH--
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAK--  310 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~--------------------le~~~~~l~~~~Gr~Pt~~ewA~--  310 (488)
                      .+|+++.||++|++.||||++||++|+++||.++.                    |++++..|++.+|++||..|||.  
T Consensus        58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~  137 (415)
T PRK07598         58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA  137 (415)
T ss_pred             CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence            47899999999999999999999999999999999                    89999999999999999999994  


Q ss_pred             --------------------HhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhH
Q 011324          311 --------------------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV  370 (488)
Q Consensus       311 --------------------a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAi  370 (488)
                                          ++||++++|+..++.|..|+++||.+|+++|+++|++|.++|++++||||||+||||+|+
T Consensus       138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rav  217 (415)
T PRK07598        138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV  217 (415)
T ss_pred             CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence                                455677778888889999999999999999999999999999999999999999999999


Q ss_pred             HhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHH
Q 011324          371 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER  450 (488)
Q Consensus       371 ekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~  450 (488)
                      ++|||++|++|+||++||||++|.+++++++++|++|.++.+.+++++++.+.|.+.+|+.|+.+|||+.|||++++|+.
T Consensus       218 ekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~  297 (415)
T PRK07598        218 EKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE  297 (415)
T ss_pred             HHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324          451 LIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD  486 (488)
Q Consensus       451 ~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped  486 (488)
                      ++..++.++|||.+++++++..+.|++.++..+|++
T Consensus       298 ~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pee  333 (415)
T PRK07598        298 VLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEE  333 (415)
T ss_pred             HHHHccCCcccccccCCCccccHHHhccCCCCCHHH
Confidence            999999999999999988888899999887777764

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=4.9e-46  Score=380.77  Aligned_cols=234  Identities=37%  Similarity=0.625  Sum_probs=226.2

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHH
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~Arek  332 (488)
                      ..|++..||++|+++|+||++||++|+++|+.++.+++.+..|+..+|++|+..+||.+++|++.+|+..++.|+.|++.
T Consensus        16 ~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~   95 (327)
T PRK05949         16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQK   95 (327)
T ss_pred             CCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011324          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (488)
Q Consensus       333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e  412 (488)
                      ||..|+++|+++|++|.+++.+++|||||||||||+++++|||++|++|+|||+||||++|.++|+++++.||+|.++..
T Consensus        96 Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~  175 (327)
T PRK05949         96 MIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITE  175 (327)
T ss_pred             HHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD  486 (488)
Q Consensus       413 ~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped  486 (488)
                      .++++.++.+.+...+|+.|+.+|||+.+|+++++|..++..++.++|||.+++++++.++.++++|+..+|++
T Consensus       176 ~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~~~pe~  249 (327)
T PRK05949        176 KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQ  249 (327)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCCCCHHH
Confidence            99999999999999999999999999999999999999999999999999999887778899999988777764

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

Probab=100.00  E-value=4.7e-46  Score=375.39  Aligned_cols=232  Identities=42%  Similarity=0.697  Sum_probs=222.3

Q ss_pred             cHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHH
Q 011324          255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  334 (488)
Q Consensus       255 d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLI  334 (488)
                      |++..||++++++|+||++||.+|++++++++.+++.+..|+++.|++|+..+||+++|+++.+|+.+++.|..|+++||
T Consensus         1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv   80 (298)
T TIGR02997         1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI   80 (298)
T ss_pred             CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence            36788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHH
Q 011324          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  414 (488)
Q Consensus       335 esnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l  414 (488)
                      .+|+++|+++|++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.++.+.+|+|.++...+
T Consensus        81 ~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~  160 (298)
T TIGR02997        81 KANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKL  160 (298)
T ss_pred             HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324          415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD  486 (488)
Q Consensus       415 ~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped  486 (488)
                      ++++++...+...+|+.|+.+|||+.+|+++++|..++..+...+|||.+++++++.++.++++|...+|++
T Consensus       161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~pe~  232 (298)
T TIGR02997       161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEE  232 (298)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCCCCHHH
Confidence            999999999999999999999999999999999999999999999999999877667888888887666653

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).

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=9.6e-46  Score=384.22  Aligned_cols=233  Identities=36%  Similarity=0.691  Sum_probs=225.2

Q ss_pred             CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHH
Q 011324          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (488)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekL  333 (488)
                      .|++..||++|+++|+||++||++|+++|++++.+++.+..|++..|++|+..+||.++|++..+|..++..|..|+++|
T Consensus        62 ~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L  141 (373)
T PRK07406         62 EDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKM  141 (373)
T ss_pred             CCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHH
Q 011324          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL  413 (488)
Q Consensus       334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~  413 (488)
                      |.+|+++|+++|++|.++|++++||+||||||||+|+++||+.+|++|+|||+||||++|.++|+++++.||+|.++.+.
T Consensus       142 i~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~  221 (373)
T PRK07406        142 VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYET  221 (373)
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324          414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD  486 (488)
Q Consensus       414 l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped  486 (488)
                      +++++++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.+++++++.++.|+++|+..+|++
T Consensus       222 ~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~~~pee  294 (373)
T PRK07406        222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPED  294 (373)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCCCCHHH
Confidence            9999999999999999999999999999999999999999889999999999887777899999987666653

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=1.1e-44  Score=369.32  Aligned_cols=234  Identities=39%  Similarity=0.620  Sum_probs=225.4

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHH
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~Arek  332 (488)
                      .+|++..||++|+++|+||++||++|+++|++++.+++++..|++++|++|+..+||.++++++.+|+..++.|+.|+++
T Consensus         6 ~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~   85 (317)
T PRK07405          6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK   85 (317)
T ss_pred             CCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011324          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (488)
Q Consensus       333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e  412 (488)
                      ||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|+++++.||+|.++..
T Consensus        86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~  165 (317)
T PRK07405         86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE  165 (317)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCCCCCC
Q 011324          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSHLPSD  486 (488)
Q Consensus       413 ~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~~ped  486 (488)
                      .+++++++...+...+|+.||.+|||+.+|+++++|..++...+..+|||.+++++++.++.++++|...+|++
T Consensus       166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~~~pe~  239 (317)
T PRK07405        166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPED  239 (317)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCCCCHHH
Confidence            99999999999999999999999999999999999999999889999999999887777899999987766664

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

Probab=100.00  E-value=4.9e-42  Score=350.54  Aligned_cols=234  Identities=35%  Similarity=0.601  Sum_probs=215.7

Q ss_pred             CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hhCCCCcHH---------------HHHHHhcCCH-
Q 011324          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC-  316 (488)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~-~~Gr~Pt~~---------------ewA~a~gm~e-  316 (488)
                      .|.+..|+.+++..++++.++|..+.+.++....+......+.. ..|..|+..               +|+..+..++ 
T Consensus         8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee   87 (342)
T COG0568           8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE   87 (342)
T ss_pred             hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence            57889999999999999999999999999888777677777777 677888876               6666665555 


Q ss_pred             HHHHHHhhhc--H-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324          317 RDLKSELHSG--N-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (488)
Q Consensus       317 eeLi~~l~~G--d-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI  393 (488)
                      ..|..++..|  + .|+.+||++|+|||++||++|.|+|+.+.||||||+||||+|++||||++|+||||||+||||++|
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            6688888888  4 699999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCcc
Q 011324          394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  473 (488)
Q Consensus       394 ~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl  473 (488)
                      .++|.++.|+||+|.|+.+.++++.+..+.+.++++++|+.+|||+.||++.++|+.++.++..++|||.|+|++++..+
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            99999999999999999999999999999999999999999999999999999999999999999999999999988899


Q ss_pred             ccccCCCCC-CCCCC
Q 011324          474 QVMPLLLSH-LPSDI  487 (488)
Q Consensus       474 ~e~i~D~s~-~ped~  487 (488)
                      +|+++|+.. +|+++
T Consensus       248 ~d~leD~~~~~p~~~  262 (342)
T COG0568         248 GDFLEDDKSVSPEDA  262 (342)
T ss_pred             HHHhhcCCcCCHHHH
Confidence            999999965 77754

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=4.5e-41  Score=360.10  Aligned_cols=220  Identities=35%  Similarity=0.550  Sum_probs=197.6

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHH
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~Arek  332 (488)
                      ..|+++.||++|+++|+||++||++|+++|+.+..++..   +.       ...+|+.   ....+|...+..|..|+++
T Consensus       209 ~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~  275 (509)
T PRK05901        209 TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDP---ELRRDLQWIGRDGKRAKNH  275 (509)
T ss_pred             cccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchh---hhhhhhhhhccchHHHHHH
Confidence            478999999999999999999999999999986433321   11       1122432   2456788888999999999


Q ss_pred             HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011324          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (488)
Q Consensus       333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e  412 (488)
                      ||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.||+|.++.+
T Consensus       276 LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e  355 (509)
T PRK05901        276 LLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE  355 (509)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCC
Q 011324          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPS  485 (488)
Q Consensus       413 ~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~pe  485 (488)
                      .+++|.++.+.|.+.+|+.||.+|||+.|||++++|..++..++.++|||.+++++++..+.|+|+|.. ..|+
T Consensus       356 ~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~  429 (509)
T PRK05901        356 TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPV  429 (509)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHH
Confidence            999999999999999999999999999999999999999999999999999998887788999999874 3454

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=2.5e-40  Score=338.42  Aligned_cols=219  Identities=35%  Similarity=0.557  Sum_probs=197.3

Q ss_pred             CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHH
Q 011324          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (488)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekL  333 (488)
                      +|++..||++++++|+||++||.+|+++|+.+..++..           |+..+|+...  ...+|...+..|..|+++|
T Consensus        25 ~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~L   91 (324)
T PRK07921         25 ADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHL   91 (324)
T ss_pred             CChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHH
Confidence            57899999999999999999999999999987665543           1122332111  3467889999999999999


Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHH
Q 011324          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL  413 (488)
Q Consensus       334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~  413 (488)
                      |..|+++|+++|++|.++|.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.|++|.++.+.
T Consensus        92 v~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~  171 (324)
T PRK07921         92 LEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ  171 (324)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCC
Q 011324          414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPS  485 (488)
Q Consensus       414 l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~pe  485 (488)
                      ++++.++...|...+|+.||.+|||+.||+++++|..++..+...+|||.+++++++.++.|+++|+. ..|+
T Consensus       172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe  244 (324)
T PRK07921        172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAE  244 (324)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHH
Confidence            99999999999999999999999999999999999999988889999999998777778999999854 3454

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=4.8e-37  Score=318.80  Aligned_cols=197  Identities=38%  Similarity=0.687  Sum_probs=183.4

Q ss_pred             CCCCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHH
Q 011324          250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS  329 (488)
Q Consensus       250 ~~~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~A  329 (488)
                      +....|+++.||++|+++|+||++||.+|+++++.                                        ++..|
T Consensus        91 ~~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A  130 (367)
T PRK09210         91 GVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------------------GDEEA  130 (367)
T ss_pred             ccccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh----------------------------------------hHHHH
Confidence            34457899999999999999999999999987764                                        12389


Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011324          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (488)
Q Consensus       330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~  409 (488)
                      ++.||..|+++|+++|++|.++|.+++||+||||||||+|+++|||.+|++|+|||+||||++|.++|+++.+.+|+|.+
T Consensus       131 ~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~  210 (367)
T PRK09210        131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH  210 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCCC
Q 011324          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPSD  486 (488)
Q Consensus       410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~ped  486 (488)
                      +.+.++++.++.+.|..++|+.||.+|||+.||+++++|+.++..++.++|||.+++++++..+.|+++|+. ..|++
T Consensus       211 ~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~  288 (367)
T PRK09210        211 MVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAD  288 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHH
Confidence            999999999999999999999999999999999999999999999999999999999877788999999875 45654

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.6e-34  Score=317.75  Aligned_cols=158  Identities=36%  Similarity=0.711  Sum_probs=151.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP  407 (488)
                      .|+++||.+|+|||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|+++.++||+|
T Consensus       380 ~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip  459 (619)
T PRK05658        380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP  459 (619)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCCC-CCC
Q 011324          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLSH-LPS  485 (488)
Q Consensus       408 ~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s~-~pe  485 (488)
                      .++.+.++++.++.+.+.+++|+.||.+|||+.||+++++|+.++..+..++|||.|++++++.++.|+++|... +|+
T Consensus       460 ~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~  538 (619)
T PRK05658        460 VHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPI  538 (619)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChH
Confidence            999999999999999999999999999999999999999999999999999999999998888889999998743 454

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=2.3e-32  Score=275.40  Aligned_cols=194  Identities=22%  Similarity=0.411  Sum_probs=164.7

Q ss_pred             CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHH
Q 011324          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (488)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekL  333 (488)
                      .+..+.||+++.++|+||+++|.+|+++++.                                       .++..|++.|
T Consensus         5 ~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~L   45 (289)
T PRK07500          5 ASADRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRI   45 (289)
T ss_pred             hhHHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHH
Confidence            3567789999999999999999999987643                                       1234899999


Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH-
Q 011324          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT-  412 (488)
Q Consensus       334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e-  412 (488)
                      |..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+|||+||||++|.++|+++.+.+|+|.+... 
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            9999999999999999999999999999999999999999999999999999999999999999999999999987554 


Q ss_pred             -HHHHHHHHHHHH---HHhcCCCCcHHHHHHHhCCCHHHHHHHHH-HhCCCccccccCCCCCCC--ccccccCCCCCCCC
Q 011324          413 -LLSKVLEAKRLY---IQEGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQVMPLLLSHLPS  485 (488)
Q Consensus       413 -~l~kI~ka~~~L---~~elgr~pS~eEIAe~LGIS~etVk~~L~-~ar~~lSLD~~i~~d~~~--tl~e~i~D~s~~pe  485 (488)
                       ...++.+....+   ...+++.||.+|||+.||+++++|..+.. .....+|||.+++++++.  ++.|+++|+..+|+
T Consensus       126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~~pe  205 (289)
T PRK07500        126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPD  205 (289)
T ss_pred             HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCCCch
Confidence             333444444433   34678899999999999999999988753 345789999998765543  68899999877776


Q ss_pred             C
Q 011324          486 D  486 (488)
Q Consensus       486 d  486 (488)
                      +
T Consensus       206 ~  206 (289)
T PRK07500        206 E  206 (289)
T ss_pred             H
Confidence            4

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.98  E-value=1.5e-31  Score=268.81  Aligned_cols=192  Identities=27%  Similarity=0.465  Sum_probs=161.8

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcH-HHHH
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN-SSRE  331 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd-~Are  331 (488)
                      +.+.+..|+++++++|+||.++|.+|+.+.+.                                        .|+ .|++
T Consensus        12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~----------------------------------------~Gd~~a~~   51 (284)
T PRK06596         12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE----------------------------------------HGDLEAAK   51 (284)
T ss_pred             CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH----------------------------------------cCCHHHHH
Confidence            46789999999999999999999999886432                                        234 8999


Q ss_pred             HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHH
Q 011324          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  411 (488)
Q Consensus       332 kLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~  411 (488)
                      .||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++|+++.+.+++|.+..
T Consensus        52 ~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~  131 (284)
T PRK06596         52 QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKA  131 (284)
T ss_pred             HHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999887889998654


Q ss_pred             H--HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh-CCCccccccCCCCC--CCccccccCCCCCCCCC
Q 011324          412 T--LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQ--DTTFQVMPLLLSHLPSD  486 (488)
Q Consensus       412 e--~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a-r~~lSLD~~i~~d~--~~tl~e~i~D~s~~ped  486 (488)
                      .  ...++.+....+.  .++.|+.+|||+.||+++++|..++... ...+|||.++++++  +.++.++++|+..+|++
T Consensus       132 ~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~~~p~~  209 (284)
T PRK06596        132 QRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPAD  209 (284)
T ss_pred             HHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCCCCchH
Confidence            2  2233433333332  3479999999999999999999987643 46899999987553  34688999998767754

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.97  E-value=3.1e-31  Score=264.12  Aligned_cols=190  Identities=26%  Similarity=0.493  Sum_probs=156.8

Q ss_pred             HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHH
Q 011324          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (488)
Q Consensus       256 ~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIe  335 (488)
                      ++..||++++++|+|++++|.+|+.++..                                       .++..|++.||.
T Consensus         2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv~   42 (270)
T TIGR02392         2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLVL   42 (270)
T ss_pred             hHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence            57889999999999999999999886432                                       123489999999


Q ss_pred             HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHH--HH
Q 011324          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL  413 (488)
Q Consensus       336 snlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~--e~  413 (488)
                      .|+++|+++|++|.+++.+++||+||||+||++|+++|||++|++|+|||+||||++|.++|+++.+.+++|.+..  ..
T Consensus        43 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~~  122 (270)
T TIGR02392        43 SHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKL  122 (270)
T ss_pred             HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999877889996543  33


Q ss_pred             HHHHHHHHHHHHHhcCCCC-cHHHHHHHhCCCHHHHHHHHHHhC-CCccccccCCCCCC--CccccccCCCCCCCCC
Q 011324          414 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFITR-MPLSMQQPVWADQD--TTFQVMPLLLSHLPSD  486 (488)
Q Consensus       414 l~kI~ka~~~L~~elgr~p-S~eEIAe~LGIS~etVk~~L~~ar-~~lSLD~~i~~d~~--~tl~e~i~D~s~~ped  486 (488)
                      ..++.+....+.  ..+.| +.+|||+.||+++++|..++.... ..+|||.+++++++  .++.+++.|+..+|++
T Consensus       123 ~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~~~pe~  197 (270)
T TIGR02392       123 FFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKTSDPED  197 (270)
T ss_pred             HHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCCCChHH
Confidence            444444444332  22345 699999999999999999875443 47999999876544  3678888888766654

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=99.97  E-value=5.5e-31  Score=262.19  Aligned_cols=153  Identities=22%  Similarity=0.346  Sum_probs=140.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP  407 (488)
                      .++++||..|++||+++|++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|+++.+.|++|
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             hhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH--hCCCccccccCCCCCC--CccccccCCC
Q 011324          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQD--TTFQVMPLLL  480 (488)
Q Consensus       408 ~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~--ar~~lSLD~~i~~d~~--~tl~e~i~D~  480 (488)
                      .++.+.+.+++++...|.+.+|+.||.+|||+.||+++++|..++..  ...++|||.+++++++  ..+.+.++|.
T Consensus       120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~~~  196 (264)
T PRK07122        120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDV  196 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccCCc
Confidence            99999999999999999999999999999999999999999998864  4578999999875433  3455655553

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

Probab=99.97  E-value=3.6e-31  Score=258.63  Aligned_cols=157  Identities=39%  Similarity=0.724  Sum_probs=148.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccch
Q 011324          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (488)
Q Consensus       329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~  408 (488)
                      |+++||..|+++|+++|++|.++|.+++||+|||+|||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
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             hHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCC
Q 011324          409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPS  485 (488)
Q Consensus       409 ~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~pe  485 (488)
                      ++.+.++++.++...+...+|+.||.+|||+.||+++++|..++......+|||.+++++++.++.|+++|+. ..|+
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~  158 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPD  158 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChH
Confidence            9999999999999999999999999999999999999999999988888999999998777678889998875 3454

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.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=99.97  E-value=9e-30  Score=260.70  Aligned_cols=193  Identities=35%  Similarity=0.594  Sum_probs=176.4

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHH
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~Arek  332 (488)
                      ..|.++.||.+|+..|+||+++|..|+.+++.                                        ++..|++.
T Consensus        51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~   90 (325)
T PRK05657         51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR   90 (325)
T ss_pred             cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence            47799999999999999999999998886653                                        23489999


Q ss_pred             HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011324          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (488)
Q Consensus       333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e  412 (488)
                      ||..|.++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+||++||||..|.++++++.+.+++|.++..
T Consensus        91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~  170 (325)
T PRK05657         91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK  170 (325)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC-CCCC
Q 011324          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS-HLPS  485 (488)
Q Consensus       413 ~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s-~~pe  485 (488)
                      .++.+.++.+.|...+++.|+.+|||+.||+++++|+.++.......|||.++..+...++.|.++|.. ..|+
T Consensus       171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe  244 (325)
T PRK05657        171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPE  244 (325)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHH
Confidence            888888888889999999999999999999999999999988778899999988777778888888764 3443

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=99.97  E-value=7.9e-30  Score=252.41  Aligned_cols=158  Identities=27%  Similarity=0.467  Sum_probs=143.2

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccCC-CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324          325 SGN-SSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (488)
Q Consensus       325 ~Gd-~ArekLIesnlrLV~sIAkry~~~-g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr  402 (488)
                      .|+ .|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+|+|.+++|++.+
T Consensus        21 ~gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~  100 (256)
T PRK07408         21 NPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSP  100 (256)
T ss_pred             CCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence            445 899999999999999999999876 667999999999999999999999999999999999999999999999999


Q ss_pred             CcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH--HhCCCccccccCCCCCC--CccccccC
Q 011324          403 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQD--TTFQVMPL  478 (488)
Q Consensus       403 ~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~--~ar~~lSLD~~i~~d~~--~tl~e~i~  478 (488)
                      .+++|+++.+.++++.++...|.+.+|+.|+.+|||+.||+++++|..++.  .....+|||.+++++++  .++.+.++
T Consensus       101 ~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~  180 (256)
T PRK07408        101 TVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLP  180 (256)
T ss_pred             eeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccC
Confidence            999999999999999999999999999999999999999999999999865  34568999999865443  36777777


Q ss_pred             CCCC
Q 011324          479 LLSH  482 (488)
Q Consensus       479 D~s~  482 (488)
                      |+..
T Consensus       181 d~~~  184 (256)
T PRK07408        181 DPRY  184 (256)
T ss_pred             Cccc
Confidence            7653

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=99.96  E-value=7.4e-29  Score=244.72  Aligned_cols=177  Identities=27%  Similarity=0.430  Sum_probs=159.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHH
Q 011324          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (488)
Q Consensus       264 i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~s  343 (488)
                      .+++|+||++||.+|+.+++.                                        ++..|++.||..|.++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence            467899999999888776543                                        2348999999999999999


Q ss_pred             HHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHH
Q 011324          344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  423 (488)
Q Consensus       344 IAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~  423 (488)
                      +|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|++++|++. .+++|.++.+.+.++.++...
T Consensus        50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~  128 (254)
T TIGR02850        50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK  128 (254)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999975 789999999999999999999


Q ss_pred             HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCC--CccccccCCCC
Q 011324          424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQVMPLLLS  481 (488)
Q Consensus       424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~tl~e~i~D~s  481 (488)
                      +..++|+.||.+|||+.||+++++|..++.....++|||.++.++++  .++.+.+.|+.
T Consensus       129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~  188 (254)
T TIGR02850       129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEK  188 (254)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCcc
Confidence            99999999999999999999999999999988889999999865443  35678887754

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.

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=99.96  E-value=7.7e-28  Score=237.79  Aligned_cols=177  Identities=27%  Similarity=0.448  Sum_probs=158.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHH
Q 011324          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (488)
Q Consensus       264 i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~s  343 (488)
                      ..++|+|+++|+..|+.+++.                                        ++..|++.||..|.++|++
T Consensus        13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~   52 (258)
T PRK08215         13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS   52 (258)
T ss_pred             CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence            356789999999888876543                                        2348999999999999999


Q ss_pred             HHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHH
Q 011324          344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  423 (488)
Q Consensus       344 IAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~  423 (488)
                      +|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.+++|++. .+++|.++.....++.++...
T Consensus        53 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~  131 (258)
T PRK08215         53 VIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREK  131 (258)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999985 789999999999999999999


Q ss_pred             HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCC--ccccccCCCC
Q 011324          424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQVMPLLLS  481 (488)
Q Consensus       424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~--tl~e~i~D~s  481 (488)
                      +..++++.|+.+|||+.||+++++|...+.....++|||.+++++++.  ++.|.++|+.
T Consensus       132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~  191 (258)
T PRK08215        132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEK  191 (258)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCcc
Confidence            999999999999999999999999999998888889999998655432  4667777654

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=99.95  E-value=2.3e-26  Score=230.71  Aligned_cols=192  Identities=35%  Similarity=0.557  Sum_probs=173.1

Q ss_pred             CCCCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHH
Q 011324          250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS  329 (488)
Q Consensus       250 ~~~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~A  329 (488)
                      .....+.+++||.+|+.+|.||.++|.+|+..++.                                        ++..|
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~a   47 (285)
T TIGR02394         8 ETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFEA   47 (285)
T ss_pred             ccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHHH
Confidence            34468899999999999999999999988887654                                        22489


Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011324          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (488)
Q Consensus       330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~  409 (488)
                      ++.||..|.++|+++|++|.+++.+++||+||||||||+|+++||+.+|++|+||+.|||+.++.++++++.+.+++|.+
T Consensus        48 ~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~  127 (285)
T TIGR02394        48 RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVH  127 (285)
T ss_pred             HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCCC
Q 011324          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLLS  481 (488)
Q Consensus       410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~s  481 (488)
                      +...++.+.+..+.+...+++.|+..|+|+.+|++++.|..++..+...+|||.++.+++..++.+.+.++.
T Consensus       128 ~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~  199 (285)
T TIGR02394       128 VIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQ  199 (285)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCC
Confidence            999999888887777788888999999999999999999999998888999999887666556667766553

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).

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=99.95  E-value=1e-26  Score=230.57  Aligned_cols=155  Identities=22%  Similarity=0.328  Sum_probs=137.6

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011324          325 SGN-SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (488)
Q Consensus       325 ~Gd-~ArekLIesnlrLV~sIAkry~~---~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~  400 (488)
                      .|+ .|++.||..|+++|+++|++|.+   .+++++||+|||+||||+|+++|||++|++|+|||+||||++|.+++|++
T Consensus        19 ~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~   98 (257)
T PRK05911         19 TQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQ   98 (257)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhc
Confidence            445 89999999999999999999852   35689999999999999999999999999999999999999999999998


Q ss_pred             cCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC--CCccccccCCC--C--CCCccc
Q 011324          401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--D--QDTTFQ  474 (488)
Q Consensus       401 sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i~~--d--~~~tl~  474 (488)
                      .   ++|+++.+.++++.++...|.+.+|+.|+.+|||+.||+++++|..++..++  ..+|||.++..  +  ++.++.
T Consensus        99 ~---~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~  175 (257)
T PRK05911         99 D---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALE  175 (257)
T ss_pred             C---CCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchh
Confidence            6   4899999999999999999999999999999999999999999999987664  46899988643  2  234678


Q ss_pred             cccCCCCC
Q 011324          475 VMPLLLSH  482 (488)
Q Consensus       475 e~i~D~s~  482 (488)
                      +.++|+..
T Consensus       176 ~~l~d~~~  183 (257)
T PRK05911        176 ERIADERA  183 (257)
T ss_pred             hhccCCCC
Confidence            88888654

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=99.94  E-value=2.2e-26  Score=223.12  Aligned_cols=159  Identities=26%  Similarity=0.392  Sum_probs=145.1

Q ss_pred             HhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011324          322 ELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (488)
Q Consensus       322 ~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~  400 (488)
                      +++.|+ .|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.+++|++
T Consensus         4 ~~~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~   83 (231)
T TIGR02885         4 LAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDD   83 (231)
T ss_pred             HHHcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhC
Confidence            344555 8999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCC--CccccccC
Q 011324          401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQVMPL  478 (488)
Q Consensus       401 sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~tl~e~i~  478 (488)
                      . .+++|+++.....++.++...+..++|+.||.+|||+.||+++++|..++..+....|||.+++++++  .++.|.+.
T Consensus        84 ~-~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~  162 (231)
T TIGR02885        84 G-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIA  162 (231)
T ss_pred             C-CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcC
Confidence            6 78999999999999999999999999999999999999999999999999888889999999876543  25667777


Q ss_pred             CCC
Q 011324          479 LLS  481 (488)
Q Consensus       479 D~s  481 (488)
                      |+.
T Consensus       163 ~~~  165 (231)
T TIGR02885       163 DKG  165 (231)
T ss_pred             CCC
Confidence            763

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.

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

Probab=99.94  E-value=6.8e-26  Score=223.90  Aligned_cols=152  Identities=28%  Similarity=0.506  Sum_probs=139.4

Q ss_pred             HHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC-CHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (488)
Q Consensus       318 eLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~-d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~  395 (488)
                      .++...+.|+ .++ .||+.|+|||.++|++|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||..+|+++|++
T Consensus        13 ~~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d   91 (247)
T COG1191          13 KLLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILD   91 (247)
T ss_pred             HHHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHH
Confidence            3455566677 788 9999999999999999998887 999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC--CCccccccCCCCCCC
Q 011324          396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDT  471 (488)
Q Consensus       396 ~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i~~d~~~  471 (488)
                      ++|++. .+++|+.+.+..+++..+...|..++||.||.+|||+.|||+.++|...+....  ..+|+|..+..+++.
T Consensus        92 ~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~  168 (247)
T COG1191          92 YLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDD  168 (247)
T ss_pred             HHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhcccccc
Confidence            999999 999999999999999999999999999999999999999999999999988664  789999877654433

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=99.93  E-value=3.7e-25  Score=220.04  Aligned_cols=180  Identities=21%  Similarity=0.303  Sum_probs=153.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHH
Q 011324          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (488)
Q Consensus       264 i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~s  343 (488)
                      .+.+|+||.++|.+|+..++.                                       .++..+++.|+..|.++|+.
T Consensus         6 ~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~~   46 (268)
T PRK06288          6 SGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVKY   46 (268)
T ss_pred             cCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHH
Confidence            378999999999999987653                                       12347999999999999999


Q ss_pred             HHHHcc-C--CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHH
Q 011324          344 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA  420 (488)
Q Consensus       344 IAkry~-~--~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka  420 (488)
                      +|++|. +  .+.+++||+||||+|||+++++||+.+|++|+||+++||||.|.+++|+..   ++|+++.....++.++
T Consensus        47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~  123 (268)
T PRK06288         47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERA  123 (268)
T ss_pred             HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHH
Confidence            999986 2  567899999999999999999999998999999999999999999999754   6899999999999999


Q ss_pred             HHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCCC---CCccccccCCCC-CCCC
Q 011324          421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQVMPLLLS-HLPS  485 (488)
Q Consensus       421 ~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~---~~tl~e~i~D~s-~~pe  485 (488)
                      ...|...+++.||.+|||+.+|++.+.|..++...  ...+|||.++..++   ..++.+.++++. .+|+
T Consensus       124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe  194 (268)
T PRK06288        124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPD  194 (268)
T ss_pred             HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHH
Confidence            99999999999999999999999999999998754  45799999874222   245777776643 3443

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=99.93  E-value=1.4e-24  Score=213.78  Aligned_cols=144  Identities=23%  Similarity=0.364  Sum_probs=135.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl  406 (488)
                      ..|+++||..|.++|+++|++|.+++.+++||+||||+|||+++++||++.|.+|.||+++||+|.|.+++|++.+.+++
T Consensus        28 ~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri  107 (255)
T TIGR02941        28 GEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHV  107 (255)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999989999


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCCCC
Q 011324          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQD  470 (488)
Q Consensus       407 P~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~  470 (488)
                      |.++.+...+++++...+...+|+.|+.+|||+.||++.+.+..++...  ...+|||.+++.+++
T Consensus       108 ~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~  173 (255)
T TIGR02941       108 PRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD  173 (255)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence            9999999999999999999999999999999999999999999887654  467899999876544

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

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

Probab=99.93  E-value=9.1e-25  Score=211.07  Aligned_cols=153  Identities=25%  Similarity=0.425  Sum_probs=139.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl  406 (488)
                      ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+|+++||+.+|.+|+||+++||+|.|.++++++.+.+++
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            36899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC--CccccccCCCCC--CCccccccCC
Q 011324          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQ--DTTFQVMPLL  479 (488)
Q Consensus       407 P~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~--~lSLD~~i~~d~--~~tl~e~i~D  479 (488)
                      |.++...+.+++++...+.+.+++.|+.+|||+.||+++++|..++.....  .+|||.++.+++  +.++.+.+.+
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~  158 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGD  158 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCC
Confidence            999999999999999999999999999999999999999999998886655  899999987332  2345555554

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=99.92  E-value=1.6e-23  Score=206.49  Aligned_cols=178  Identities=26%  Similarity=0.382  Sum_probs=155.7

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHH
Q 011324          262 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV  341 (488)
Q Consensus       262 ~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV  341 (488)
                      +.-+..|.||.+++.+|+..++.                                        ++..|++.||..|.++|
T Consensus         6 ~~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v   45 (252)
T PRK05572          6 KNKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLV   45 (252)
T ss_pred             ccCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHH
Confidence            34467899999988877765432                                        23489999999999999


Q ss_pred             HHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHH
Q 011324          342 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK  421 (488)
Q Consensus       342 ~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~  421 (488)
                      +++|++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||+|.|.+++|+.. .+++|..+.....+++++.
T Consensus        46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~  124 (252)
T PRK05572         46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK  124 (252)
T ss_pred             HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999988889999999999999999999885 7899999999999999999


Q ss_pred             HHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCC--CccccccCCC
Q 011324          422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQVMPLLL  480 (488)
Q Consensus       422 ~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~tl~e~i~D~  480 (488)
                      ..+..++++.|+..|||+.+|++++.|..++.......||+.++.+++.  .++.|.+.++
T Consensus       125 ~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~  185 (252)
T PRK05572        125 DELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQ  185 (252)
T ss_pred             HHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCC
Confidence            9998888999999999999999999999998888888999998865543  2345555554

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=99.91  E-value=1.4e-23  Score=206.61  Aligned_cols=161  Identities=22%  Similarity=0.283  Sum_probs=139.7

Q ss_pred             HHHHHHHh-hhcH-HHHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011324          316 CRDLKSEL-HSGN-SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (488)
Q Consensus       316 eeeLi~~l-~~Gd-~ArekLIesnlrLV~sIAkry~~---~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIR  390 (488)
                      +..|+.++ ..|+ .|++.||..|.++|+++|++|.+   ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+
T Consensus         8 e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~ir   87 (251)
T PRK07670          8 EQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIR   87 (251)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence            45666664 4445 89999999999999999999965   6889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH--HhCCCccccccCCCC
Q 011324          391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWAD  468 (488)
Q Consensus       391 naI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~--~ar~~lSLD~~i~~d  468 (488)
                      |.|++++|++.   ++|..+.+.+.+++++...+.+.+|+.|+.+|||+.||+++++|+.++.  .....+|||.++.++
T Consensus        88 n~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~  164 (251)
T PRK07670         88 GAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQ  164 (251)
T ss_pred             HHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCC
Confidence            99999999876   6999999999999999999999999999999999999999999999986  345789999998655


Q ss_pred             CCC-ccccccCC
Q 011324          469 QDT-TFQVMPLL  479 (488)
Q Consensus       469 ~~~-tl~e~i~D  479 (488)
                      ++. .+.+.+.|
T Consensus       165 ~~~~~~~~~~~~  176 (251)
T PRK07670        165 DDGENVSVTIRD  176 (251)
T ss_pred             CCcchhhhhhcC
Confidence            432 33344433

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=99.91  E-value=7.2e-23  Score=201.96  Aligned_cols=143  Identities=24%  Similarity=0.375  Sum_probs=133.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl  406 (488)
                      ..|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.+++|++...+++
T Consensus        28 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i  107 (257)
T PRK08583         28 EEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHV  107 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCC
Confidence            48999999999999999999999999999999999999999999999999888999999999999999999999999999


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCCC
Q 011324          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ  469 (488)
Q Consensus       407 P~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~  469 (488)
                      |+++.+..+++..+...+...+++.|+.+|+|+.+|++.+.|..++...  ...+|+|.+++.++
T Consensus       108 ~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~  172 (257)
T PRK08583        108 PRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADS  172 (257)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCC
Confidence            9999999999999999998888999999999999999999998887654  46789999886544

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=99.90  E-value=5.9e-23  Score=200.86  Aligned_cols=139  Identities=22%  Similarity=0.309  Sum_probs=124.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011324          328 SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~---~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i  404 (488)
                      .....|+..|+++|.++|++|.+   .+.+.+||+|||+||||+|+++||+.+| +|+||++|||||+|.+++|+..   
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            34567899999999999999875   4679999999999999999999998665 8999999999999999999865   


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH--hCCCccccccCCCCCC
Q 011324          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQD  470 (488)
Q Consensus       405 rlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~--ar~~lSLD~~i~~d~~  470 (488)
                      +.|+.+....++++++...+.+.+|+.|+.+|||+.||+++++|..++..  +...+|||.+++++++
T Consensus        91 ~~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~  158 (231)
T PRK12427         91 WRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAH  158 (231)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCc
Confidence            57999999999999999999999999999999999999999999998764  4578999999876543

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

Probab=99.89  E-value=9.6e-23  Score=197.03  Aligned_cols=150  Identities=21%  Similarity=0.327  Sum_probs=130.7

Q ss_pred             HHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011324          333 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (488)
Q Consensus       333 LIesnlrLV~sIAkry~~---~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~  409 (488)
                      ||..|.++|+++|++|.+   ++.+++||+||||+|||+++++||+.+|++|+||+++||+|.|++++|+..   ++|..
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            688999999999999986   789999999999999999999999999999999999999999999999865   68999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCC-CCCccccccCC-CCCCCC
Q 011324          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWAD-QDTTFQVMPLL-LSHLPS  485 (488)
Q Consensus       410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d-~~~tl~e~i~D-~s~~pe  485 (488)
                      +...++++.++...+...+|+.|+.+|||+.||++++.|..++..+  ...+|+|..+.++ +..++.+++++ ...+|+
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE  157 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence            9999999999999999999999999999999999999999998644  4568899876543 33466666663 333443

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.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=99.87  E-value=1.9e-21  Score=189.54  Aligned_cols=143  Identities=21%  Similarity=0.389  Sum_probs=128.6

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHcc---CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011324          325 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (488)
Q Consensus       325 ~Gd~ArekLIesnlrLV~sIAkry~---~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~s  401 (488)
                      .|.-+++.||..|.++|+.+|++|.   +++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|++.
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            5667999999999999999999997   6789999999999999999999999999999999999999999999999976


Q ss_pred             CCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCCCC
Q 011324          402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQD  470 (488)
Q Consensus       402 r~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~  470 (488)
                         ++|..+.....++.++...+.+.+++.|+.+|||+.||+++++|..++...  ...+|++..++++++
T Consensus        85 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~  152 (236)
T PRK06986         85 ---WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGD  152 (236)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCc
Confidence               478888888888888888898899999999999999999999999988743  456789988766544

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.85  E-value=2.1e-20  Score=182.11  Aligned_cols=163  Identities=21%  Similarity=0.342  Sum_probs=127.9

Q ss_pred             HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHH
Q 011324          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (488)
Q Consensus       256 ~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIe  335 (488)
                      .|..|+.+++..|+||+++|..|+..++.                                        ++..|++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence            67889999999999999999887765443                                        23489999999


Q ss_pred             HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---cc------
Q 011324          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI---RL------  406 (488)
Q Consensus       336 snlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i---rl------  406 (488)
                      .|.++|+++|.+|.+++.+++|++|||||+||+++++||+++|.+|.||+++|++|.|++++|+..+..   .+      
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            999999999999999999999999999999999999999988889999999999999999999765321   00      


Q ss_pred             -------------c------hhH-H--HHHHHHHHHHHHHH--------Hhc----CCCCcHHHHHHHhCCCHHHHHHHH
Q 011324          407 -------------P------ENI-Y--TLLSKVLEAKRLYI--------QEG----NHSPDKEDLARRVGITVEKLERLI  452 (488)
Q Consensus       407 -------------P------~~v-~--e~l~kI~ka~~~L~--------~el----gr~pS~eEIAe~LGIS~etVk~~L  452 (488)
                                   +      ... .  .....+.++...|+        ..+    ..+.|++|||+.||+|.++|+.++
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                         0      000 0  11112333332221        112    357899999999999999999998


Q ss_pred             HHhCCC
Q 011324          453 FITRMP  458 (488)
Q Consensus       453 ~~ar~~  458 (488)
                      ++|+..
T Consensus       217 ~rA~~k  222 (233)
T PRK05803        217 KRALKK  222 (233)
T ss_pred             HHHHHH
Confidence            887654

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.77  E-value=7.4e-18  Score=163.83  Aligned_cols=141  Identities=25%  Similarity=0.392  Sum_probs=108.9

Q ss_pred             HHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHH
Q 011324          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  396 (488)
Q Consensus       318 eLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~  396 (488)
                      .|+.+++.|+ .|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.|+++
T Consensus        41 ~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~  120 (234)
T PRK08301         41 YLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMY  120 (234)
T ss_pred             HHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHH
Confidence            3444444555 899999999999999999999999999999999999999999999999888899999999999999999


Q ss_pred             HHHhcCCcc---c--c--------------------h---hHH---HHHHHHHHHHHHHHH--------hc----CCCCc
Q 011324          397 IFQHSRTIR---L--P--------------------E---NIY---TLLSKVLEAKRLYIQ--------EG----NHSPD  433 (488)
Q Consensus       397 IRk~sr~ir---l--P--------------------~---~v~---e~l~kI~ka~~~L~~--------el----gr~pS  433 (488)
                      +|++.+...   +  +                    .   ...   .....+.+++..|+.        .+    ..+.|
T Consensus       121 lRk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s  200 (234)
T PRK08301        121 LRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKT  200 (234)
T ss_pred             HHHHhccccccccccccccccCCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCC
Confidence            998654211   0  0                    0   000   011123344433321        12    35889


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          434 KEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       434 ~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      ++|||+.||+|+++|+..+++++..
T Consensus       201 ~~EIA~~lgis~~tVk~~~~rA~~~  225 (234)
T PRK08301        201 QKEVADMLGISQSYISRLEKRIIKR  225 (234)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999888654

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.77  E-value=9.1e-18  Score=163.19  Aligned_cols=140  Identities=24%  Similarity=0.422  Sum_probs=107.1

Q ss_pred             HHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011324          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  397 (488)
Q Consensus       319 Li~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~I  397 (488)
                      |+.+++.|+ .|++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++++|+++++.+|.||+++|++|.|++++
T Consensus        38 li~~~~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~  117 (227)
T TIGR02846        38 YLDRLKEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHL  117 (227)
T ss_pred             HHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHH
Confidence            333334455 8999999999999999999999999999999999999999999999998888899999999999999999


Q ss_pred             HHhcCCcc-c----------------------c-----hh---HHHHHHHHHHHHHHHH--------Hhc----CCCCcH
Q 011324          398 FQHSRTIR-L----------------------P-----EN---IYTLLSKVLEAKRLYI--------QEG----NHSPDK  434 (488)
Q Consensus       398 Rk~sr~ir-l----------------------P-----~~---v~e~l~kI~ka~~~L~--------~el----gr~pS~  434 (488)
                      |+..+..+ .                      +     ..   ..+....+.+++..|.        ..+    ..+.|+
T Consensus       118 Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~  197 (227)
T TIGR02846       118 RALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQ  197 (227)
T ss_pred             HHHhccccceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCH
Confidence            98754211 0                      0     00   0011122333333322        122    257899


Q ss_pred             HHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          435 EDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       435 eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      +|||+.||+++++|+.++++++..
T Consensus       198 ~EIAe~lgis~~tV~~~~~rAl~~  221 (227)
T TIGR02846       198 REIAKILGISRSYVSRIEKRALMK  221 (227)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHH
Confidence            999999999999999999887654

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.

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.76  E-value=1e-17  Score=163.43  Aligned_cols=129  Identities=19%  Similarity=0.280  Sum_probs=111.1

Q ss_pred             HhhhcHHHHHHHHHHHHHHHHHHHHHccCCC--CCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011324          322 ELHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ  399 (488)
Q Consensus       322 ~l~~Gd~ArekLIesnlrLV~sIAkry~~~g--~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk  399 (488)
                      .++.|+..++.||..|.|+|.++|.+|.+++  .+.+|++|+|+||||+|+++||+++|.+|.|||.+||+++|++++|+
T Consensus         3 ~~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk   82 (218)
T TIGR02895         3 PIQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRK   82 (218)
T ss_pred             hhhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4567886699999999999999999998775  58999999999999999999999999999999999999999999999


Q ss_pred             hc---CCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHH------hCCCHHHHHH
Q 011324          400 HS---RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR------VGITVEKLER  450 (488)
Q Consensus       400 ~s---r~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~------LGIS~etVk~  450 (488)
                      ..   ..+++|....+....+..+...+....++.++.+||+..      .||+.+.+-+
T Consensus        83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~  142 (218)
T TIGR02895        83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK  142 (218)
T ss_pred             cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh
Confidence            87   456788766666667777777888888889999999853      4888776643

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).

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.74  E-value=4.7e-17  Score=158.86  Aligned_cols=135  Identities=24%  Similarity=0.379  Sum_probs=105.8

Q ss_pred             hhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324          324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (488)
Q Consensus       324 ~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr  402 (488)
                      ..|+ .|++.|+..|.+.|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+++++|++.+
T Consensus        47 ~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r  126 (234)
T TIGR02835        47 TQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNK  126 (234)
T ss_pred             HcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence            3444 899999999999999999999999999999999999999999999998878889999999999999999998764


Q ss_pred             Ccc-cc----------------------h-----hH---HHHHHHHHHHHHHHHH--------hc----CCCCcHHHHHH
Q 011324          403 TIR-LP----------------------E-----NI---YTLLSKVLEAKRLYIQ--------EG----NHSPDKEDLAR  439 (488)
Q Consensus       403 ~ir-lP----------------------~-----~v---~e~l~kI~ka~~~L~~--------el----gr~pS~eEIAe  439 (488)
                      ... .+                      .     ..   ......+.+++..|+.        .+    ..+.|++|||+
T Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~  206 (234)
T TIGR02835       127 TRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVAD  206 (234)
T ss_pred             ccCcccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHH
Confidence            211 00                      0     00   0011224444443321        12    25789999999


Q ss_pred             HhCCCHHHHHHHHHHhCCC
Q 011324          440 RVGITVEKLERLIFITRMP  458 (488)
Q Consensus       440 ~LGIS~etVk~~L~~ar~~  458 (488)
                      .||+|+++|+..+++++..
T Consensus       207 ~Lgis~~tV~~~l~ra~~~  225 (234)
T TIGR02835       207 MLGISQSYISRLEKRILKR  225 (234)
T ss_pred             HHCCCHHHHHHHHHHHHHH
Confidence            9999999999999887643

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.

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.74  E-value=2.3e-17  Score=156.20  Aligned_cols=146  Identities=23%  Similarity=0.284  Sum_probs=114.0

Q ss_pred             cCCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (488)
Q Consensus       313 gm~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn  391 (488)
                      .++++.|+..++.|+ .|++.|+..|.++|+.+|++|.+++.+++|++||+|++||+++.+||+.+|.+|.||++.+++|
T Consensus         8 ~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n   87 (208)
T PRK08295          8 ELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITR   87 (208)
T ss_pred             CCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHH
Confidence            456778888888888 8999999999999999999999999999999999999999999999998778999999999999


Q ss_pred             HHHHHHHHhcCCccc--------------------------------chh-H--HHHH--------HHHHHHHHH-HHHh
Q 011324          392 TIRKAIFQHSRTIRL--------------------------------PEN-I--YTLL--------SKVLEAKRL-YIQE  427 (488)
Q Consensus       392 aI~~~IRk~sr~irl--------------------------------P~~-v--~e~l--------~kI~ka~~~-L~~e  427 (488)
                      .+.+++++..+..+.                                |.. +  .+..        ..+....+. +.. 
T Consensus        88 ~~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-  166 (208)
T PRK08295         88 QIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-  166 (208)
T ss_pred             HHHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-
Confidence            999999864332111                                000 0  0011        111112122 222 


Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          428 GNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      +..+.+++|||+.||+|+++|+..+++++..+
T Consensus       167 ~~e~~s~~EIA~~lgis~~tV~~~l~rar~~L  198 (208)
T PRK08295        167 YLDGKSYQEIAEELNRHVKSIDNALQRVKRKL  198 (208)
T ss_pred             HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            44578999999999999999999999887653

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.74  E-value=2.6e-17  Score=154.50  Aligned_cols=146  Identities=23%  Similarity=0.295  Sum_probs=113.3

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      |++.+|+..++.|+ .|++.||..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++..+..|.||++.+|++.
T Consensus         4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~   83 (198)
T TIGR02859         4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ   83 (198)
T ss_pred             cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence            56788899999988 89999999999999999999999999999999999999999999999987779999999999999


Q ss_pred             HHHHHHHhcCCcc--------------------------------cchhH---HHHHHHHHHHHHH--------HHHhcC
Q 011324          393 IRKAIFQHSRTIR--------------------------------LPENI---YTLLSKVLEAKRL--------YIQEGN  429 (488)
Q Consensus       393 I~~~IRk~sr~ir--------------------------------lP~~v---~e~l~kI~ka~~~--------L~~elg  429 (488)
                      |++++++..+..+                                -|...   .+....+.+++..        +...+-
T Consensus        84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~  163 (198)
T TIGR02859        84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL  163 (198)
T ss_pred             HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            9888874311100                                01100   0111122233332        222233


Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .+.|++|||+.||+|+++|+.++++++..+
T Consensus       164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L  193 (198)
T TIGR02859       164 DGKSYQEIACDLNRHVKSIDNALQRVKRKL  193 (198)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            478999999999999999999999887653

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.

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.72  E-value=7.3e-17  Score=150.93  Aligned_cols=145  Identities=17%  Similarity=0.194  Sum_probs=114.6

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      ++++.|+..+..|+ .|++.|+..|.++|+.+|++|.+++.+++|++||+|++||+++.+|++. +.+|.+|++.+++|.
T Consensus         5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~   83 (186)
T PRK05602          5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL   83 (186)
T ss_pred             ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence            56778888888888 8999999999999999999999999999999999999999999999975 457999999999999


Q ss_pred             HHHHHHHhcCCcc--c---------chh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHH
Q 011324          393 IRKAIFQHSRTIR--L---------PEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLER  450 (488)
Q Consensus       393 I~~~IRk~sr~ir--l---------P~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~  450 (488)
                      +.+++|++.....  +         |..   ..+....+.+++..|.        ..+..+.+++|||+.||+|..+|+.
T Consensus        84 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~  163 (186)
T PRK05602         84 CYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALES  163 (186)
T ss_pred             HHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHH
Confidence            9999998764211  1         111   0011122333333322        2233478999999999999999999


Q ss_pred             HHHHhCCCc
Q 011324          451 LIFITRMPL  459 (488)
Q Consensus       451 ~L~~ar~~l  459 (488)
                      .+++++..+
T Consensus       164 ~l~Rar~~L  172 (186)
T PRK05602        164 LLARGRRAL  172 (186)
T ss_pred             HHHHHHHHH
Confidence            999987654

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.70  E-value=1.9e-16  Score=149.11  Aligned_cols=144  Identities=15%  Similarity=0.196  Sum_probs=114.7

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      ++++.|+..+..|+ .|++.|+..|.+.|+++|+++.++..+++|++||+|+++|+++++|++.  ..|.+|++++++|.
T Consensus        11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~   88 (194)
T PRK12513         11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL   88 (194)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence            45788999999888 8999999999999999999999999999999999999999999999974  36999999999999


Q ss_pred             HHHHHHHhcCCcccc-----------------hhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCC
Q 011324          393 IRKAIFQHSRTIRLP-----------------ENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGIT  444 (488)
Q Consensus       393 I~~~IRk~sr~irlP-----------------~~v---~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS  444 (488)
                      +++++|+..+....+                 ...   .+....+.+++..|...        +..+.|++|||+.||||
T Consensus        89 ~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis  168 (194)
T PRK12513         89 LIDHWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVP  168 (194)
T ss_pred             HHHHHHHhccccccccccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHCCC
Confidence            999999876533221                 000   01122344444444322        22467999999999999


Q ss_pred             HHHHHHHHHHhCCCc
Q 011324          445 VEKLERLIFITRMPL  459 (488)
Q Consensus       445 ~etVk~~L~~ar~~l  459 (488)
                      +++|+..+++|+..+
T Consensus       169 ~~tV~~~l~ra~~~L  183 (194)
T PRK12513        169 EETVKSRLRYALQKL  183 (194)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999887654

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.69  E-value=2.4e-16  Score=148.42  Aligned_cols=144  Identities=14%  Similarity=0.220  Sum_probs=111.8

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCC---CCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV  389 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g---~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wI  389 (488)
                      ++++.|+..+..|+ .|++.|+..|.++|++++.++.+++   .+++|++||++++||+++++|++..+ .|.||++.++
T Consensus         3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia   81 (189)
T PRK06811          3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS   81 (189)
T ss_pred             CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence            67788999999988 8999999999999999999998753   57999999999999999999997544 7999999999


Q ss_pred             HHHHHHHHHHhcCCcccc---h-------h-------------HHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCH
Q 011324          390 RQTIRKAIFQHSRTIRLP---E-------N-------------IYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITV  445 (488)
Q Consensus       390 RnaI~~~IRk~sr~irlP---~-------~-------------v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~  445 (488)
                      +|.+++++|++.+.....   .       .             +...+.++....+.+. ..+..+.+++|||+.||+|.
T Consensus        82 rn~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~  161 (189)
T PRK06811         82 KYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTR  161 (189)
T ss_pred             HHHHHHHHHHhccccccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCH
Confidence            999999999876432211   0       0             1112222222222222 12234789999999999999


Q ss_pred             HHHHHHHHHhCCC
Q 011324          446 EKLERLIFITRMP  458 (488)
Q Consensus       446 etVk~~L~~ar~~  458 (488)
                      .+|+..+++++..
T Consensus       162 ~~V~~~l~Ra~~~  174 (189)
T PRK06811        162 SAIDNRLSRGRKK  174 (189)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999988653

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.69  E-value=2.3e-16  Score=149.08  Aligned_cols=144  Identities=9%  Similarity=0.069  Sum_probs=112.2

Q ss_pred             CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (488)
Q Consensus       315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI  393 (488)
                      +...|+..+..|+ .+++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++.+||+.+| .|.+|++.+++|.+
T Consensus        16 ~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~   94 (194)
T PRK09646         16 DLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRA   94 (194)
T ss_pred             cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHH
Confidence            4567888888887 899999999999999999999999999999999999999999999998655 79999999999999


Q ss_pred             HHHHHHhcCCccc---------c------hh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011324          394 RKAIFQHSRTIRL---------P------EN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK  447 (488)
Q Consensus       394 ~~~IRk~sr~irl---------P------~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~et  447 (488)
                      ++++|++.+..+.         .      ..   ..+....+.+++..|.        ..+..+.+++|||+.||+++++
T Consensus        95 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~t  174 (194)
T PRK09646         95 VDRVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGT  174 (194)
T ss_pred             HHHHHhhccccccccccccccccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHh
Confidence            9999986532110         0      00   0011122333333222        2233478999999999999999


Q ss_pred             HHHHHHHhCCCc
Q 011324          448 LERLIFITRMPL  459 (488)
Q Consensus       448 Vk~~L~~ar~~l  459 (488)
                      |+..+++++..+
T Consensus       175 Vk~~l~ra~~~L  186 (194)
T PRK09646        175 VKTRMRDGLIRL  186 (194)
T ss_pred             HHHHHHHHHHHH
Confidence            999999887543

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

Probab=99.68  E-value=4.5e-16  Score=143.25  Aligned_cols=144  Identities=15%  Similarity=0.169  Sum_probs=113.8

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      |++++|+..+..|+ .|++.|+..|.+.|++++.++.++..+++|++||+|+.+|+.+++|++.  ..|.||++.+++|.
T Consensus         1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~   78 (169)
T TIGR02954         1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE   78 (169)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence            45678888888888 8999999999999999999999999999999999999999999999974  36999999999999


Q ss_pred             HHHHHHHhcCCcccch-----------------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324          393 IRKAIFQHSRTIRLPE-----------------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFI  454 (488)
Q Consensus       393 I~~~IRk~sr~irlP~-----------------~v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~  454 (488)
                      +++++|+..+...++.                 .+...+.++....+++. ..+..+.+++|||+.||+|+++|+..+.+
T Consensus        79 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~R  158 (169)
T TIGR02954        79 CIDLLKKKKKVIPFDPNTSIEKGECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHR  158 (169)
T ss_pred             HHHHHHhcCCcCccccccccccchhhhchHHHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            9999998765332211                 01122223322222222 22334789999999999999999999998


Q ss_pred             hCCCc
Q 011324          455 TRMPL  459 (488)
Q Consensus       455 ar~~l  459 (488)
                      ++..+
T Consensus       159 a~~~L  163 (169)
T TIGR02954       159 ALKKL  163 (169)
T ss_pred             HHHHH
Confidence            87543

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.

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.68  E-value=3.9e-16  Score=145.07  Aligned_cols=142  Identities=12%  Similarity=0.178  Sum_probs=110.2

Q ss_pred             HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHH
Q 011324          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  394 (488)
Q Consensus       316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~  394 (488)
                      ++.|+..++.|+ .+++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++..  .|.+|++.+++|.+.
T Consensus         5 ~~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~   82 (187)
T TIGR02948         5 IKKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTI   82 (187)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHH
Confidence            356777888888 89999999999999999999999999999999999999999999999865  599999999999999


Q ss_pred             HHHHHhcCCcccc----------------------hhH-H--HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHh
Q 011324          395 KAIFQHSRTIRLP----------------------ENI-Y--TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRV  441 (488)
Q Consensus       395 ~~IRk~sr~irlP----------------------~~v-~--e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~L  441 (488)
                      +++|+..+.....                      ... .  +....+.++...|+        ..+..+.+++|||+.|
T Consensus        83 ~~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l  162 (187)
T TIGR02948        83 DRLRKRKPDFYLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEIL  162 (187)
T ss_pred             HHHHhhcccccccccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHH
Confidence            9999865421100                      000 0  01112333333322        1133478999999999


Q ss_pred             CCCHHHHHHHHHHhCCCc
Q 011324          442 GITVEKLERLIFITRMPL  459 (488)
Q Consensus       442 GIS~etVk~~L~~ar~~l  459 (488)
                      |+++++|+..+++++..+
T Consensus       163 gis~~~v~~~l~Rar~~L  180 (187)
T TIGR02948       163 DLPVGTVKTRIHRGREAL  180 (187)
T ss_pred             CCCHHHHHHHHHHHHHHH
Confidence            999999999999887543

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

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.67  E-value=5e-16  Score=144.87  Aligned_cols=145  Identities=14%  Similarity=0.126  Sum_probs=112.7

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      +++.+|+..+..|+ .|++.|+..|.+.|+.++++|.+++.+++|++||+|+++|+++++|++.. ..|.+|++++++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~   86 (186)
T PRK13919          8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHA   86 (186)
T ss_pred             cCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHH
Confidence            46778888888888 89999999999999999999999999999999999999999999998754 36999999999999


Q ss_pred             HHHHHHHhcCCcc-c------------c-----hhHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011324          393 IRKAIFQHSRTIR-L------------P-----ENIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE  446 (488)
Q Consensus       393 I~~~IRk~sr~ir-l------------P-----~~v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~e  446 (488)
                      +++++|+..+... +            +     .........+.+++..|.        ..+..+.+++|||+.||||++
T Consensus        87 ~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~  166 (186)
T PRK13919         87 AVDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLG  166 (186)
T ss_pred             HHHHHHhhhcccccccccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence            9999998653211 0            0     000011112333333332        123347899999999999999


Q ss_pred             HHHHHHHHhCCCc
Q 011324          447 KLERLIFITRMPL  459 (488)
Q Consensus       447 tVk~~L~~ar~~l  459 (488)
                      +|+..+++++..+
T Consensus       167 ~V~~~l~ra~~~L  179 (186)
T PRK13919        167 TLKTRARRALSRL  179 (186)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999887543

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.67  E-value=6e-16  Score=145.40  Aligned_cols=145  Identities=13%  Similarity=0.087  Sum_probs=114.5

Q ss_pred             hcCCHHHHHHHhhh---cH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHH
Q 011324          312 IGLSCRDLKSELHS---GN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW  387 (488)
Q Consensus       312 ~gm~eeeLi~~l~~---Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~  387 (488)
                      ..++++.|+..++.   |+ .|++.|+..|.+.|+.+|.+|.++..+++|++||+|++||+++++|++.  ..|.+|+++
T Consensus         6 ~~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~   83 (188)
T PRK09640          6 RELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYS   83 (188)
T ss_pred             CCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHH
Confidence            35778888888875   35 8999999999999999999999999999999999999999999999863  479999999


Q ss_pred             HHHHHHHHHHHHhcCCcccch------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCC
Q 011324          388 WVRQTIRKAIFQHSRTIRLPE------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGIT  444 (488)
Q Consensus       388 wIRnaI~~~IRk~sr~irlP~------------~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS  444 (488)
                      +++|.+++++|+..+......            .   ..+....+.++...|+..        +..+.+++|||+.||||
T Consensus        84 ia~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis  163 (188)
T PRK09640         84 ITYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMG  163 (188)
T ss_pred             HHHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCC
Confidence            999999999997654222110            0   011223345555555432        22367999999999999


Q ss_pred             HHHHHHHHHHhCCC
Q 011324          445 VEKLERLIFITRMP  458 (488)
Q Consensus       445 ~etVk~~L~~ar~~  458 (488)
                      .++|+..+.+|+..
T Consensus       164 ~~tV~~~l~Ra~~~  177 (188)
T PRK09640        164 LSATKMRYKRALDK  177 (188)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999988754

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.67  E-value=7.4e-16  Score=144.51  Aligned_cols=141  Identities=18%  Similarity=0.213  Sum_probs=108.6

Q ss_pred             HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCC----CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (488)
Q Consensus       317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~----g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn  391 (488)
                      ..|+..+..|+ .|++.|+..|.+.|+++|.++.++    +.+++|++||+|++||+++.+|+.. +..|.+|++.+++|
T Consensus        12 ~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n   90 (189)
T PRK09648         12 DALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAH   90 (189)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHH
Confidence            45788888887 899999999999999999998764    4689999999999999999999864 45799999999999


Q ss_pred             HHHHHHHHhcCCcccc--------------hh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011324          392 TIRKAIFQHSRTIRLP--------------EN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE  446 (488)
Q Consensus       392 aI~~~IRk~sr~irlP--------------~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~e  446 (488)
                      .+++++|++.+....+              ..   ..+....+.+++..|+        ..+..+.+++|||+.||+|++
T Consensus        91 ~~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~  170 (189)
T PRK09648         91 KVADAHRAAGRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPG  170 (189)
T ss_pred             HHHHHHHHhCCCccccccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH
Confidence            9999999877532211              00   0111122333333322        223347899999999999999


Q ss_pred             HHHHHHHHhCCC
Q 011324          447 KLERLIFITRMP  458 (488)
Q Consensus       447 tVk~~L~~ar~~  458 (488)
                      +|+..+++++..
T Consensus       171 tV~~~l~Ra~~~  182 (189)
T PRK09648        171 AVRVAQHRALAR  182 (189)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988654

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=6.2e-16  Score=143.64  Aligned_cols=145  Identities=10%  Similarity=0.060  Sum_probs=111.6

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      ++...|+..+..|+ .+++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++.+++|.
T Consensus         4 ~~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~   82 (179)
T PRK12514          4 DDIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNH   82 (179)
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHH
Confidence            34567777777787 89999999999999999999999999999999999999999999998653 46999999999999


Q ss_pred             HHHHHHHhcCCcc-c------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011324          393 IRKAIFQHSRTIR-L------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL  448 (488)
Q Consensus       393 I~~~IRk~sr~ir-l------------P~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etV  448 (488)
                      |++++|++.+... +            |...   .+....+..++..|.        ..+..+.|++|||+.||||+++|
T Consensus        83 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV  162 (179)
T PRK12514         83 AIDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTM  162 (179)
T ss_pred             HHHHHHhcCCcccccccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHH
Confidence            9999998664210 0            1100   011112333333322        22334789999999999999999


Q ss_pred             HHHHHHhCCCc
Q 011324          449 ERLIFITRMPL  459 (488)
Q Consensus       449 k~~L~~ar~~l  459 (488)
                      +..+++++..+
T Consensus       163 ~~~l~Rar~~L  173 (179)
T PRK12514        163 RTWLRRSLLKL  173 (179)
T ss_pred             HHHHHHHHHHH
Confidence            99999987543

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=6.2e-16  Score=144.58  Aligned_cols=144  Identities=11%  Similarity=0.163  Sum_probs=113.3

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      ++..+|+..+..|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++.+++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~   86 (182)
T PRK12537          8 FDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHL   86 (182)
T ss_pred             hhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHH
Confidence            45667888888888 89999999999999999999999999999999999999999999998643 37999999999999


Q ss_pred             HHHHHHHhcCCcccch-------------h---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011324          393 IRKAIFQHSRTIRLPE-------------N---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL  448 (488)
Q Consensus       393 I~~~IRk~sr~irlP~-------------~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etV  448 (488)
                      +++++|++.+......             .   ..+....+.++...|+        .....+.+++|||+.||||+++|
T Consensus        87 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV  166 (182)
T PRK12537         87 ALNVLRDTRREVVLDDDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTV  166 (182)
T ss_pred             HHHHHHhccccCccccchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhH
Confidence            9999999865322110             0   0011222333333322        22334789999999999999999


Q ss_pred             HHHHHHhCCC
Q 011324          449 ERLIFITRMP  458 (488)
Q Consensus       449 k~~L~~ar~~  458 (488)
                      +..+++++..
T Consensus       167 ~~~l~ra~~~  176 (182)
T PRK12537        167 KAWIKRSLKA  176 (182)
T ss_pred             HHHHHHHHHH
Confidence            9999988754

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

Probab=99.66  E-value=9.6e-16  Score=140.13  Aligned_cols=138  Identities=15%  Similarity=0.149  Sum_probs=106.8

Q ss_pred             HHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011324          320 KSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  398 (488)
Q Consensus       320 i~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IR  398 (488)
                      +.++.+|+ .|++.|+..|.+.+++++.++.++..+++|++||+|+++|+++++|+...+ .|.+|++.+++|.+++++|
T Consensus         2 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R   80 (170)
T TIGR02952         2 LERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFR   80 (170)
T ss_pred             hHHHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHH
Confidence            44566677 899999999999999999999988899999999999999999999986544 8999999999999999999


Q ss_pred             HhcCCcccc--------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324          399 QHSRTIRLP--------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIF  453 (488)
Q Consensus       399 k~sr~irlP--------------~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~  453 (488)
                      ++.+....+              ...   .+....+.++...|+        ..+..+.+++|||+.||||+++|+..++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~  160 (170)
T TIGR02952        81 GSKRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQF  160 (170)
T ss_pred             hcCCCCCCcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            876433221              000   011122333333222        2233478999999999999999999999


Q ss_pred             HhCCC
Q 011324          454 ITRMP  458 (488)
Q Consensus       454 ~ar~~  458 (488)
                      +++..
T Consensus       161 ra~~~  165 (170)
T TIGR02952       161 RAIKK  165 (170)
T ss_pred             HHHHH
Confidence            88654

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.

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=8.8e-16  Score=145.33  Aligned_cols=146  Identities=18%  Similarity=0.172  Sum_probs=114.5

Q ss_pred             cCCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (488)
Q Consensus       313 gm~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn  391 (488)
                      .+++..|+.++..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++. ...|.||++.+++|
T Consensus        10 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~-~~~~~~wl~~ia~n   88 (196)
T PRK12524         10 DVSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQG-EARVSTWLYRVVCN   88 (196)
T ss_pred             CcCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhccccc-cchHHHHHHHHHHH
Confidence            456788999999888 8999999999999999999999999999999999999999999999853 34799999999999


Q ss_pred             HHHHHHHHhcCCc-cc----------c--hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011324          392 TIRKAIFQHSRTI-RL----------P--ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK  447 (488)
Q Consensus       392 aI~~~IRk~sr~i-rl----------P--~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~et  447 (488)
                      .+++++|++.+.. .+          +  ...   .+....+.+++..|+        ..+..+.+++|||+.||+|..+
T Consensus        89 ~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~t  168 (196)
T PRK12524         89 LCTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEA  168 (196)
T ss_pred             HHHHHHHhhcCCCCCccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence            9999999865421 10          0  010   011122333333322        2233578999999999999999


Q ss_pred             HHHHHHHhCCCc
Q 011324          448 LERLIFITRMPL  459 (488)
Q Consensus       448 Vk~~L~~ar~~l  459 (488)
                      |+..+++|+..+
T Consensus       169 V~~~l~Ra~~~L  180 (196)
T PRK12524        169 VESLTARGKRAL  180 (196)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988654

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.66  E-value=1.2e-15  Score=137.76  Aligned_cols=130  Identities=16%  Similarity=0.181  Sum_probs=100.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC----
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT----  403 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~----  403 (488)
                      .|++.|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.+|++.+++|.+++++|++.+.    
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            689999999999999999986 56679999999999999999999997666 799999999999999999987421    


Q ss_pred             --cccchh----------HHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          404 --IRLPEN----------IYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       404 --irlP~~----------v~e~l~kI~ka~~~L-~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                        ...|..          +...+.++....+.+ ...+..+.|++|||+.||+|+++|+.++.+++..+
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              111211          122222332222222 23344578999999999999999999999886543

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.65  E-value=1.3e-15  Score=141.63  Aligned_cols=143  Identities=13%  Similarity=0.192  Sum_probs=111.2

Q ss_pred             CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (488)
Q Consensus       315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI  393 (488)
                      ..+.|+..++.|+ .+++.|+..|.++|+++|+++.++..+++|++||+|++||+++.+|++..  +|.+|++.+++|.+
T Consensus         4 ~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~   81 (187)
T PRK09641          4 LIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLT   81 (187)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHH
Confidence            3567788888888 89999999999999999999999999999999999999999999999753  69999999999999


Q ss_pred             HHHHHHhcCCccc----------------------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHH
Q 011324          394 RKAIFQHSRTIRL----------------------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARR  440 (488)
Q Consensus       394 ~~~IRk~sr~irl----------------------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~  440 (488)
                      ++++|+..+....                      |..   ..+....+.++...|+.        .+..+.+++|||+.
T Consensus        82 ~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~~  161 (187)
T PRK09641         82 IDRLRKRKPDYYLDAEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEI  161 (187)
T ss_pred             HHHHHhcCccccccccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHHH
Confidence            9999987542210                      000   00111223333333321        12347799999999


Q ss_pred             hCCCHHHHHHHHHHhCCCc
Q 011324          441 VGITVEKLERLIFITRMPL  459 (488)
Q Consensus       441 LGIS~etVk~~L~~ar~~l  459 (488)
                      ||||+++|+..+++++..+
T Consensus       162 lgis~~~v~~~l~Rar~~L  180 (187)
T PRK09641        162 LDLPVGTVKTRIHRGREAL  180 (187)
T ss_pred             HCCCHHHHHHHHHHHHHHH
Confidence            9999999999999887543

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.65  E-value=1.9e-15  Score=139.63  Aligned_cols=144  Identities=13%  Similarity=0.141  Sum_probs=113.4

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      |++..++..+..|+ .|++.|+..|.+.|+.+|++|.++..+++|++||+|+++|+++++|++.  .+|.+|++.+++|.
T Consensus         3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~   80 (176)
T PRK09638          3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL   80 (176)
T ss_pred             ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence            56777888888888 8999999999999999999999999999999999999999999999864  47999999999999


Q ss_pred             HHHHHHHhcCCcccch------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011324          393 IRKAIFQHSRTIRLPE------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE  449 (488)
Q Consensus       393 I~~~IRk~sr~irlP~------------~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk  449 (488)
                      +++++|+..+......            .   .......+.+....|+..        +..+.+++|||+.||+++.+|+
T Consensus        81 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V~  160 (176)
T PRK09638         81 YKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVK  160 (176)
T ss_pred             HHHHHHHhccccchhhhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHHCCChhHHH
Confidence            9999998764322110            0   011222333444433322        2246799999999999999999


Q ss_pred             HHHHHhCCCc
Q 011324          450 RLIFITRMPL  459 (488)
Q Consensus       450 ~~L~~ar~~l  459 (488)
                      ..+.+++..+
T Consensus       161 ~~l~ra~~~l  170 (176)
T PRK09638        161 SRVHHGIKQL  170 (176)
T ss_pred             HHHHHHHHHH
Confidence            9999887543

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.65  E-value=2.1e-15  Score=142.60  Aligned_cols=144  Identities=16%  Similarity=0.120  Sum_probs=113.9

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      +++..++..+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|+..  ..|.+|++.+++|.
T Consensus        12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~   89 (192)
T PRK09643         12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNA   89 (192)
T ss_pred             cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHH
Confidence            46778888888888 8999999999999999999999999999999999999999999999964  36999999999999


Q ss_pred             HHHHHHHhcCCcccc-----------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHH
Q 011324          393 IRKAIFQHSRTIRLP-----------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLER  450 (488)
Q Consensus       393 I~~~IRk~sr~irlP-----------~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~  450 (488)
                      +++++|+..+....+           ..   ..+....+.+++..|+.        .+..+.+++|||+.||++..+|+.
T Consensus        90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~  169 (192)
T PRK09643         90 CLDRLRRAKARPTVPLDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKS  169 (192)
T ss_pred             HHHHHHccccCCCCCccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Confidence            999999875432211           00   01112233333333322        233478999999999999999999


Q ss_pred             HHHHhCCCc
Q 011324          451 LIFITRMPL  459 (488)
Q Consensus       451 ~L~~ar~~l  459 (488)
                      .+++++..+
T Consensus       170 rl~rar~~L  178 (192)
T PRK09643        170 RCARGRARL  178 (192)
T ss_pred             HHHHHHHHH
Confidence            999987654

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.64  E-value=1.5e-15  Score=139.26  Aligned_cols=136  Identities=20%  Similarity=0.260  Sum_probs=104.4

Q ss_pred             HhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011324          322 ELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (488)
Q Consensus       322 ~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~  400 (488)
                      +++.|+ .|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++.+|+  .+.+|.+|++.++++.+.+++|+.
T Consensus         3 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~   80 (182)
T PRK09652          3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQ   80 (182)
T ss_pred             hhhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcc
Confidence            345666 89999999999999999999999999999999999999999999999  356899999999999999999986


Q ss_pred             cCCcccc----------------------hhHH---HHHHHHHHHHHHH-------H-HhcCCCCcHHHHHHHhCCCHHH
Q 011324          401 SRTIRLP----------------------ENIY---TLLSKVLEAKRLY-------I-QEGNHSPDKEDLARRVGITVEK  447 (488)
Q Consensus       401 sr~irlP----------------------~~v~---e~l~kI~ka~~~L-------~-~elgr~pS~eEIAe~LGIS~et  447 (488)
                      .+....+                      ....   .....+..+...|       . ..+..+.+++|||+.||+|+.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t  160 (182)
T PRK09652         81 GRRPPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT  160 (182)
T ss_pred             cCCCCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHH
Confidence            5432211                      0000   1122222222222       1 2233478999999999999999


Q ss_pred             HHHHHHHhCCCc
Q 011324          448 LERLIFITRMPL  459 (488)
Q Consensus       448 Vk~~L~~ar~~l  459 (488)
                      |+..+++++..+
T Consensus       161 V~~~l~ra~~~L  172 (182)
T PRK09652        161 VRSRIFRAREAL  172 (182)
T ss_pred             HHHHHHHHHHHH
Confidence            999998876543

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=1.7e-15  Score=141.55  Aligned_cols=143  Identities=13%  Similarity=0.073  Sum_probs=110.9

Q ss_pred             HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHH
Q 011324          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  394 (488)
Q Consensus       316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~  394 (488)
                      ...++..+..|+ .+++.|+..|.++|+.+|++|.++..+++|++||+|+++|+++++|++.++ .|.||++.+++|.++
T Consensus        12 ~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~   90 (187)
T PRK12534         12 TGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAI   90 (187)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHH
Confidence            455666666777 899999999999999999999999999999999999999999999997644 689999999999999


Q ss_pred             HHHHHhcCCcc------c---------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHH
Q 011324          395 KAIFQHSRTIR------L---------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKL  448 (488)
Q Consensus       395 ~~IRk~sr~ir------l---------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etV  448 (488)
                      +++|+..+...      .         |..   ..+....+..++..|+.        .+..+.+++|||+.||+|+++|
T Consensus        91 d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v  170 (187)
T PRK12534         91 DHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTV  170 (187)
T ss_pred             HHHHhcccccccccccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHH
Confidence            99998653210      0         000   11122334444433322        2334789999999999999999


Q ss_pred             HHHHHHhCCCc
Q 011324          449 ERLIFITRMPL  459 (488)
Q Consensus       449 k~~L~~ar~~l  459 (488)
                      +..+++++..+
T Consensus       171 ~~~l~Rar~~L  181 (187)
T PRK12534        171 KSWIRRGLAKL  181 (187)
T ss_pred             HHHHHHHHHHH
Confidence            99999987643

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=2.3e-15  Score=147.69  Aligned_cols=145  Identities=14%  Similarity=0.174  Sum_probs=113.2

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      .++..|+..+..|+ .+++.|+..|.+.|+.+++++.++..+++|++||+|+++|+.+++|++..+ .|.+|++.+++|.
T Consensus        48 ~~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~  126 (233)
T PRK12538         48 DEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNR  126 (233)
T ss_pred             ccHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHH
Confidence            45678888888888 899999999999999999999999999999999999999999999986444 7999999999999


Q ss_pred             HHHHHHHhcCCcc---------cch--h-H--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHH
Q 011324          393 IRKAIFQHSRTIR---------LPE--N-I--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLER  450 (488)
Q Consensus       393 I~~~IRk~sr~ir---------lP~--~-v--~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~  450 (488)
                      +++++|++.+...         .+.  . +  .+....+.+++..|+.        .+..+.+++|||+.||+|+++|+.
T Consensus       127 ~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~  206 (233)
T PRK12538        127 CIDLRRKPRTENVDAVPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVES  206 (233)
T ss_pred             HHHHHHhhcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHH
Confidence            9999998643210         011  0 0  1111223333333322        233478999999999999999999


Q ss_pred             HHHHhCCCc
Q 011324          451 LIFITRMPL  459 (488)
Q Consensus       451 ~L~~ar~~l  459 (488)
                      .+++++..+
T Consensus       207 ~l~RAr~kL  215 (233)
T PRK12538        207 LLKRGRQQL  215 (233)
T ss_pred             HHHHHHHHH
Confidence            999987654

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=3e-15  Score=143.23  Aligned_cols=140  Identities=12%  Similarity=0.125  Sum_probs=107.0

Q ss_pred             HHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011324          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  397 (488)
Q Consensus       319 Li~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~I  397 (488)
                      |+..+..|+ .+++.|+..|.+.|+.++.++.++..+++|++||+|+++|+++.+|++.++ .|.||++.+++|.+++++
T Consensus        28 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~  106 (206)
T PRK12526         28 LILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDML  106 (206)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHH
Confidence            445556566 899999999999999999999999899999999999999999999997655 599999999999999999


Q ss_pred             HHhcCCccc-------c------------hhHHH--HHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHH
Q 011324          398 FQHSRTIRL-------P------------ENIYT--LLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKL  448 (488)
Q Consensus       398 Rk~sr~irl-------P------------~~v~e--~l~kI~ka~~~L--------~~elgr~pS~eEIAe~LGIS~etV  448 (488)
                      |++.+....       +            .....  ....+.+++..|        ...+..+.+++|||+.||+|+++|
T Consensus       107 Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV  186 (206)
T PRK12526        107 RKIKAKKEQNLGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTV  186 (206)
T ss_pred             HHhccccccccccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHH
Confidence            986542110       0            00000  011233333322        222334789999999999999999


Q ss_pred             HHHHHHhCCCc
Q 011324          449 ERLIFITRMPL  459 (488)
Q Consensus       449 k~~L~~ar~~l  459 (488)
                      +..+++++..+
T Consensus       187 ~~~l~Ra~~~L  197 (206)
T PRK12526        187 KSRLRLALAKL  197 (206)
T ss_pred             HHHHHHHHHHH
Confidence            99999887654

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=2.1e-15  Score=142.54  Aligned_cols=142  Identities=11%  Similarity=0.091  Sum_probs=109.3

Q ss_pred             HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (488)
Q Consensus       317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~  395 (488)
                      .+|+..+..|+ .+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+.+|++.++ .|.+|++.+++|.+++
T Consensus        15 ~~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld   93 (194)
T PRK12531         15 LECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFD   93 (194)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHH
Confidence            45777888888 899999999999999999999999899999999999999999999987544 7999999999999999


Q ss_pred             HHHHhcCCc-cc------ch-----------hHH--HHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHH
Q 011324          396 AIFQHSRTI-RL------PE-----------NIY--TLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEK  447 (488)
Q Consensus       396 ~IRk~sr~i-rl------P~-----------~v~--e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~et  447 (488)
                      ++|+..+.. ..      +.           ...  .....+.+++..|+.        .+-.+.+++|||+.||||+++
T Consensus        94 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~t  173 (194)
T PRK12531         94 LLRKQKGKDLHIHADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGT  173 (194)
T ss_pred             HHHHhcccccccchhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHH
Confidence            999865321 10      00           000  011223333333221        233478999999999999999


Q ss_pred             HHHHHHHhCCCc
Q 011324          448 LERLIFITRMPL  459 (488)
Q Consensus       448 Vk~~L~~ar~~l  459 (488)
                      |+..+++++..+
T Consensus       174 Vk~rl~ra~~~L  185 (194)
T PRK12531        174 VKSRLRLAVEKL  185 (194)
T ss_pred             HHHHHHHHHHHH
Confidence            999999887543

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.63  E-value=3.1e-15  Score=139.38  Aligned_cols=144  Identities=19%  Similarity=0.260  Sum_probs=111.6

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      .++..|+..+..|+ .+++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++.  ..|.+|++.+++|.
T Consensus         5 ~~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~   82 (190)
T TIGR02939         5 ELDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNT   82 (190)
T ss_pred             ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHH
Confidence            35667888888888 8999999999999999999999999999999999999999999999974  36999999999999


Q ss_pred             HHHHHHHhcCCccc----------------------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHH
Q 011324          393 IRKAIFQHSRTIRL----------------------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLAR  439 (488)
Q Consensus       393 I~~~IRk~sr~irl----------------------P~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe  439 (488)
                      +++++++..+....                      |...   .+....+.++...|+.        .+..+.+++|||+
T Consensus        83 ~~~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~  162 (190)
T TIGR02939        83 AKNHLVAQGRRPPTSDVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIAR  162 (190)
T ss_pred             HHHHHHHhccCCCcccccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHH
Confidence            99999876542211                      1000   0011123333333322        1234679999999


Q ss_pred             HhCCCHHHHHHHHHHhCCCc
Q 011324          440 RVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       440 ~LGIS~etVk~~L~~ar~~l  459 (488)
                      .|||++++|+..+++++..+
T Consensus       163 ~lgis~~tv~~~l~rar~~L  182 (190)
T TIGR02939       163 IMDCPVGTVRSRIFRAREAI  182 (190)
T ss_pred             HHCcCHHHHHHHHHHHHHHH
Confidence            99999999999999987643

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.

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=2.6e-15  Score=141.13  Aligned_cols=142  Identities=20%  Similarity=0.218  Sum_probs=109.7

Q ss_pred             CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (488)
Q Consensus       315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI  393 (488)
                      ++.+|+..+..|+ .+++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++.++ .|.||++.+++|.+
T Consensus        15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~   92 (194)
T PRK12519         15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA   92 (194)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence            4577888888888 899999999999999999999999999999999999999976 67886554 79999999999999


Q ss_pred             HHHHHHhcCCcccc----------------h-h--HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHH
Q 011324          394 RKAIFQHSRTIRLP----------------E-N--IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVE  446 (488)
Q Consensus       394 ~~~IRk~sr~irlP----------------~-~--v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~e  446 (488)
                      ++++|++.+.....                . .  ..+....+..++..|..        .+..+.+++|||+.||+|+.
T Consensus        93 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~  172 (194)
T PRK12519         93 IDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLG  172 (194)
T ss_pred             HHHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHH
Confidence            99999875421110                0 0  00111223333333322        12347899999999999999


Q ss_pred             HHHHHHHHhCCC
Q 011324          447 KLERLIFITRMP  458 (488)
Q Consensus       447 tVk~~L~~ar~~  458 (488)
                      +|+..+++++..
T Consensus       173 tV~~~l~Ra~~~  184 (194)
T PRK12519        173 TVKARARQGLLK  184 (194)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988654

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.62  E-value=4.7e-15  Score=139.31  Aligned_cols=143  Identities=15%  Similarity=0.215  Sum_probs=110.2

Q ss_pred             CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (488)
Q Consensus       315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI  393 (488)
                      +++.|+..++.|+ .+++.|+..|.+.|+.+++++.++..+++|++||+|+++|+++.+|++..  .|.+|++.+++|.+
T Consensus         6 ~~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~   83 (193)
T PRK11923          6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTA   83 (193)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHH
Confidence            3567788888887 89999999999999999999999989999999999999999999999864  49999999999999


Q ss_pred             HHHHHHhcCCcc---c-------------------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHH
Q 011324          394 RKAIFQHSRTIR---L-------------------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARR  440 (488)
Q Consensus       394 ~~~IRk~sr~ir---l-------------------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~  440 (488)
                      ++++|++.+...   .                   |..   ..+....+.++...|+.        .+-.+.+++|||+.
T Consensus        84 ~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~  163 (193)
T PRK11923         84 KNHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASV  163 (193)
T ss_pred             HHHHHHhcCCCccccccccchhhhcccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHH
Confidence            999987654311   0                   000   00011123333332222        12346799999999


Q ss_pred             hCCCHHHHHHHHHHhCCCc
Q 011324          441 VGITVEKLERLIFITRMPL  459 (488)
Q Consensus       441 LGIS~etVk~~L~~ar~~l  459 (488)
                      ||+|+++|+..+.+++..|
T Consensus       164 lgis~~tv~~~l~Rar~~L  182 (193)
T PRK11923        164 MQCPVGTVRSRIFRAREAI  182 (193)
T ss_pred             HCCCHHHHHHHHHHHHHHH
Confidence            9999999999999887543

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.62  E-value=4.3e-15  Score=144.72  Aligned_cols=143  Identities=15%  Similarity=0.193  Sum_probs=113.2

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      ++++.|+..+..|+ .|++.|+..|.+.|+++|+++.+.+.+++|++||+|++||+++++|++.  ..|.+|++.+++|.
T Consensus        15 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~   92 (231)
T PRK11922         15 ASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNE   92 (231)
T ss_pred             ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHH
Confidence            45667888887777 8999999999999999999999999999999999999999999999975  47999999999999


Q ss_pred             HHHHHHHhcCCcccch-----------------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHH
Q 011324          393 IRKAIFQHSRTIRLPE-----------------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLA  438 (488)
Q Consensus       393 I~~~IRk~sr~irlP~-----------------------~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIA  438 (488)
                      +++++|+..+....+.                       .   ..+....+.+++..|...        +..+.+++|||
T Consensus        93 ~~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA  172 (231)
T PRK11922         93 ALGRLRRRRRLVNLAEMVMASTIAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETA  172 (231)
T ss_pred             HHHHHHhhcccccchhcccccccccccccccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHH
Confidence            9999998764322110                       0   011122344444443322        22467999999


Q ss_pred             HHhCCCHHHHHHHHHHhCCC
Q 011324          439 RRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       439 e~LGIS~etVk~~L~~ar~~  458 (488)
                      +.||+|.++|+..+++++..
T Consensus       173 e~lgis~~tVk~~l~Rar~k  192 (231)
T PRK11922        173 QALGLPEETVKTRLHRARRL  192 (231)
T ss_pred             HHHCcCHHHHHHHHHHHHHH
Confidence            99999999999999988754

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.61  E-value=8e-15  Score=136.96  Aligned_cols=142  Identities=10%  Similarity=0.046  Sum_probs=108.4

Q ss_pred             HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccC-CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (488)
Q Consensus       316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~-~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI  393 (488)
                      ...++..+..|+ .|++.|+..|.+.|+.++.++.+ ...+++|++||+|++||+.++.|++.  ..|.+|++.+++|.+
T Consensus         8 ~~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~   85 (181)
T PRK12536          8 LRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKL   85 (181)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHH
Confidence            345777777777 89999999999999999988764 57899999999999999999999974  469999999999999


Q ss_pred             HHHHHHhcCCcccc--------------hhHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011324          394 RKAIFQHSRTIRLP--------------ENIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERL  451 (488)
Q Consensus       394 ~~~IRk~sr~irlP--------------~~v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~  451 (488)
                      ++++|+..+.....              ....+....+.+++..|+        ..+-.+.+++|||+.||||+++|+..
T Consensus        86 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~  165 (181)
T PRK12536         86 MDFLRSRARREALHDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVG  165 (181)
T ss_pred             HHHHHHHhccccccCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence            99999965421100              011112222334443332        12234789999999999999999999


Q ss_pred             HHHhCCCc
Q 011324          452 IFITRMPL  459 (488)
Q Consensus       452 L~~ar~~l  459 (488)
                      +++++..+
T Consensus       166 l~rar~~L  173 (181)
T PRK12536        166 IHRGLKAL  173 (181)
T ss_pred             HHHHHHHH
Confidence            99887543

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.61  E-value=8.3e-15  Score=137.22  Aligned_cols=141  Identities=11%  Similarity=0.125  Sum_probs=108.7

Q ss_pred             HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHH----HccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011324          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAK----QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (488)
Q Consensus       316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAk----ry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIR  390 (488)
                      ...|+..+..|+ .|++.|+..|.+.|+.+|+    ++.++..+++|++||+|+.+|+.+..|++..  .|.+|++.+++
T Consensus         8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~   85 (184)
T PRK12539          8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR   85 (184)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence            566777888887 8999999999999999986    4557889999999999999999999999753  69999999999


Q ss_pred             HHHHHHHHHhcCCc-ccc---------h---hHHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011324          391 QTIRKAIFQHSRTI-RLP---------E---NIYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE  449 (488)
Q Consensus       391 naI~~~IRk~sr~i-rlP---------~---~v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk  449 (488)
                      |.+++++|+..+.. ..+         .   ...+....+..+...|+..        +..+.+++|||+.||+|+++|+
T Consensus        86 n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~  165 (184)
T PRK12539         86 YKLIDHLRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK  165 (184)
T ss_pred             HHHHHHHHHHhccccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHH
Confidence            99999999865421 111         0   0112223344444333221        2247899999999999999999


Q ss_pred             HHHHHhCCC
Q 011324          450 RLIFITRMP  458 (488)
Q Consensus       450 ~~L~~ar~~  458 (488)
                      ..+++++..
T Consensus       166 ~~l~ra~~~  174 (184)
T PRK12539        166 VSVHRGLKA  174 (184)
T ss_pred             HHHHHHHHH
Confidence            999988754

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.60  E-value=9.6e-15  Score=137.18  Aligned_cols=145  Identities=14%  Similarity=0.134  Sum_probs=112.8

Q ss_pred             cCCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (488)
Q Consensus       313 gm~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn  391 (488)
                      .++++.|+..+..|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+++.+|++.  ..|.+|++.+++|
T Consensus         6 ~~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n   83 (189)
T PRK12515          6 ATTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARF   83 (189)
T ss_pred             ccCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHH
Confidence            356788888888888 8999999999999999999999999999999999999999999999963  4799999999999


Q ss_pred             HHHHHHHHhcCCccc-------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011324          392 TIRKAIFQHSRTIRL-------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK  447 (488)
Q Consensus       392 aI~~~IRk~sr~irl-------------P~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~et  447 (488)
                      .+.+++|+..+....             |...   .+....+.++...|+        ..+..+.+++|||+.||+|+++
T Consensus        84 ~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~t  163 (189)
T PRK12515         84 KALSALRRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPEST  163 (189)
T ss_pred             HHHHHHHccCCCCCccccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHH
Confidence            999999976532110             0000   001111222222221        2233478999999999999999


Q ss_pred             HHHHHHHhCCCc
Q 011324          448 LERLIFITRMPL  459 (488)
Q Consensus       448 Vk~~L~~ar~~l  459 (488)
                      |+..+.+++..+
T Consensus       164 V~~~l~Rar~~L  175 (189)
T PRK12515        164 VKTRMFYARKKL  175 (189)
T ss_pred             HHHHHHHHHHHH
Confidence            999999987654

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=4.3e-15  Score=139.08  Aligned_cols=135  Identities=16%  Similarity=0.103  Sum_probs=104.8

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324          325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (488)
Q Consensus       325 ~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~  403 (488)
                      .|+ .+++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|+++.+|+...+..|.||++.+++|.+++++|++.+.
T Consensus         5 ~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~   84 (185)
T PRK12542          5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRH   84 (185)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            455 8999999999999999999999999999999999999999999999865445799999999999999999987643


Q ss_pred             cccc------------hhH------HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          404 IRLP------------ENI------YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       404 irlP------------~~v------~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                      ....            ...      ......+.+++..|+.        .+..+.+++|||+.||+|+++|+..+.+++.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~  164 (185)
T PRK12542         85 ETFLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARK  164 (185)
T ss_pred             hhhhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2110            000      0011223333333321        1334789999999999999999999999876


Q ss_pred             Cc
Q 011324          458 PL  459 (488)
Q Consensus       458 ~l  459 (488)
                      .+
T Consensus       165 ~L  166 (185)
T PRK12542        165 RV  166 (185)
T ss_pred             HH
Confidence            54

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

Probab=99.58  E-value=1.3e-14  Score=134.91  Aligned_cols=141  Identities=17%  Similarity=0.194  Sum_probs=106.5

Q ss_pred             HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC-----CHhHHHHHHHHHHHH-hHHhhCCCCCCchhhHHHHH
Q 011324          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWW  388 (488)
Q Consensus       316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~-----d~EDLIQEG~IGL~r-AiekFDpskG~rFSTYA~~w  388 (488)
                      ...|+..+..|+ .|++.|+..|.+.|+.+|++|.++..     +++|++||+|+.+|+ ...+|++.  ..|.+|++.+
T Consensus         4 ~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i   81 (183)
T TIGR02999         4 VTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKA   81 (183)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHH
Confidence            356777888888 89999999999999999999998877     899999999999998 78889754  3699999999


Q ss_pred             HHHHHHHHHHHhcCCcc------c------c---hhHHHH---HHH-------HHHHHHH-HHHhcCCCCcHHHHHHHhC
Q 011324          389 VRQTIRKAIFQHSRTIR------L------P---ENIYTL---LSK-------VLEAKRL-YIQEGNHSPDKEDLARRVG  442 (488)
Q Consensus       389 IRnaI~~~IRk~sr~ir------l------P---~~v~e~---l~k-------I~ka~~~-L~~elgr~pS~eEIAe~LG  442 (488)
                      ++|.+++++|+..+..+      .      +   ....+.   +..       +....+. +...+..+.|++|||+.||
T Consensus        82 ~~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lg  161 (183)
T TIGR02999        82 MRRILVDHARRRRAQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLG  161 (183)
T ss_pred             HHHHHHHHHHHHHHHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence            99999999997542111      0      0   011111   111       2221122 2222334789999999999


Q ss_pred             CCHHHHHHHHHHhCCC
Q 011324          443 ITVEKLERLIFITRMP  458 (488)
Q Consensus       443 IS~etVk~~L~~ar~~  458 (488)
                      ||+++|+..+++++..
T Consensus       162 is~~tVk~~l~Rar~~  177 (183)
T TIGR02999       162 VSVRTVERDWRFARAW  177 (183)
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            9999999999998754

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.

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

Probab=99.57  E-value=2.2e-14  Score=141.90  Aligned_cols=145  Identities=12%  Similarity=0.044  Sum_probs=113.1

Q ss_pred             hcCCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHH-------hHHhhCCCCCCchhh
Q 011324          312 IGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFAS  383 (488)
Q Consensus       312 ~gm~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~r-------AiekFDpskG~rFST  383 (488)
                      ++.++..|+..++.|+ .|++.|+..|.+.|+.+++++.++..+++|++||.|+.+|.       .+.+|++.  ..|.|
T Consensus        22 ~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~t   99 (244)
T TIGR03001        22 LHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLS   99 (244)
T ss_pred             ccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHh
Confidence            3456788999999998 89999999999999999999999999999999999999994       78889863  36999


Q ss_pred             HHHHHHHHHHHHHHHHhcCCccc---------------chhH-H------HHHHHHHHHHHHHHHh--------cCCCCc
Q 011324          384 YAYWWVRQTIRKAIFQHSRTIRL---------------PENI-Y------TLLSKVLEAKRLYIQE--------GNHSPD  433 (488)
Q Consensus       384 YA~~wIRnaI~~~IRk~sr~irl---------------P~~v-~------e~l~kI~ka~~~L~~e--------lgr~pS  433 (488)
                      |++.+++|.+++++|++.+...+               |... .      +....+.+++..|+..        +-.+.|
T Consensus       100 WL~~Ia~N~~id~lRk~~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S  179 (244)
T TIGR03001       100 WVRIVATRIALELQAQERRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGLS  179 (244)
T ss_pred             HHHHHHHHHHHHHHHHhcccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCC
Confidence            99999999999999976542211               0100 0      0112244444444322        224789


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          434 KEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       434 ~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      ++|||+.||||+++|+..+++++..
T Consensus       180 ~~EIA~~Lgis~~TVk~rl~RAr~~  204 (244)
T TIGR03001       180 MDRIGAMYQVHRSTVSRWVAQARER  204 (244)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            9999999999999999999988753

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.

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

Probab=99.57  E-value=2.3e-14  Score=129.83  Aligned_cols=130  Identities=15%  Similarity=0.142  Sum_probs=101.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP  407 (488)
                      ++++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++..  .|.+|++.+++|.+++++|++.+....-
T Consensus         1 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~   78 (159)
T TIGR02989         1 EAFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVF   78 (159)
T ss_pred             CHHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            37899999999999999999999999999999999999999999999753  5999999999999999999876542210


Q ss_pred             -hh----------------HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          408 -EN----------------IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       408 -~~----------------v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                       ..                ..+....+.+++..|+.        ..-.+.+++|||+.||||.++|+..+++++..+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~L  155 (159)
T TIGR02989        79 DDELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRL  155 (159)
T ss_pred             CHHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence             00                01111223333333321        133478999999999999999999999987654

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).

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.57  E-value=1.9e-14  Score=135.43  Aligned_cols=142  Identities=19%  Similarity=0.154  Sum_probs=109.4

Q ss_pred             HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (488)
Q Consensus       317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~  395 (488)
                      ..|+.++..|+ .|++.|+..|.+.|+.+++ +.++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++
T Consensus        12 ~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d   88 (185)
T PRK09649         12 TALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVAD   88 (185)
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHH
Confidence            45777777887 8999999999999999995 67788899999999999999999999864  46999999999999999


Q ss_pred             HHHHhcCCccc-----chh---------HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011324          396 AIFQHSRTIRL-----PEN---------IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIF  453 (488)
Q Consensus       396 ~IRk~sr~irl-----P~~---------v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~  453 (488)
                      ++|+..+....     +..         ..+....+.+++..|+..        +..+.+++|||+.||+|+++|+..+.
T Consensus        89 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~  168 (185)
T PRK09649         89 HIRHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVA  168 (185)
T ss_pred             HHHHhccccccccccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            99986432211     000         011222344444433222        33478999999999999999999999


Q ss_pred             HhCCCccc
Q 011324          454 ITRMPLSM  461 (488)
Q Consensus       454 ~ar~~lSL  461 (488)
                      +++..+--
T Consensus       169 Rar~~Lr~  176 (185)
T PRK09649        169 RARDALLA  176 (185)
T ss_pred             HHHHHHHh
Confidence            99876543

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.57  E-value=2.9e-14  Score=130.47  Aligned_cols=139  Identities=14%  Similarity=0.127  Sum_probs=106.7

Q ss_pred             HHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011324          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  397 (488)
Q Consensus       319 Li~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~I  397 (488)
                      |...+..|+ .|++.|+..|.+.|+.+|+++.++..+++|++||+|++||+++++|+  .+..|.+|++.++++.+.+++
T Consensus         3 ~~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~   80 (179)
T PRK11924          3 LMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLL   80 (179)
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHH
Confidence            455666777 89999999999999999999999999999999999999999999998  345899999999999999999


Q ss_pred             HHhcCCcccch-------------h-------------HHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHH
Q 011324          398 FQHSRTIRLPE-------------N-------------IYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLER  450 (488)
Q Consensus       398 Rk~sr~irlP~-------------~-------------v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~  450 (488)
                      ++..+......             .             +...+.++....+.+. ..+..+.+.+|||+.||+|..+|+.
T Consensus        81 r~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~  160 (179)
T PRK11924         81 RRRRREKAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKS  160 (179)
T ss_pred             HhcccccccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence            97654322110             0             1112222222222221 2223478999999999999999999


Q ss_pred             HHHHhCCCc
Q 011324          451 LIFITRMPL  459 (488)
Q Consensus       451 ~L~~ar~~l  459 (488)
                      .+++++..+
T Consensus       161 ~~~ra~~~l  169 (179)
T PRK11924        161 RLRRARQLL  169 (179)
T ss_pred             HHHHHHHHH
Confidence            999886543

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.56  E-value=4.5e-14  Score=131.73  Aligned_cols=140  Identities=14%  Similarity=0.167  Sum_probs=106.2

Q ss_pred             HHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCC----CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       318 eLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~----g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      .|+..+..|+ .|++.|+..|.+.|+.+|++++++    ..+++|++||+|+.+|+..++|+..  ..|.+|++.+++|.
T Consensus        11 ~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~   88 (184)
T PRK12512         11 DLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNK   88 (184)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHH
Confidence            4566666666 999999999999999999998752    4689999999999999999999863  47999999999999


Q ss_pred             HHHHHHHhcCCcccc---------h-h--HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHH
Q 011324          393 IRKAIFQHSRTIRLP---------E-N--IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLI  452 (488)
Q Consensus       393 I~~~IRk~sr~irlP---------~-~--v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L  452 (488)
                      +.+++|++.+....+         . .  -......+.++...|+..        +-.+.+++|||+.||+|..+|+..+
T Consensus        89 ~~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l  168 (184)
T PRK12512         89 LIDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVAL  168 (184)
T ss_pred             HHHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            999999876532211         0 0  011122333333333221        2247899999999999999999999


Q ss_pred             HHhCCCc
Q 011324          453 FITRMPL  459 (488)
Q Consensus       453 ~~ar~~l  459 (488)
                      ++++..+
T Consensus       169 ~ra~~~L  175 (184)
T PRK12512        169 HRGLAAL  175 (184)
T ss_pred             HHHHHHH
Confidence            9887543

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

Probab=99.55  E-value=5.6e-14  Score=131.56  Aligned_cols=134  Identities=16%  Similarity=0.202  Sum_probs=106.3

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (488)
Q Consensus       324 ~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~  403 (488)
                      .++..+++.++..|.+.++.+|+++.++..+++||+||+|+.+|+++..| .. +..|.||++.+++|.+++++|+..+.
T Consensus        11 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~r~   88 (182)
T COG1595          11 RGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRKRR   88 (182)
T ss_pred             hcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhccc
Confidence            34448999999999999999999999998899999999999999999999 33 45799999999999999999987654


Q ss_pred             ccc-c-------------h-h----HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324          404 IRL-P-------------E-N----IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITR  456 (488)
Q Consensus       404 irl-P-------------~-~----v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~ar  456 (488)
                      ... +             . .    ..+....+.++...|+..        ...+.|++|||+.|||++++|+..+++++
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~  168 (182)
T COG1595          89 RARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRAR  168 (182)
T ss_pred             ccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            321 0             1 1    122334455555544332        33478999999999999999999999987


Q ss_pred             CCc
Q 011324          457 MPL  459 (488)
Q Consensus       457 ~~l  459 (488)
                      ..+
T Consensus       169 ~~l  171 (182)
T COG1595         169 KKL  171 (182)
T ss_pred             HHH
Confidence            653

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=99.55  E-value=4e-14  Score=123.99  Aligned_cols=127  Identities=24%  Similarity=0.393  Sum_probs=100.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc--
Q 011324          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL--  406 (488)
Q Consensus       329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl--  406 (488)
                      |++.|+..|.++|+++++++.+++.+.+|++|||+++++++++.|++.  .+|.+|+++++++.+.++++++.+ .+.  
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~-~~~~~   78 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR-LRREL   78 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc-CCcch
Confidence            789999999999999999999999999999999999999999999997  689999999999999999999874 110  


Q ss_pred             ------------ch----------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          407 ------------PE----------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       407 ------------P~----------~v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                                  |.          .+...+..+....+.+. ..+..+.+..|||+.+|+|..+|+.++.+++..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~k  153 (158)
T TIGR02937        79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKK  153 (158)
T ss_pred             hhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                        10          01222333333333332 222447899999999999999999999887543

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.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.54  E-value=4.8e-14  Score=131.54  Aligned_cols=133  Identities=16%  Similarity=0.186  Sum_probs=102.7

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324          325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (488)
Q Consensus       325 ~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~  403 (488)
                      .|+ .|++.|+..|.+.|+.++++|.++..+++|++||+|+.+|+++.+|++..  .|.+|++.+++|.+.+++|+..+.
T Consensus         3 ~~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~   80 (179)
T PRK12543          3 SGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRR   80 (179)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhccc
Confidence            345 89999999999999999999999999999999999999999999999864  599999999999999999865421


Q ss_pred             cc---------------cchhH--HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          404 IR---------------LPENI--YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       404 ir---------------lP~~v--~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      .+               .|..+  .+....+.++...|+        ..+..+.+++|||+.||||+++|+..+++++..
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~  160 (179)
T PRK12543         81 FRIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK  160 (179)
T ss_pred             cccccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            11               11111  111223333333332        123347899999999999999999999988765


Q ss_pred             c
Q 011324          459 L  459 (488)
Q Consensus       459 l  459 (488)
                      +
T Consensus       161 L  161 (179)
T PRK12543        161 L  161 (179)
T ss_pred             H
Confidence            4

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.54  E-value=6e-14  Score=129.82  Aligned_cols=130  Identities=10%  Similarity=0.075  Sum_probs=101.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-  406 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl-  406 (488)
                      ..++.|+..|.++|+.+|++|.++..+++|++||+|+.||+++++|++..  +|.+|++.+++|.+++++|++.+.... 
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            45899999999999999999999999999999999999999999999753  799999999999999999987543210 


Q ss_pred             --------------------chhH--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324          407 --------------------PENI--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITR  456 (488)
Q Consensus       407 --------------------P~~v--~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar  456 (488)
                                          +...  .+....+.+++..|+.        .+..+.+++|||+.||+++++|+..+.+++
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                                0000  0111223333333322        233478999999999999999999999887


Q ss_pred             CCc
Q 011324          457 MPL  459 (488)
Q Consensus       457 ~~l  459 (488)
                      ..+
T Consensus       161 ~~L  163 (173)
T PRK12522        161 KQM  163 (173)
T ss_pred             HHH
Confidence            654

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.54  E-value=4.6e-14  Score=132.75  Aligned_cols=129  Identities=16%  Similarity=0.176  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccch
Q 011324          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (488)
Q Consensus       329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~  408 (488)
                      +++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|+..  .+|.||++.+++|.+++++|++.+......
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            689999999999999999999999999999999999999999999864  369999999999999999998765322110


Q ss_pred             ------------------------------hH------HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCC
Q 011324          409 ------------------------------NI------YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGIT  444 (488)
Q Consensus       409 ------------------------------~v------~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS  444 (488)
                                                    ..      .+....+..++..|+.        .+..+.|++|||+.||+|
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      0111223333333322        223467999999999999


Q ss_pred             HHHHHHHHHHhCCCc
Q 011324          445 VEKLERLIFITRMPL  459 (488)
Q Consensus       445 ~etVk~~L~~ar~~l  459 (488)
                      +++|+..+++++..+
T Consensus       161 ~~tV~~~l~Rar~~L  175 (191)
T PRK12520        161 ATNAWVLLYRARMRL  175 (191)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999987654

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

Probab=99.53  E-value=4.3e-14  Score=133.15  Aligned_cols=130  Identities=16%  Similarity=0.152  Sum_probs=102.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP  407 (488)
                      .+|+.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+.+|++.  ..|.+|++.+++|.+++++|++.+.....
T Consensus        11 ~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~~   88 (193)
T TIGR02947        11 QRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQS   88 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCcccc
Confidence            7999999999999999999999999999999999999999999999864  46999999999999999999876432110


Q ss_pred             --hhH------------------H-------HHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHH
Q 011324          408 --ENI------------------Y-------TLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLI  452 (488)
Q Consensus       408 --~~v------------------~-------e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L  452 (488)
                        ...                  .       .....+..++..|+..        +..+.+++|||+.||||+++|+..+
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l  168 (193)
T TIGR02947        89 DDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRL  168 (193)
T ss_pred             cchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHHH
Confidence              000                  0       0113344445444333        2246799999999999999999999


Q ss_pred             HHhCCCc
Q 011324          453 FITRMPL  459 (488)
Q Consensus       453 ~~ar~~l  459 (488)
                      ++++..+
T Consensus       169 ~Rar~~L  175 (193)
T TIGR02947       169 HRGRKQL  175 (193)
T ss_pred             HHHHHHH
Confidence            9987654

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.

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.52  E-value=8.9e-14  Score=129.89  Aligned_cols=131  Identities=12%  Similarity=0.081  Sum_probs=101.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl  406 (488)
                      ..|++.|+..|.+.|+++|+++.++..+++|++||+|+.+|+++.+|+..  ..|.+|++.+++|.+++++|+..+....
T Consensus        15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~   92 (179)
T PRK09415         15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVI   92 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccccc
Confidence            38999999999999999999999999999999999999999999999864  3699999999999999999985322111


Q ss_pred             ---------------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          407 ---------------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       407 ---------------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                                     |..   ..+....+.++...|+.        ....+.+++|||+.||||+++|+..+++++..+
T Consensus        93 ~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~L  171 (179)
T PRK09415         93 VTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELL  171 (179)
T ss_pred             ccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                           000   11112223333333322        122367999999999999999999999987654

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.52  E-value=1e-13  Score=127.93  Aligned_cols=136  Identities=18%  Similarity=0.193  Sum_probs=102.7

Q ss_pred             HHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011324          321 SELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ  399 (488)
Q Consensus       321 ~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk  399 (488)
                      ..++.|+ .+++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++.  ..|.+|++.+++|.+++++|+
T Consensus         3 ~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~   79 (175)
T PRK12518          3 LRCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQ   79 (175)
T ss_pred             hHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHH
Confidence            4455666 89999999999999999999875 4789999999999999999999974  469999999999999999997


Q ss_pred             hcCCcc----cc-----------hhHH--HHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324          400 HSRTIR----LP-----------ENIY--TLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFI  454 (488)
Q Consensus       400 ~sr~ir----lP-----------~~v~--e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~  454 (488)
                      ..+...    .+           ....  +....+.++...|+..        +..+.+++|||+.||+|+++|+..+++
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~R  159 (175)
T PRK12518         80 FAQRPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFY  159 (175)
T ss_pred             hhccccchhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            643211    00           0110  0111233344444322        223679999999999999999999998


Q ss_pred             hCCCc
Q 011324          455 TRMPL  459 (488)
Q Consensus       455 ar~~l  459 (488)
                      ++..+
T Consensus       160 ar~~L  164 (175)
T PRK12518        160 ARRQL  164 (175)
T ss_pred             HHHHH
Confidence            87654

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.52  E-value=1.1e-13  Score=127.76  Aligned_cols=132  Identities=11%  Similarity=0.067  Sum_probs=101.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011324          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (488)
Q Consensus       326 Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir  405 (488)
                      +..+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++. ...|.+|++.+++|.+++++|++.+...
T Consensus         7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~-~~~~~~wL~~iarn~~~d~~Rk~~~~~~   85 (173)
T PRK09645          7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADT-GRSARAWLFTVARNLVIDERRSARARPV   85 (173)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcc-cccHHHHHHHHHHHHHHHHHHhhccccc
Confidence            348999999999999999999999998999999999999999999999743 2479999999999999999997653211


Q ss_pred             --------c-----chhHHH--HHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          406 --------L-----PENIYT--LLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       406 --------l-----P~~v~e--~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                              .     +..+..  ....+..++..|+        ..+..+.+++|||+.||+|+++|+..+++++..
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~  161 (173)
T PRK09645         86 EGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRA  161 (173)
T ss_pred             ccccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence                    1     011110  1112333333322        223347899999999999999999999988754

>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1

Probab=99.52  E-value=7e-14  Score=125.59  Aligned_cols=129  Identities=19%  Similarity=0.221  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-  406 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl-  406 (488)
                      .|++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++.  .+|.+|++.++++.+.+++++..+.... 
T Consensus         1 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~~   78 (161)
T TIGR02985         1 KAFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKYQ   78 (161)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHHH
Confidence            3789999999999999999999998999999999999999999999863  4799999999999999999977532110 


Q ss_pred             ---------------chh----------HHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          407 ---------------PEN----------IYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       407 ---------------P~~----------v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                                     |..          +...+..+....+.+. ..+..+.+.+|||+.||+|..+|+..+++++..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~  156 (161)
T TIGR02985        79 EEILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALKE  156 (161)
T ss_pred             HHHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                           000          1111222222222222 213347899999999999999999999988654

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.

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.52  E-value=1.1e-13  Score=130.84  Aligned_cols=132  Identities=17%  Similarity=0.151  Sum_probs=103.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011324          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (488)
Q Consensus       326 Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir  405 (488)
                      ++.+++.|+..|.+.|+.+|++++++..+++|++||.|+.+|+..++|+..  ..|.+|++.+++|.+++++|++.+...
T Consensus         8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~   85 (187)
T PRK12516          8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQ   85 (187)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence            348999999999999999999999999999999999999999999999864  369999999999999999998765321


Q ss_pred             cch-------------hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          406 LPE-------------NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       406 lP~-------------~v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ...             ........+..++..|+.        ....+.+++|||+.||||+++|+..+.+++..|
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             001112233333333322        233478999999999999999999999887643

>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1

Probab=99.51  E-value=1.3e-13  Score=128.13  Aligned_cols=134  Identities=16%  Similarity=0.179  Sum_probs=100.3

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHcc----CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011324          325 SGN-SSREKLINANLRLVVHVAKQYQ----GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ  399 (488)
Q Consensus       325 ~Gd-~ArekLIesnlrLV~sIAkry~----~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk  399 (488)
                      .|+ .|++.|+..|.+.|+.+|++|.    ++..+++|++||+|+.+|+++.+|+...+..|.+|++.+++|.+.+++|+
T Consensus         3 ~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~   82 (189)
T TIGR02984         3 GGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR   82 (189)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence            445 8999999999999999999874    35678999999999999999999987656689999999999999999987


Q ss_pred             hc----CCc----cc-----------------------chh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHH
Q 011324          400 HS----RTI----RL-----------------------PEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDL  437 (488)
Q Consensus       400 ~s----r~i----rl-----------------------P~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEI  437 (488)
                      ..    +..    .+                       |..   ..+....+.+++..|.        ..+..+.+++||
T Consensus        83 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eI  162 (189)
T TIGR02984        83 HLGAQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEV  162 (189)
T ss_pred             HHHHHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHH
Confidence            51    110    00                       000   0111122333332221        223347899999


Q ss_pred             HHHhCCCHHHHHHHHHHhCCC
Q 011324          438 ARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       438 Ae~LGIS~etVk~~L~~ar~~  458 (488)
                      |+.||||+++|+..+++++..
T Consensus       163 A~~lgis~~~v~~~l~Ra~~~  183 (189)
T TIGR02984       163 AERMDRSEGAVSMLWVRGLAR  183 (189)
T ss_pred             HHHHCcCHHHHHHHHHHHHHH
Confidence            999999999999999988654

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).

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.51  E-value=1.2e-13  Score=141.18  Aligned_cols=141  Identities=13%  Similarity=0.153  Sum_probs=109.7

Q ss_pred             HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (488)
Q Consensus       317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~  395 (488)
                      .+|+.++..|+ .+++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++
T Consensus         7 ~~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d   84 (339)
T PRK08241          7 AALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLD   84 (339)
T ss_pred             HHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHH
Confidence            46888888888 8999999999999999999999999999999999999999999999853  46999999999999999


Q ss_pred             HHHHhcCCcc---c----------------------------------chhH---HHHH-HHHHHHHHHHHHh-------
Q 011324          396 AIFQHSRTIR---L----------------------------------PENI---YTLL-SKVLEAKRLYIQE-------  427 (488)
Q Consensus       396 ~IRk~sr~ir---l----------------------------------P~~v---~e~l-~kI~ka~~~L~~e-------  427 (488)
                      ++|++.+...   .                                  |...   .+.+ ..+.+++..|+..       
T Consensus        85 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L  164 (339)
T PRK08241         85 ALEGRARRPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLIL  164 (339)
T ss_pred             HHHhhccccCccccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhh
Confidence            9998653210   0                                  0000   0101 1233344433322       


Q ss_pred             -cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          428 -GNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       428 -lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                       +..+.+++|||+.||+|+++|+..+++++..+
T Consensus       165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~L  197 (339)
T PRK08241        165 RDVLGWSAAEVAELLDTSVAAVNSALQRARATL  197 (339)
T ss_pred             HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence             23467999999999999999999999887544

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.49  E-value=2.8e-13  Score=124.68  Aligned_cols=130  Identities=15%  Similarity=0.110  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl  406 (488)
                      +..|..++..|.+.|+.+|+++.++..+++|++||+|+.+|+...+|+..  ..|.+|++.+++|.+++++|+..+....
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~~   82 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQD   82 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            46899999999999999999999999999999999999999999999864  3599999999999999999976543211


Q ss_pred             c------------h-hHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          407 P------------E-NIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       407 P------------~-~v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      .            . ........+..++..|+        ..+-.+.+++|||+.||||+++|+..+++++..
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~  155 (164)
T PRK12547         83 SDGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNR  155 (164)
T ss_pred             ccccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            0            0 00011122333333332        222347899999999999999999999988754

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.49  E-value=2e-13  Score=127.61  Aligned_cols=135  Identities=13%  Similarity=0.055  Sum_probs=100.5

Q ss_pred             hhcH-HHHHHHHHHHHHHHHHHHHHccC--CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011324          324 HSGN-SSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (488)
Q Consensus       324 ~~Gd-~ArekLIesnlrLV~sIAkry~~--~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~  400 (488)
                      ..|+ .+++.|+..|.+.|+.++.++.+  +..+++|++||.|+.+|+...+|+......|.||++.+++|.+++++|++
T Consensus         8 ~~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~   87 (178)
T PRK12529          8 LSADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQ   87 (178)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHH
Confidence            4455 89999999999999998766555  45789999999999999999999754345799999999999999999976


Q ss_pred             cCCcc--------------cchh---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324          401 SRTIR--------------LPEN---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFIT  455 (488)
Q Consensus       401 sr~ir--------------lP~~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~a  455 (488)
                      .+...              -|..   ..+....|.+++..|+.+        .-.+.+++|||+.||+|+++|+..++++
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rA  167 (178)
T PRK12529         88 SLELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQA  167 (178)
T ss_pred             HHHhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            42110              1111   112223344444444322        2236899999999999999999999887


Q ss_pred             CCC
Q 011324          456 RMP  458 (488)
Q Consensus       456 r~~  458 (488)
                      ...
T Consensus       168 l~~  170 (178)
T PRK12529        168 YVT  170 (178)
T ss_pred             HHH
Confidence            543

>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family

Probab=99.49  E-value=2.9e-13  Score=123.38  Aligned_cols=132  Identities=14%  Similarity=0.117  Sum_probs=101.5

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011324          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (488)
Q Consensus       326 Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir  405 (488)
                      +..+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|+.  ...|.+|++.+++|.+++++|+..+...
T Consensus         4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~~~   81 (162)
T TIGR02983         4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLLEL   81 (162)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccccc
Confidence            44899999999999999999999999999999999999999999999964  3479999999999999999998754110


Q ss_pred             ----cc-------h-------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          406 ----LP-------E-------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       406 ----lP-------~-------~v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                          .+       .       .+...+.++....+.+. ..+-.+.+++|||+.||+|+++|+..+.+++..+
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                00       0       01122222222222221 2223478999999999999999999999887643

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.

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.48  E-value=3.6e-13  Score=123.03  Aligned_cols=130  Identities=12%  Similarity=0.132  Sum_probs=100.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl  406 (488)
                      ..+++.++..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++.   .|.||++.+++|.+++++|+..+....
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            37999999999999999999999999999999999999999999999863   599999999999999999986542211


Q ss_pred             c------------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          407 P------------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       407 P------------~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .            ..   ..+....+..+...|+.        ....+.+++|||+.||+|.++|+..+++++..+
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            0            00   01111222223222222        123478999999999999999999999987543

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.47  E-value=3.9e-13  Score=128.12  Aligned_cols=139  Identities=15%  Similarity=0.109  Sum_probs=106.2

Q ss_pred             HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011324          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (488)
Q Consensus       317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~  395 (488)
                      .+|+..+..|+ .+++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++.  ..|.+|++.+++|.+++
T Consensus        13 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id   89 (196)
T PRK12535         13 TDLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVD   89 (196)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHH
Confidence            45777777777 8999999999999999975 56888899999999999999999999863  36999999999999999


Q ss_pred             HHHHhcCCccc--------------ch--hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHH
Q 011324          396 AIFQHSRTIRL--------------PE--NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERL  451 (488)
Q Consensus       396 ~IRk~sr~irl--------------P~--~v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~  451 (488)
                      ++|+..+..+.              |.  ...+....+.+++..|+.        .+-.+.+++|||+.||+++++|+..
T Consensus        90 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~  169 (196)
T PRK12535         90 NIRHDMARPRKSATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSR  169 (196)
T ss_pred             HHHhhccCCCcccccccccccccCCcchhHHHHHHHHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHH
Confidence            99986532210              00  011112234444433322        2223679999999999999999999


Q ss_pred             HHHhCCC
Q 011324          452 IFITRMP  458 (488)
Q Consensus       452 L~~ar~~  458 (488)
                      +++++..
T Consensus       170 l~Rar~~  176 (196)
T PRK12535        170 VARARAD  176 (196)
T ss_pred             HHHHHHH
Confidence            9988654

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.47  E-value=7.9e-13  Score=130.63  Aligned_cols=91  Identities=21%  Similarity=0.337  Sum_probs=81.9

Q ss_pred             CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC--CHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011324          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (488)
Q Consensus       315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~--d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRn  391 (488)
                      +.++|+..++.|+ .|++.|+..|.++|+++|.+|+++..  +.+|++|||++++|+++++|++.+|..|.+|++++|+|
T Consensus         4 ~~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn   83 (237)
T PRK08311          4 SLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKR   83 (237)
T ss_pred             cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence            3466778888887 89999999999999999999998875  58999999999999999999999888899999999999


Q ss_pred             HHHHHHHHhcCCcc
Q 011324          392 TIRKAIFQHSRTIR  405 (488)
Q Consensus       392 aI~~~IRk~sr~ir  405 (488)
                      .+++++|++.+...
T Consensus        84 ~~iDylRk~~~~~~   97 (237)
T PRK08311         84 RLIDYFRKESKHNL   97 (237)
T ss_pred             HHHHHHHHhhcccc
Confidence            99999998876433

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=99.47  E-value=2.7e-13  Score=137.29  Aligned_cols=131  Identities=15%  Similarity=0.158  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR-  405 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir-  405 (488)
                      ..+++.|+..|.+.|+++|++++++..+++|++||.|+.+|+.+.+|+..  ..|.+|++.+++|.|++++|++.+... 
T Consensus         4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~   81 (324)
T TIGR02960         4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRP   81 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCc
Confidence            38999999999999999999999999999999999999999999999864  469999999999999999998654211 


Q ss_pred             -------------------------cc--------------hhH---HHHH-HHHHHHHHHHHH--------hcCCCCcH
Q 011324          406 -------------------------LP--------------ENI---YTLL-SKVLEAKRLYIQ--------EGNHSPDK  434 (488)
Q Consensus       406 -------------------------lP--------------~~v---~e~l-~kI~ka~~~L~~--------elgr~pS~  434 (488)
                                               ++              ...   .+.+ ..+.+++..|+.        .+..+.++
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~  161 (324)
T TIGR02960        82 VGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRA  161 (324)
T ss_pred             cccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCCCH
Confidence                                     00              000   0111 123333333322        22346799


Q ss_pred             HHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          435 EDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       435 eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      +|||+.||+|+++|+..+++++..|
T Consensus       162 ~EIA~~lgis~~tV~~~l~Rar~~L  186 (324)
T TIGR02960       162 AETAELLGTSTASVNSALQRARATL  186 (324)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999887543

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=99.47  E-value=4.9e-13  Score=129.93  Aligned_cols=134  Identities=14%  Similarity=0.096  Sum_probs=103.8

Q ss_pred             hhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324          323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (488)
Q Consensus       323 l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr  402 (488)
                      +.....+++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+.+|++  + .|.+|++++++|.+++++|++++
T Consensus        13 ~~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~--~-~~~aWL~~IarN~~~d~~Rk~~~   89 (216)
T PRK12533         13 AAARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG--D-NARPWLLAIVRHTWYSEWRRRAN   89 (216)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCc--c-chHhHHHHHHHHHHHHHHHhhcc
Confidence            34456899999999999999999999999999999999999999999999985  2 49999999999999999998753


Q ss_pred             Cccc------c---------------hh---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHH
Q 011324          403 TIRL------P---------------EN---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLER  450 (488)
Q Consensus       403 ~irl------P---------------~~---v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~  450 (488)
                      ....      .               ..   ..+....+.+++..|...        +-.+.+++|||+.||||+++|+.
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~  169 (216)
T PRK12533         90 AHEVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMS  169 (216)
T ss_pred             cccccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHH
Confidence            2110      0               00   011223344444433221        23478999999999999999999


Q ss_pred             HHHHhCCCc
Q 011324          451 LIFITRMPL  459 (488)
Q Consensus       451 ~L~~ar~~l  459 (488)
                      .+++++..|
T Consensus       170 ~L~RAr~~L  178 (216)
T PRK12533        170 RLARARRRL  178 (216)
T ss_pred             HHHHHHHHH
Confidence            999887654

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.46  E-value=4.2e-13  Score=123.29  Aligned_cols=127  Identities=14%  Similarity=0.117  Sum_probs=98.4

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc--
Q 011324          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP--  407 (488)
Q Consensus       330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP--  407 (488)
                      ++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|+++++|++.   +|.+|++.+++|.+.+++|+..+.....  
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            57899999999999999999999999999999999999999999862   5999999999999999999876532211  


Q ss_pred             ----------hhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          408 ----------ENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       408 ----------~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                                ...   .+....+.++...|+.        ....+.+++|||+.||+|+++|+..+++++..+
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   1111223333332221        223467999999999999999999999887643

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.46  E-value=2.2e-13  Score=126.11  Aligned_cols=133  Identities=11%  Similarity=0.055  Sum_probs=100.4

Q ss_pred             hhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324          324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (488)
Q Consensus       324 ~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr  402 (488)
                      +.|+ .++..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+. ..|...  ..|.+|++.+++|.+++++|++.+
T Consensus         5 ~~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~   81 (172)
T PRK12523          5 QSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAAL   81 (172)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566 899999999999999999999999999999999999999987 446543  369999999999999999998653


Q ss_pred             Ccc--------------cchh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          403 TIR--------------LPEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       403 ~ir--------------lP~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                      ...              -|..   ..+....+.+++..|+        ..+..+.+++|||+.||||+++|+..+++++.
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~  161 (172)
T PRK12523         82 EQAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR  161 (172)
T ss_pred             HHHHHHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            110              0111   0111223333333332        22334789999999999999999999998865


Q ss_pred             Cc
Q 011324          458 PL  459 (488)
Q Consensus       458 ~l  459 (488)
                      .+
T Consensus       162 ~~  163 (172)
T PRK12523        162 QC  163 (172)
T ss_pred             HH
Confidence            54

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.43  E-value=8.8e-13  Score=120.51  Aligned_cols=128  Identities=18%  Similarity=0.116  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl  406 (488)
                      +.+++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|++  .|+.  +..|.+|++.+++|.+.+++|+..+....
T Consensus         2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~   77 (166)
T PRK09639          2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR   77 (166)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence            3689999999999999999999999999999999999999999  6764  34799999999999999999987643211


Q ss_pred             ---------------chhH---HHHHHHHHHHHHH--------HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          407 ---------------PENI---YTLLSKVLEAKRL--------YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       407 ---------------P~~v---~e~l~kI~ka~~~--------L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                                     |...   .+....+.++...        +...+ .+.+++|||+.||+|+++|+..+.+++..+
T Consensus        78 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~L  155 (166)
T PRK09639         78 ILGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKF  155 (166)
T ss_pred             ccchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                           1000   1112223333322        22335 688999999999999999999999887543

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.43  E-value=8.2e-13  Score=126.00  Aligned_cols=126  Identities=13%  Similarity=0.166  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc----
Q 011324          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP----  407 (488)
Q Consensus       332 kLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP----  407 (488)
                      .++..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++++|++.+...++    
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~   89 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSALDA   89 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            348899999999999999999999999999999999999999875  36999999999999999999876532211    


Q ss_pred             -------------------------------hhHH---HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCH
Q 011324          408 -------------------------------ENIY---TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITV  445 (488)
Q Consensus       408 -------------------------------~~v~---e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~  445 (488)
                                                     ....   +....+.+++..|+        ..+..+.+++|||+.||+|+
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~  169 (201)
T PRK12545         90 ELDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTA  169 (201)
T ss_pred             ccchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence                                           0000   01112333333322        22334789999999999999


Q ss_pred             HHHHHHHHHhCCCc
Q 011324          446 EKLERLIFITRMPL  459 (488)
Q Consensus       446 etVk~~L~~ar~~l  459 (488)
                      ++|+..+.+++..+
T Consensus       170 ~tVk~~l~RAr~~L  183 (201)
T PRK12545        170 NHCSVLLYRARTRL  183 (201)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999887643

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.43  E-value=9.3e-13  Score=120.35  Aligned_cols=127  Identities=14%  Similarity=0.122  Sum_probs=97.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI---  404 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i---  404 (488)
                      .|++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..+.|++   ..|.+|++++++|.+++++|+..+..   
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~~~   80 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERAYL   80 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            689999999999999999999999999999999999999999988864   36999999999999999999854211   


Q ss_pred             ----ccc-----h--h---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          405 ----RLP-----E--N---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       405 ----rlP-----~--~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                          ..+     .  .   ..+....+.+++..|+        .....+.+++|||+.||+|+++|+..+++++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~  155 (161)
T PRK12528         81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM  155 (161)
T ss_pred             HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                011     0  0   0111122333333322        22334789999999999999999999988754

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.43  E-value=4.7e-13  Score=122.02  Aligned_cols=122  Identities=11%  Similarity=0.062  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-c-------
Q 011324          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR-L-------  406 (488)
Q Consensus       335 esnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir-l-------  406 (488)
                      +.|.+.|+.+|.++.++..+++|++||+|+.+|+++++|++ .  .|.+|++.+++|.+++++|++.+... .       
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~-~--~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~   78 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQF-R--GLKTWMARIATNHAIDYKRKKARENEELSLCKETE   78 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccccccc-c--hhHHHHHHHHHHHHHHHHHHhcccccccccchhhh
Confidence            57899999999999999999999999999999999999986 2  49999999999999999998654211 0       


Q ss_pred             --------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          407 --------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       407 --------P~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                              |...   .+....+.+++..|+.        .+..+.+++|||+.||+|+++|+..+++++..+
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   0111123333333322        233478999999999999999999999987653

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.43  E-value=1.3e-12  Score=123.11  Aligned_cols=130  Identities=19%  Similarity=0.216  Sum_probs=101.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-  406 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl-  406 (488)
                      .++..++..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++..  .|.+|++.+++|.+++++|++.+.... 
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            57788999999999999999999999999999999999999999998653  699999999999999999986643210 


Q ss_pred             -----------chh-HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          407 -----------PEN-IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       407 -----------P~~-v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                                 +.. .......+.+++..|+        ..+..+.+++|||+.||||+++|+..+++++..+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~L  155 (182)
T PRK12540         83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL  155 (182)
T ss_pred             cccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                       100 0111122333333332        2233478999999999999999999999987654

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.42  E-value=1.3e-12  Score=125.50  Aligned_cols=129  Identities=21%  Similarity=0.277  Sum_probs=100.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc--c
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI--R  405 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i--r  405 (488)
                      .+++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+.+|++  + .|.+|++.+++|.+++++|+..+..  .
T Consensus        28 ~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~~~~~  104 (203)
T PRK09647         28 PSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARIRMEA  104 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccCcccc
Confidence            899999999999999999999999999999999999999999999985  3 6999999999999999999875321  0


Q ss_pred             c-------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          406 L-------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       406 l-------------P~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .             |...   .+....+..++..|.        .....+.+++|||+.|||++++|+..+.+++..+
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~L  182 (203)
T PRK09647        105 LPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL  182 (203)
T ss_pred             ccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            0             0000   011222333333222        1223478999999999999999999999987653

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.42  E-value=1.1e-12  Score=123.92  Aligned_cols=126  Identities=14%  Similarity=0.197  Sum_probs=95.6

Q ss_pred             HHHHHHHHHHHHHHHHHccCCCCC-HhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc---
Q 011324          331 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL---  406 (488)
Q Consensus       331 ekLIesnlrLV~sIAkry~~~g~d-~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl---  406 (488)
                      +..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++++|+..  .+|.+|++.+++|.+++++|++.+....   
T Consensus         8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~   85 (195)
T PRK12532          8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL   85 (195)
T ss_pred             hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence            456778999999999999998888 9999999999999999999864  4799999999999999999987643211   


Q ss_pred             -------------------------------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCC
Q 011324          407 -------------------------------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGIT  444 (488)
Q Consensus       407 -------------------------------P~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS  444 (488)
                                                     |...   .+....+.++...|..        .+..+.+++|||+.||+|
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                                           0000   0111123333333322        223468999999999999


Q ss_pred             HHHHHHHHHHhCCC
Q 011324          445 VEKLERLIFITRMP  458 (488)
Q Consensus       445 ~etVk~~L~~ar~~  458 (488)
                      +++|+..+++++..
T Consensus       166 ~~tVk~~l~Rar~~  179 (195)
T PRK12532        166 TSNYHTIMHRARES  179 (195)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999988754

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.40  E-value=2.5e-12  Score=121.64  Aligned_cols=134  Identities=13%  Similarity=0.031  Sum_probs=102.1

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (488)
Q Consensus       324 ~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~  403 (488)
                      ..+..+++.++..|.+.|+.+|+++.++..+++|++||.|+.+|+.++.|++.  ..|.+|++.+++|.+.+..++..+.
T Consensus        19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~   96 (188)
T PRK12517         19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD   96 (188)
T ss_pred             hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC
Confidence            34558999999999999999999999999999999999999999999999864  3699999999999998887764432


Q ss_pred             cc------cc------hhHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          404 IR------LP------ENIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       404 ir------lP------~~v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ..      .+      .........+..++..|+.        .+..+.+++|||+.|||++++|+..+++++..+
T Consensus        97 ~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L  172 (188)
T PRK12517         97 LVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQL  172 (188)
T ss_pred             ccCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            10      00      0001111223444443332        233478999999999999999999999887643

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.40  E-value=3.1e-12  Score=120.28  Aligned_cols=127  Identities=15%  Similarity=0.195  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011324          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (488)
Q Consensus       330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~  409 (488)
                      ++.|++.|.+.|+.+|.++.++..+++|++||.|+.+|+.+..|+.  +..|.+|++.+++|.+++++|++.+...++..
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~--~~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~   80 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKD--GSSIKSWLYQIANNTIIDFYRKKNRSEELPDD   80 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhcc--ccchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence            6789999999999999999999999999999999999999999985  34799999999999999999987654332210


Q ss_pred             -------------------HHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          410 -------------------IYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       410 -------------------v~e~l~kI~ka~~~L-~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                                         +...+.++....+.+ ......+.+.+|||+.||+|+++|+..+.+++..
T Consensus        81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~  149 (181)
T PRK09637         81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVK  149 (181)
T ss_pred             hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence                               111112222222221 1223347899999999999999999999888653

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.40  E-value=1.7e-12  Score=122.51  Aligned_cols=126  Identities=14%  Similarity=0.150  Sum_probs=95.4

Q ss_pred             HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc---
Q 011324          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP---  407 (488)
Q Consensus       331 ekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP---  407 (488)
                      +.-|..|.+.|+.+|.++.++..+++|++||.|+.+|+.+.+|++.  .+|.+|++++++|.+++++|++.+.....   
T Consensus        10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~   87 (189)
T PRK12530         10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNESELI   87 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCccccc
Confidence            4457788999999999999999999999999999999999999864  36999999999999999999876432110   


Q ss_pred             ----------------------h------h-H--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHH
Q 011324          408 ----------------------E------N-I--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKL  448 (488)
Q Consensus       408 ----------------------~------~-v--~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etV  448 (488)
                                            .      . +  .+....+..++..|+.        .+..+.+++|||+.||+|+++|
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV  167 (189)
T PRK12530         88 EEDSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNL  167 (189)
T ss_pred             ccccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHH
Confidence                                  0      0 0  0001123333333322        2223789999999999999999


Q ss_pred             HHHHHHhCCC
Q 011324          449 ERLIFITRMP  458 (488)
Q Consensus       449 k~~L~~ar~~  458 (488)
                      +..+++++..
T Consensus       168 k~~l~RAr~~  177 (189)
T PRK12530        168 HVLLYRARLQ  177 (189)
T ss_pred             HHHHHHHHHH
Confidence            9999988754

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=99.40  E-value=1.9e-12  Score=122.23  Aligned_cols=127  Identities=11%  Similarity=0.164  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc---
Q 011324          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP---  407 (488)
Q Consensus       331 ekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP---  407 (488)
                      .+.+..|.+.|+.+|+++.++..+++|++||+|+.+|+..++|++.  .+|.+|++.+++|.+++++|++.+....+   
T Consensus         5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~   82 (188)
T TIGR02943         5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLD   82 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccccc
Confidence            3577889999999999999999999999999999999999999864  47999999999999999999876432111   


Q ss_pred             ------------------------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011324          408 ------------------------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE  446 (488)
Q Consensus       408 ------------------------------~~v---~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~e  446 (488)
                                                    ...   .+....+.+++..|+        ..+..+.+++|||+.||+|++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~  162 (188)
T TIGR02943        83 DELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTS  162 (188)
T ss_pred             cccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHH
Confidence                                          000   001122333333322        223347899999999999999


Q ss_pred             HHHHHHHHhCCCc
Q 011324          447 KLERLIFITRMPL  459 (488)
Q Consensus       447 tVk~~L~~ar~~l  459 (488)
                      +|+..+.+++..+
T Consensus       163 tvk~rl~Rar~~L  175 (188)
T TIGR02943       163 NCHVLLYRARLSL  175 (188)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999987654

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.

>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=1e-12  Score=103.51  Aligned_cols=70  Identities=23%  Similarity=0.432  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011324          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (488)
Q Consensus       333 LIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr  402 (488)
                      |++.|.++|++++++|.+++.+.+|++||++++||+++++||+++|..|.+|++.+++|.+.+++|++.+
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            7899999999999999999999999999999999999999999999899999999999999999998764

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 ....

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.39  E-value=2.4e-12  Score=123.87  Aligned_cols=129  Identities=14%  Similarity=0.212  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc-
Q 011324          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP-  407 (488)
Q Consensus       329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP-  407 (488)
                      .-..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|+..  .+|.+|++++++|.+++++|+..+....+ 
T Consensus        19 ~~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~   96 (206)
T PRK12544         19 QDPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASS   96 (206)
T ss_pred             hhHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccccc
Confidence            346788999999999999999999999999999999999999999864  46999999999999999999865432111 


Q ss_pred             ---------------------------------hhHH---HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCC
Q 011324          408 ---------------------------------ENIY---TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGI  443 (488)
Q Consensus       408 ---------------------------------~~v~---e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGI  443 (488)
                                                       ....   +....+.+++..|+        ..+..+.+++|||+.||+
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgi  176 (206)
T PRK12544         97 LLRDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDL  176 (206)
T ss_pred             cccccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCc
Confidence                                             0000   01112222333222        122347799999999999


Q ss_pred             CHHHHHHHHHHhCCCc
Q 011324          444 TVEKLERLIFITRMPL  459 (488)
Q Consensus       444 S~etVk~~L~~ar~~l  459 (488)
                      |+++|+..+++++..+
T Consensus       177 s~~tV~~~l~RAr~~L  192 (206)
T PRK12544        177 SVSNLNVLLYRARLRL  192 (206)
T ss_pred             CHHHHHHHHHHHHHHH
Confidence            9999999999987653

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.39  E-value=1.8e-12  Score=116.80  Aligned_cols=122  Identities=12%  Similarity=0.129  Sum_probs=94.5

Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-------
Q 011324          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-------  406 (488)
Q Consensus       334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl-------  406 (488)
                      +..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++   .+|.||++.++++.+.++++++.+....       
T Consensus         1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~   77 (154)
T TIGR02950         1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGD   77 (154)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccHhhhhh
Confidence            357899999999999998899999999999999999999997   4799999999999999999976532211       


Q ss_pred             --------chhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          407 --------PENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       407 --------P~~v---~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                              |...   .+....+.+++..|+..        ...+.+++|||+.||+|+++|+..+++++..
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~  148 (154)
T TIGR02950        78 LEQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKE  148 (154)
T ss_pred             ccccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                    1100   11123344555544322        2246799999999999999999999988654

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.

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.38  E-value=4.4e-12  Score=120.31  Aligned_cols=128  Identities=17%  Similarity=0.190  Sum_probs=97.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP  407 (488)
                      ++++.|+. |.+.|+++|+++.++..+++|++||.|+.+|+.+..|+..  ..|.+|++.+++|.+++++|+..+.....
T Consensus         8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~~   84 (188)
T PRK12546          8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPDP   84 (188)
T ss_pred             hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccCc
Confidence            56777766 7799999999999999999999999999999999999863  46999999999999999999876432110


Q ss_pred             ------------hh-HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          408 ------------EN-IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       408 ------------~~-v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                                  .. .......+..++..|+.        .+..+.+.+|||+.||||+.+|+..+.+++..
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~  156 (188)
T PRK12546         85 EGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARAR  156 (188)
T ss_pred             ccccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                        00 00111223333333322        12347899999999999999999999988754

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.36  E-value=4.4e-12  Score=117.67  Aligned_cols=123  Identities=19%  Similarity=0.234  Sum_probs=94.5

Q ss_pred             HHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhH----
Q 011324          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI----  410 (488)
Q Consensus       335 esnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v----  410 (488)
                      ..|.+.|+.+++++.++..+++|++||+|+.+|+++.+|+.  +.+|.+|++.+++|.+++++|+..+...++...    
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~--~~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~   79 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKD--GQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD   79 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCC--cccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence            46889999999999999999999999999999999999986  357999999999999999999987544322110    


Q ss_pred             --------HHHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          411 --------YTLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       411 --------~e~l~kI~ka~~~L--------~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                              .+....+.+++..|        ......+.+++|||+.||||+.+|+..+++++..+
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                    11111222222222        12233478999999999999999999999887653

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=99.33  E-value=9.8e-12  Score=117.24  Aligned_cols=128  Identities=13%  Similarity=0.114  Sum_probs=97.2

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc---
Q 011324          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL---  406 (488)
Q Consensus       330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl---  406 (488)
                      .+..+..+.+.|+.+|.++.++..+++|++||.|+.+|+.+..|+..  ..|.+|++.+++|.+++++|++.+....   
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~~~   83 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRADE   83 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccccc
Confidence            44567889999999999999999999999999999999999999863  3699999999999999999986542110   


Q ss_pred             ---------ch--hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          407 ---------PE--NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       407 ---------P~--~v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                               +.  ........+.+++..|+.        .+-.+.+++|||+.||||+++|+..+++++..+
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~L  155 (182)
T PRK12511         84 LAVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL  155 (182)
T ss_pred             hhhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence                     00  011112223333333322        133478999999999999999999999887643

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.32  E-value=2e-11  Score=113.41  Aligned_cols=129  Identities=11%  Similarity=0.080  Sum_probs=97.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR-  405 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir-  405 (488)
                      ..|++.++..|.+.++.++.++.++..+++|++||.|+.+|+. ..|++-.  .|.+|++.+++|.+++++|++.+... 
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            3799999999999999999999999999999999999999998 3565432  58999999999999999997542110 


Q ss_pred             -------------cchhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          406 -------------LPENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       406 -------------lP~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                                   -|...   .+....+.+++..|+.        .+..+.+++|||+.||+++++|+..+++++..
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~  162 (172)
T PRK09651         86 LEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEH  162 (172)
T ss_pred             hhHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence                         01111   1122233334433322        23347799999999999999999999988653

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.28  E-value=2.3e-11  Score=119.62  Aligned_cols=134  Identities=15%  Similarity=0.075  Sum_probs=97.7

Q ss_pred             HHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011324          320 KSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  398 (488)
Q Consensus       320 i~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IR  398 (488)
                      .+....|+ .+++.+++.| +.|+++|.++.++..+++||+||.|+.+|+.   |+..  ..|.+|++.+++|.+++++|
T Consensus         9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~R   82 (228)
T PRK06704          9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIK   82 (228)
T ss_pred             HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHh
Confidence            33444555 7888888877 7899999999999999999999999999985   5543  35999999999999999999


Q ss_pred             HhcCCcccc--------hh-HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          399 QHSRTIRLP--------EN-IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       399 k~sr~irlP--------~~-v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ++.+...+.        .. ..+....+.++...|+..        ...+.|++|||+.||+|+++|+..+++++..+
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            876432211        00 111112233333333221        22367999999999999999999999998754

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.27  E-value=3e-11  Score=110.24  Aligned_cols=124  Identities=17%  Similarity=0.200  Sum_probs=92.4

Q ss_pred             HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc------
Q 011324          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR------  405 (488)
Q Consensus       332 kLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~ir------  405 (488)
                      .++..|.+.|+++|.++.++..+++|++||+++++|+....|++.   .|.+|++.+++|.+++++|++.+...      
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            367889999999999999999999999999999999998877653   48899999999999999997653211      


Q ss_pred             ----cc------hh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          406 ----LP------EN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       406 ----lP------~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                          .+      ..   ..+....+..+...|+        ..+..+.+++|||+.||+|+++|+..+.+++..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~  152 (163)
T PRK07037         79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVH  152 (163)
T ss_pred             cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                11      00   0011222233332221        223347899999999999999999999887653

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.26  E-value=5.3e-11  Score=109.99  Aligned_cols=128  Identities=9%  Similarity=0.055  Sum_probs=95.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc--
Q 011324          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI--  404 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i--  404 (488)
                      +.++.+++..|.+.++++|.++.++..+++|++||.|+.+|+..+.++.   ..|.+|++++++|.+++++|+.....  
T Consensus         8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~   84 (168)
T PRK12525          8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAY   84 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3789999999999999999999999999999999999999986665542   36999999999999999998753210  


Q ss_pred             ------------ccchh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          405 ------------RLPEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       405 ------------rlP~~---v~e~l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                                  ..|..   ..+....+.+++..|+        ..+..+.+++|||+.||+|+++|+..+.+++.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~  160 (168)
T PRK12525         85 LQSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK  160 (168)
T ss_pred             HHHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                        01111   1111222333333322        22334789999999999999999999988754

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.26  E-value=2.8e-11  Score=110.35  Aligned_cols=123  Identities=11%  Similarity=0.083  Sum_probs=91.8

Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-------
Q 011324          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-------  406 (488)
Q Consensus       334 IesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl-------  406 (488)
                      +..|.+.++.++.++.++..+++|++||.|+.+|+..+.|++   .+|.||++.+++|.+++++|++.+....       
T Consensus         1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~   77 (159)
T PRK12527          1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDE   77 (159)
T ss_pred             ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcccccchhhhhc
Confidence            357889999999999999899999999999999999999875   3799999999999999999976421110       


Q ss_pred             --------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          407 --------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       407 --------P~~v---~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                              |...   .+....+..++..|+.        ....+.+++|||+.||+|+++|+..+.+++..+
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~L  149 (159)
T PRK12527         78 EERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC  149 (159)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence                    1111   1112223333333322        233478999999999999999999999886543

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.21  E-value=1e-10  Score=117.82  Aligned_cols=128  Identities=12%  Similarity=0.046  Sum_probs=94.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC--c-
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT--I-  404 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~--i-  404 (488)
                      ..+..|++.|.+.++.+|+++.++..++||++||.|+. |.....|+   ...|.+|++++++|.|++++|++.+.  . 
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~   79 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRETY   79 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhcccccc
Confidence            34678999999999999999999999999999999999 55567775   34799999999999999999976421  1 


Q ss_pred             ---cc----------chhH---HHHH-HHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          405 ---RL----------PENI---YTLL-SKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       405 ---rl----------P~~v---~e~l-~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                         .+          |...   .+.+ ..+..++..|+        .....+.+++|||+.||+|+++|+.++++++..+
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               11          1110   1111 11223333222        1222367999999999999999999999887543

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=99.13  E-value=3.8e-10  Score=113.41  Aligned_cols=124  Identities=17%  Similarity=0.079  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc------c
Q 011324          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI------R  405 (488)
Q Consensus       332 kLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i------r  405 (488)
                      +++..|.+.++.+|+++.++..++||++||+|+.+++.  .|+.  ...|.+|++++++|.|++++|+..+..      .
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~   76 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREVYVGPW   76 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence            37899999999999999999999999999999998775  5543  236999999999999999999764211      1


Q ss_pred             cc----------hhHH---HHHH-HHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          406 LP----------ENIY---TLLS-KVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       406 lP----------~~v~---e~l~-kI~ka~~~L--------~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      +|          ....   +.+. .+..+...|        ......+.+++|||+.||+|+.+|+.++++++..+
T Consensus        77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~L  152 (281)
T TIGR02957        77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHL  152 (281)
T ss_pred             CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            11          1111   1111 111222222        11222367999999999999999999999887654

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.

>PRK09191 two-component response regulator; Provisional

Probab=99.12  E-value=3.2e-10  Score=109.78  Aligned_cols=129  Identities=14%  Similarity=0.086  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC-cccc
Q 011324          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT-IRLP  407 (488)
Q Consensus       329 ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~-irlP  407 (488)
                      ++..|+..|.+.|+++|.++.++..+++|++||+|+.+|+...+|++.  ..|.+|+++++++...+........ ....
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~~~~~~~~~   79 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGANDPEPGSPFE   79 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccCCCCCCCch
Confidence            578999999999999999999999999999999999999999999864  4699999999988764432221100 0011


Q ss_pred             hhHHHHHHHHHHHHHH-HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          408 ENIYTLLSKVLEAKRL-YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       408 ~~v~e~l~kI~ka~~~-L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ..+...+.++....+. +....-.+.|++|||+.||+++++|+..+.+++..+
T Consensus        80 ~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l  132 (261)
T PRK09191         80 ARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEI  132 (261)
T ss_pred             HHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            1234444444433333 222233478999999999999999999998876543

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.12  E-value=2.8e-10  Score=115.36  Aligned_cols=128  Identities=12%  Similarity=-0.039  Sum_probs=94.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC--c-
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT--I-  404 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~--i-  404 (488)
                      ..+..+++.|.+.++.+|+++.++..++||++||.|+.+|++...+    ...|.+|++.+++|.|++++|+..+.  . 
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~~~rr~~~   80 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSASTRRERP   80 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence            5788999999999999999999999999999999999999987543    13599999999999999999975321  0 


Q ss_pred             -----ccc----------hhH---HHH-HHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          405 -----RLP----------ENI---YTL-LSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       405 -----rlP----------~~v---~e~-l~kI~ka~~~L~--------~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                           ..|          ...   .+. ...+..+...|.        .....+.+++|||+.||+|+.+|+.++++++.
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                 111          000   010 112222222221        11223679999999999999999999998876


Q ss_pred             Cc
Q 011324          458 PL  459 (488)
Q Consensus       458 ~l  459 (488)
                      .+
T Consensus       161 ~L  162 (290)
T PRK09635        161 KI  162 (290)
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=99.10  E-value=1.2e-10  Score=95.08  Aligned_cols=75  Identities=29%  Similarity=0.416  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCCCccccccCCC-CCCCCC
Q 011324          412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVMPLLL-SHLPSD  486 (488)
Q Consensus       412 e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~tl~e~i~D~-s~~ped  486 (488)
                      +.+++|.++.+.|.+++||.||.+|||+.|||++++|+.++..++..+|||.+++.+++.++.++|.|+ ..+|++
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e   76 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEE   76 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHH
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhh
Confidence            467899999999999999999999999999999999999999999999999999988889999999998 556654

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 ....

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.06  E-value=9.3e-10  Score=98.71  Aligned_cols=113  Identities=11%  Similarity=0.056  Sum_probs=80.2

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHh-----hCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011324          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (488)
Q Consensus       330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiek-----FDpskG~rFSTYA~~wIRnaI~~~IRk~sr~i  404 (488)
                      ++.|+..|.++++.+|++|..    .+| +||.|+.+|+.+.+     |++  +..|.||++.+++|.+++++|++.+..
T Consensus         1 f~~~~~~y~~~l~~~~~~~~~----~~~-~qdvf~~~w~~~~~~~~~~~~~--~~~~~~wL~~iarN~~id~~Rk~~~~~   73 (142)
T TIGR03209         1 FEEIYMNFKNTIDIFTRKYNL----YYD-YNDILYHLWIILKKIDLNKFNT--ENDLEKYISTSLKRYCLDICNKKNRDK   73 (142)
T ss_pred             ChHHHHHHHHHHHHHHHHhcc----hhh-HHHHHHHHHHHHHHhhhhhcCc--hhHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            468999999999999999965    224 49999999999875     543  246999999999999999999765421


Q ss_pred             cc------------c-hh--HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011324          405 RL------------P-EN--IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE  449 (488)
Q Consensus       405 rl------------P-~~--v~e~l~kI~ka~~~L~~e--------lgr~pS~eEIAe~LGIS~etVk  449 (488)
                      ..            + ..  ..+....+.+++..|+..        ...+.|++|||+.||||+++|+
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            11            0 00  001112233444433322        2246799999999999999986

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=99.01  E-value=1.2e-09  Score=99.15  Aligned_cols=107  Identities=12%  Similarity=0.080  Sum_probs=75.1

Q ss_pred             CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-----------------------
Q 011324          350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-----------------------  406 (488)
Q Consensus       350 ~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irl-----------------------  406 (488)
                      ++..+++|++||+|+.+|+.+..+ +  +..|.+|++.+++|.|++++|++.+....                       
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            345679999999999999998863 3  45799999999999999999986532111                       


Q ss_pred             --------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          407 --------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       407 --------P~~---v~e~l~kI~ka~~~L~~--------elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                              |..   ..+....+.+++..|+.        .+..+.+++|||+.||||+++|+..+++++..+
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   00111223333333322        133478999999999999999999999887543

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=98.76  E-value=1e-07  Score=90.34  Aligned_cols=141  Identities=18%  Similarity=0.185  Sum_probs=96.9

Q ss_pred             HHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCC---CCCHhH--HHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011324          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (488)
Q Consensus       317 eeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~---g~d~ED--LIQEG~IGL~rAiekFDpskG~rFSTYA~~wIR  390 (488)
                      .+|+.+++.|| .|++.|+..|.+-+..+|+++.+.   +.+.+|  |++|.|+.+++.-...+.+.-..|-.|+...++
T Consensus         5 t~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~r   84 (185)
T PF07638_consen    5 TELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMR   84 (185)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHH
Confidence            46888899999 899999999999999999876532   345555  477888877773332233333469999999999


Q ss_pred             HHHHHHHHHhcCCcc------cc---------hhHHHHHHHHHHHHH-----------HHHHhcCCCCcHHHHHHHhCCC
Q 011324          391 QTIRKAIFQHSRTIR------LP---------ENIYTLLSKVLEAKR-----------LYIQEGNHSPDKEDLARRVGIT  444 (488)
Q Consensus       391 naI~~~IRk~sr~ir------lP---------~~v~e~l~kI~ka~~-----------~L~~elgr~pS~eEIAe~LGIS  444 (488)
                      +.+++++|++.+..|      .+         ..-.+.+-.+.++..           .+......+.|.+|||+.||||
T Consensus        85 r~lid~~R~~~a~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgiS  164 (185)
T PF07638_consen   85 RKLIDHARRRQAQKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGIS  164 (185)
T ss_pred             HHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCcC
Confidence            999999997654332      11         000111112222222           1222222378999999999999


Q ss_pred             HHHHHHHHHHhCC
Q 011324          445 VEKLERLIFITRM  457 (488)
Q Consensus       445 ~etVk~~L~~ar~  457 (488)
                      +.+|+..+..++.
T Consensus       165 ~~tV~r~l~~aR~  177 (185)
T PF07638_consen  165 ERTVRRRLRRARA  177 (185)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999988764

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=97.92  E-value=2.7e-06  Score=61.14  Aligned_cols=34  Identities=41%  Similarity=0.464  Sum_probs=30.1

Q ss_pred             CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH
Q 011324          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR  287 (488)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~  287 (488)
                      +|+++.||++|+++|+||++||++|+++|+.+..
T Consensus         1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~   34 (37)
T PF00140_consen    1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE   34 (37)
T ss_dssp             HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence            3789999999999999999999999999998654

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 ....

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=97.13  E-value=0.012  Score=65.96  Aligned_cols=34  Identities=32%  Similarity=0.493  Sum_probs=31.7

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHH
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI  286 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~  286 (488)
                      .+||+++||+++|+.||||+|+|++++++|..+.
T Consensus       102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~  135 (619)
T PRK05658        102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE  135 (619)
T ss_pred             CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999998754

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

Probab=96.48  E-value=0.023  Score=55.89  Aligned_cols=33  Identities=33%  Similarity=0.579  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      +.++...+...+|++||.+|.|+.+|++.+.+.
T Consensus        89 ~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~  121 (238)
T TIGR02393        89 LIKAERQLTQELGREPTDEELAERMGMPAEKVR  121 (238)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            445667788889999999999999999987664

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.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=96.25  E-value=0.039  Score=54.64  Aligned_cols=30  Identities=0%  Similarity=0.129  Sum_probs=26.4

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      ..+.|++|||+.||+|+++|+..+++++..
T Consensus       215 ~~~~s~~EIA~~lgis~~tV~~~~~ra~~~  244 (251)
T PRK07670        215 KEELTLTEIGQVLNLSTSRISQIHSKALFK  244 (251)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            347899999999999999999999887654

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=96.17  E-value=0.031  Score=55.89  Aligned_cols=30  Identities=3%  Similarity=0.149  Sum_probs=26.1

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      ..+.|++|||+.||+|.++|+.+++++...
T Consensus       219 ~e~~t~~EIA~~lgis~~~V~~~~~ral~k  248 (257)
T PRK05911        219 YEELVLKEIGKILGVSESRVSQIHSKALLK  248 (257)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            447899999999999999999998877543

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=96.14  E-value=0.015  Score=58.14  Aligned_cols=34  Identities=29%  Similarity=0.510  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      ++.++...|...+|++|+..+.|+.+|++.+++.
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~  147 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQ  147 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHH
Confidence            3455677888899999999999999999987664

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

Probab=96.11  E-value=0.17  Score=50.89  Aligned_cols=149  Identities=19%  Similarity=0.192  Sum_probs=83.8

Q ss_pred             HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHH
Q 011324          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (488)
Q Consensus       256 ~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIe  335 (488)
                      .+..||++-.  +.--+.--.+++.      +++.+..+|+..+||+||..|.|...|++.+++...+..+.        
T Consensus        88 ei~d~LR~~~--~v~vpR~~~~~~~------~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~--------  151 (247)
T COG1191          88 EILDYLRKND--SVKVPRSLRELGR------RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAIN--------  151 (247)
T ss_pred             HHHHHHHhCC--CccCcHHHHHHHH------HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhc--------
Confidence            5667888876  2112222233333      45567788999999999999999999999877764443332        


Q ss_pred             HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHH
Q 011324          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  415 (488)
Q Consensus       336 snlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~  415 (488)
                        -.....+-......+...              +.   ..-+..+..+-.+...+.+...+.      .+|..    - 
T Consensus       152 --~~~~~sld~~~~~~~d~~--------------~~---~~~~~~~~~~~~~~~~~~l~~ai~------~L~ER----E-  201 (247)
T COG1191         152 --GSQLLSLDEDVLKDDDDD--------------VD---DQIENPDDGVEKEELLEILKEAIE------PLPER----E-  201 (247)
T ss_pred             --cccccchhhhhccccccc--------------hh---hccccchhHHHHHHHHHHHHHHHH------ccCHH----H-
Confidence              111111111111111100              11   111233445555555566665554      12211    0 


Q ss_pred             HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324          416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT  455 (488)
Q Consensus       416 kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a  455 (488)
                         +.  -+...+..+.|..|||+.||||+.+|-.+...+
T Consensus       202 ---k~--Vl~l~y~eelt~kEI~~~LgISes~VSql~kka  236 (247)
T COG1191         202 ---KL--VLVLRYKEELTQKEIAEVLGISESRVSRLHKKA  236 (247)
T ss_pred             ---HH--HHHHHHHhccCHHHHHHHhCccHHHHHHHHHHH
Confidence               11  122233447899999999999999998876654

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=96.02  E-value=0.072  Score=53.37  Aligned_cols=34  Identities=26%  Similarity=0.526  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      .+.+....|+..+|++|+..+.|...|++.+.+.
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~  152 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYN  152 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence            4555667788889999999999999999876654

>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=96.01  E-value=0.022  Score=46.00  Aligned_cols=56  Identities=18%  Similarity=0.301  Sum_probs=46.6

Q ss_pred             HHHHhhhcH-HHHHHHHHHHHHHHHHHHHHcc----C--CCCCHhHHHHHHHHHHHHhHHhhC
Q 011324          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQ----G--RGISLHDLLQEGSMGLMKSVEKFK  374 (488)
Q Consensus       319 Li~~l~~Gd-~ArekLIesnlrLV~sIAkry~----~--~g~d~EDLIQEG~IGL~rAiekFD  374 (488)
                      ++.++.+|| .|.+++++.|.+++.+.+.|-.    +  .+.--+|+-|+--..|++++-+|+
T Consensus         3 vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen    3 VIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            556677777 9999999999999999998722    2  244569999999999999999996

Some proteins with this domain are annotated as conjugative transposon proteins.

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=96.00  E-value=0.1  Score=55.01  Aligned_cols=128  Identities=20%  Similarity=0.251  Sum_probs=70.9

Q ss_pred             HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHH-HHHHH
Q 011324          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMGL  366 (488)
Q Consensus       288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQE-G~IGL  366 (488)
                      +.+...+|...+|++||..|.|+.+|++.+.+...+..                   +.+    ...+++.+.+ +-..|
T Consensus       218 ~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~-------------------~~~----~~SLd~~~~~~~~~~l  274 (367)
T PRK09210        218 LIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI-------------------AQE----PVSLETPIGEEDDSHL  274 (367)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------hcC----CCCcCCCCCCCCcchh
Confidence            45567788889999999999999999998776432211                   111    1111111111 00111


Q ss_pred             HHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhc----CCCCcHHHHHHHhC
Q 011324          367 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG----NHSPDKEDLARRVG  442 (488)
Q Consensus       367 ~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~el----gr~pS~eEIAe~LG  442 (488)
                      ...+.  |..............++..+.++|.      .+|..-.    .|      +...+    +.+.|.+|||+.||
T Consensus       275 ~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr----~V------l~lrygl~~~~~~tl~EIa~~lg  336 (367)
T PRK09210        275 GDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREE----NV------LRLRFGLDDGRTRTLEEVGKVFG  336 (367)
T ss_pred             hhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHH----HH------HHHHhccCCCCCccHHHHHHHHC
Confidence            11121  1111223344445555555555553      2332111    11      22222    35789999999999


Q ss_pred             CCHHHHHHHHHHhC
Q 011324          443 ITVEKLERLIFITR  456 (488)
Q Consensus       443 IS~etVk~~L~~ar  456 (488)
                      +|.++|+.+...|.
T Consensus       337 vs~erVrQi~~~Al  350 (367)
T PRK09210        337 VTRERIRQIEAKAL  350 (367)
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999999977663

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=95.97  E-value=0.055  Score=54.42  Aligned_cols=34  Identities=26%  Similarity=0.524  Sum_probs=28.2

Q ss_pred             HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011324          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (488)
Q Consensus       288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~  321 (488)
                      +.+...++...+|++||..|.|+.+|++.+++..
T Consensus       129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~  162 (264)
T PRK07122        129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE  162 (264)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            4456677888899999999999999999877643

>PRK05949 RNA polymerase sigma factor; Validated

Probab=95.82  E-value=0.053  Score=56.41  Aligned_cols=34  Identities=26%  Similarity=0.472  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      ++.+.+..+...+|++|+..|.|+.+|++.+.+.
T Consensus       179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~  212 (327)
T PRK05949        179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIR  212 (327)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            3455666777889999999999999999987664

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=95.75  E-value=0.16  Score=55.97  Aligned_cols=34  Identities=32%  Similarity=0.567  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      ++.+++.+|...+|++||.+|.|+.+|++.+.+.
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~  392 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVR  392 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            4556778888999999999999999999987664

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=95.69  E-value=0.13  Score=52.37  Aligned_cols=30  Identities=20%  Similarity=0.279  Sum_probs=26.2

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .+.|.+|||+.||||.++|+.+++.+...+
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~kL  273 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEARALEKL  273 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            478999999999999999999998876543

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=95.57  E-value=0.13  Score=55.32  Aligned_cols=35  Identities=20%  Similarity=0.485  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~  321 (488)
                      ++.+.+..|...+|+.|+..|.|+.+||+.+.+..
T Consensus       263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~  297 (415)
T PRK07598        263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE  297 (415)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            56677888888999999999999999999887753

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=95.41  E-value=0.043  Score=53.42  Aligned_cols=31  Identities=39%  Similarity=0.612  Sum_probs=25.8

Q ss_pred             HHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       290 ~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      +....+...+|++||..+.|+.+|++.+++.
T Consensus       101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~  131 (231)
T TIGR02885       101 YMKEELSKELGREPTINELAEALGVSPEEIV  131 (231)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHH
Confidence            3456677788999999999999999987664

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.

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=95.38  E-value=0.16  Score=52.83  Aligned_cols=34  Identities=32%  Similarity=0.460  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      ++.++..+|...+|++||..|.|+.+|++.+.+.
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~  207 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIA  207 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            4556778888899999999999999999987664

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

Probab=95.26  E-value=0.23  Score=50.64  Aligned_cols=34  Identities=26%  Similarity=0.509  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      ++.+.+..+...+|++|+..+.|+.+|++.+.+.
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~  195 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVR  195 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            4455666777889999999999999999987764

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).

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

Probab=94.85  E-value=0.25  Score=47.88  Aligned_cols=34  Identities=32%  Similarity=0.651  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      ++.++..++...+|++|+.++.|+.+|++.+++.
T Consensus        84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~  117 (224)
T TIGR02479        84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYR  117 (224)
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHH
Confidence            3455667788889999999999999999876653

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.

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=94.82  E-value=0.15  Score=52.72  Aligned_cols=34  Identities=26%  Similarity=0.522  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      ++.+.+..+...+|++|+..+.|+.+|++.+.+.
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~  202 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR  202 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            4556777788889999999999999999876653

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=94.79  E-value=0.16  Score=50.28  Aligned_cols=29  Identities=17%  Similarity=0.250  Sum_probs=25.5

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                      ..+.|++|||+.||+++++|+.++++++.
T Consensus       219 ~~g~s~~eIA~~lgis~~~V~~~~~ra~~  247 (255)
T TIGR02941       219 EENLSQKETGERLGISQMHVSRLQRQAIS  247 (255)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            44789999999999999999999887754

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

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=94.73  E-value=0.31  Score=51.79  Aligned_cols=34  Identities=32%  Similarity=0.584  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      ++.+....|...+|++||..|.|+.+|++.+.+.
T Consensus       224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~  257 (373)
T PRK07406        224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLR  257 (373)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            4556677888899999999999999999987663

>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=94.61  E-value=0.072  Score=43.20  Aligned_cols=37  Identities=30%  Similarity=0.593  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHH
Q 011324          286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  322 (488)
Q Consensus       286 ~~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~  322 (488)
                      .++.+++.+|+..+||+||.+|.|+.+|++.+++...
T Consensus         4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~   40 (78)
T PF04539_consen    4 RKIERARRELEQELGREPTDEEIAEELGISVEEVREL   40 (78)
T ss_dssp             HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHH
Confidence            3567889999999999999999999999998777543

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 ....

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=94.52  E-value=0.49  Score=47.03  Aligned_cols=35  Identities=26%  Similarity=0.297  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHH
Q 011324          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  322 (488)
Q Consensus       288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~  322 (488)
                      +.+...++...+|++|+.++.|+.+|++.+++...
T Consensus       122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~  156 (254)
T TIGR02850       122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA  156 (254)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            33456677788999999999999999998877543

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.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=93.81  E-value=0.53  Score=46.09  Aligned_cols=30  Identities=3%  Similarity=0.147  Sum_probs=26.3

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      ..+.|++|||+.||+|+++|+..+++++..
T Consensus       198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~~  227 (236)
T PRK06986        198 QEELNLKEIGAVLGVSESRVSQIHSQAIKR  227 (236)
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            347899999999999999999999887654

>PRK05572 sporulation sigma factor SigF; Validated

Probab=93.56  E-value=0.49  Score=46.92  Aligned_cols=29  Identities=21%  Similarity=0.308  Sum_probs=25.2

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      .+.|.+|||+.+|++..+|..+.+++...
T Consensus       217 ~~~s~~eIA~~lgis~~~V~~~~~ral~k  245 (252)
T PRK05572        217 KDKTQSEVAKRLGISQVQVSRLEKKILKQ  245 (252)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            47899999999999999999998876543

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=93.28  E-value=0.76  Score=45.72  Aligned_cols=33  Identities=24%  Similarity=0.307  Sum_probs=26.9

Q ss_pred             HHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011324          289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (488)
Q Consensus       289 e~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~  321 (488)
                      .+...++...+|++|+..|.|..+|++.+++..
T Consensus       126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~  158 (258)
T PRK08215        126 LQVREKLINENSKEPTVEEIAKELEVPREEVVF  158 (258)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence            345567777889999999999999999887653

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

Probab=93.18  E-value=0.47  Score=45.95  Aligned_cols=29  Identities=21%  Similarity=0.350  Sum_probs=25.6

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      .+.|++|||+.||++..+|+.+++++...
T Consensus       193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~~  221 (227)
T TIGR02980       193 EDKTQSEIAERLGISQMHVSRLLRRALKK  221 (227)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            47899999999999999999999887543

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.

>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=92.53  E-value=0.11  Score=39.34  Aligned_cols=31  Identities=16%  Similarity=0.171  Sum_probs=23.2

Q ss_pred             hcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          427 EGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       427 elgr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                      .+..+.+.+|||+.+|+|+.+|+..+.+++.
T Consensus        22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   22 RYFQGMSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             HHTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             HHHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            3455789999999999999999999988753

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.

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=92.43  E-value=1  Score=44.32  Aligned_cols=33  Identities=15%  Similarity=0.402  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011324          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (488)
Q Consensus       288 le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi  320 (488)
                      +.+....+...+|++|+..+.|+.+|++.+++.
T Consensus       103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~  135 (231)
T PRK12427        103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQ  135 (231)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence            345567788889999999999999999987764

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=92.36  E-value=0.72  Score=45.74  Aligned_cols=30  Identities=17%  Similarity=0.194  Sum_probs=26.1

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      ..+.+++|||+.||||.++|+.++++++..
T Consensus       219 ~~g~s~~eIA~~l~is~~tV~~~~~ra~~k  248 (257)
T PRK08583        219 IENLSQKETGERLGISQMHVSRLQRQAIKK  248 (257)
T ss_pred             hCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            347899999999999999999999877643

>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=91.88  E-value=0.52  Score=37.95  Aligned_cols=43  Identities=26%  Similarity=0.409  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCC-HHHHHHHHHH
Q 011324          412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI  454 (488)
Q Consensus       412 e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS-~etVk~~L~~  454 (488)
                      +.-.+|-..+..+..+.|..||+.|||+.+|+. ...|...|..
T Consensus         6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~   49 (65)
T PF01726_consen    6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA   49 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            445566677777788888899999999999997 9999988864

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.

>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=91.85  E-value=0.45  Score=35.53  Aligned_cols=31  Identities=19%  Similarity=0.239  Sum_probs=25.6

Q ss_pred             HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324          426 QEGNHSPDKEDLARRVGITVEKLERLIFITR  456 (488)
Q Consensus       426 ~elgr~pS~eEIAe~LGIS~etVk~~L~~ar  456 (488)
                      ..+..+.|.+|||+.||+|.++|+.+...+.
T Consensus        15 ~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al   45 (50)
T PF04545_consen   15 LRYFEGLTLEEIAERLGISRSTVRRILKRAL   45 (50)
T ss_dssp             HHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence            3446688999999999999999999988764

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 ....

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=91.69  E-value=0.37  Score=48.75  Aligned_cols=31  Identities=23%  Similarity=0.323  Sum_probs=27.3

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ..+.|++|||+.||+|+++|+.++++|+..+
T Consensus       240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkL  270 (285)
T TIGR02394       240 YEPATLEEVAAEVGLTRERVRQIQVEALKKL  270 (285)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999887654

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).

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=91.39  E-value=0.55  Score=44.82  Aligned_cols=66  Identities=12%  Similarity=0.151  Sum_probs=53.3

Q ss_pred             HHHHHHHHHHHHccCCCCC---HhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011324          336 ANLRLVVHVAKQYQGRGIS---LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (488)
Q Consensus       336 snlrLV~sIAkry~~~g~d---~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~s  401 (488)
                      +-+..+-.+.++|.-+|-.   -+|+|.+|.-.+++.+..||+++...+-+|+..++-++..+.|.+..
T Consensus        45 ~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk  113 (179)
T PHA02547         45 AIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK  113 (179)
T ss_pred             HHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence            3445555566665444544   59999999999999999999999999999999999999998887654

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=89.48  E-value=7.6  Score=39.53  Aligned_cols=28  Identities=14%  Similarity=0.253  Sum_probs=24.6

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                      .+.|.+|||+.||+|.++|+.+...+..
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al~  274 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEKNAMK  274 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4789999999999999999999887643

>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=87.84  E-value=1.8  Score=31.89  Aligned_cols=34  Identities=21%  Similarity=0.238  Sum_probs=23.4

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324          420 AKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI  454 (488)
Q Consensus       420 a~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~  454 (488)
                      .+-.+.+..+ ..++.|||+.+|+|..+|..++++
T Consensus         7 ~Il~~Lq~d~-r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    7 KILRLLQEDG-RRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             HHHHHHHH-T-TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHcC-CccHHHHHHHHCcCHHHHHHHHHH
Confidence            3333334445 579999999999999999998764

...

>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=85.22  E-value=1.7  Score=31.03  Aligned_cols=28  Identities=14%  Similarity=0.209  Sum_probs=24.7

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                      .+.+..+||+.+|++..+|...+..++.
T Consensus        25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~   52 (55)
T cd06171          25 EGLSYEEIAEILGISRSTVRQRLHRALK   52 (55)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4789999999999999999999887654

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

>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=84.13  E-value=2.9  Score=32.21  Aligned_cols=48  Identities=21%  Similarity=0.320  Sum_probs=35.5

Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHH
Q 011324          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI  452 (488)
Q Consensus       405 rlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L  452 (488)
                      .+|....+.+...-+....|..++....+-.|||+.+|++..+|+.=+
T Consensus         2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl   49 (50)
T PF06971_consen    2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKDL   49 (50)
T ss_dssp             S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence            467667777777777777888777778899999999999999998643

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 ....

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=82.91  E-value=4.5  Score=42.85  Aligned_cols=126  Identities=10%  Similarity=0.026  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhH
Q 011324          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  410 (488)
Q Consensus       331 ekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP~~v  410 (488)
                      +..+..-.+.+..-.-+|.++-.-.||.+||+|+..++.-.+=.+-+  .-..|++-.-||.-++.+|++.+.-..|.+.
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            33444444445544455666666789999999987665555444433  3789999999999999999987654444322


Q ss_pred             HHHH---------------------HHH---------HHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          411 YTLL---------------------SKV---------LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       411 ~e~l---------------------~kI---------~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      ....                     +-|         ......|.-..--+.|..|||...=+++.++.+++-+++..
T Consensus        86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~r  163 (415)
T COG4941          86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKAR  163 (415)
T ss_pred             cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            1111                     110         01111122222226799999999999999999998877654

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=82.86  E-value=2.3  Score=35.36  Aligned_cols=25  Identities=12%  Similarity=0.155  Sum_probs=22.7

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFI  454 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~  454 (488)
                      .+.|+.|||+.||+|+.+|+..+..
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            3789999999999999999999873

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.

>PRK06930 positive control sigma-like factor; Validated

Probab=82.54  E-value=1.3  Score=42.09  Aligned_cols=31  Identities=10%  Similarity=0.082  Sum_probs=26.9

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          428 GNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      +..+.++.|||+.||+++++|+..+.+++..
T Consensus       127 ~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~k  157 (170)
T PRK06930        127 RGYGLSYSEIADYLNIKKSTVQSMIERAEKK  157 (170)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            3347899999999999999999999988654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	488
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		2e-30
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		6e-30
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		6e-30
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		3e-29
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		1e-28
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		1e-28
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		1e-28
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		2e-26
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		3e-26
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		8e-21
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		9e-18
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		3e-10

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score =  130 bits (326), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/240 (33%), Positives = 138/240 (57%), Gaps = 23/240 (9%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 311 AIGLSC------------RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISL 355
            +G +             ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S 
Sbjct: 59  ILGTARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSF 118
Query: 356 HDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 415
            DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +RTIR+P ++   ++
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETIN 178
Query: 416 KVLEAKRLYIQEGNHSPDKEDLARRVGIT--VEKLERLIFITRMPLSMQQPVWADQDTTF 473
           K+    R   QE    P  E++A  +G     +++E  + I + P+S++ P+  ++D+ +
Sbjct: 179 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFY 238

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score =  128 bits (322), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 57/160 (35%), Positives = 106/160 (66%), Gaps = 4/160 (2%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 431
           KF+ + G +F++YA WW+RQ I ++I   +RTIR+P ++   ++K+    R  +QE    
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 432 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
           P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+D+
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517

>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613

Iteration: 1
 Score =  128 bits (322), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 57/160 (35%), Positives = 106/160 (66%), Gaps = 4/160 (2%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 431
           KF+ + G +F++YA WW+RQ I ++I   +RTIR+P ++   ++K+    R  +QE    
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 432 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
           P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+D+
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score =  126 bits (316), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 80/255 (31%), Positives = 138/255 (54%), Gaps = 38/255 (14%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 93  SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 149
Query: 311 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 340
            +G +                            ++LK  LH    G ++R+ LI ANLRL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 341 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400
           VV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT--VEKLERLIFITRMP 458
           +RTIR+P ++   ++K+    R   QE    P  E++A  +G     +++E  + I + P
Sbjct: 270 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 329
Query: 459 LSMQQPVWADQDTTF 473
           +S++ P+  ++D+ +
Sbjct: 330 VSLETPIGDEKDSFY 344

>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423

Iteration: 1
 Score =  124 bits (311), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 63/165 (38%), Positives = 106/165 (64%), Gaps = 5/165 (3%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT- 444
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 445 -VEKLERLIFITRMPLSMQQPVWADQDTTF-QVMPLLLSHLPSDI 487
             +++E  + I + P+S++ P+  ++D+ +   +P    HLPS +
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIP--DEHLPSPV 342

>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423

Iteration: 1
 Score =  124 bits (311), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 63/165 (38%), Positives = 106/165 (64%), Gaps = 5/165 (3%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT- 444
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 445 -VEKLERLIFITRMPLSMQQPVWADQDTTF-QVMPLLLSHLPSDI 487
             +++E  + I + P+S++ P+  ++D+ +   +P    HLPS +
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIP--DEHLPSPV 342

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score =  124 bits (310), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 63/165 (38%), Positives = 106/165 (64%), Gaps = 5/165 (3%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT- 444
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 445 -VEKLERLIFITRMPLSMQQPVWADQDTTF-QVMPLLLSHLPSDI 487
             +++E  + I + P+S++ P+  ++D+ +   +P    HLPS +
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIP--DEHLPSPV 362

>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 =  116 bits (291), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 60/150 (40%), Positives = 97/150 (64%), Gaps = 5/150 (3%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 92  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 151
Query: 374 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 433
           + +   +F++YA WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P 
Sbjct: 152 EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPS 211
Query: 434 KEDLARRVGIT--VEKLERLIFITRMPLSM 461
            E++A  +G     +++E  + I + P+S+
Sbjct: 212 YEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241

>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 =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 60/150 (40%), Positives = 97/150 (64%), Gaps = 5/150 (3%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 96  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 155
Query: 374 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 433
           + +   +F++YA WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P 
Sbjct: 156 EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPS 215
Query: 434 KEDLARRVGIT--VEKLERLIFITRMPLSM 461
            E++A  +G     +++E  + I + P+S+
Sbjct: 216 YEEIAEAMGPGWDAKRVEETLKIAQEPVSL 245

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 98.6 bits (244), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 45/89 (50%), Positives = 65/89 (73%), Gaps = 3/89 (3%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 91  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 374 KPQAGCRFASYAYWWVRQTIRKAIFQHSR 402
           + + G  F++YA WW+RQ I +AI   +R
Sbjct: 151 EYKRGFAFSTYATWWIRQAINRAIADQAR 179

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 88.2 bits (217), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 34/74 (45%), Positives = 58/74 (78%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 389 VRQTIRKAIFQHSR 402
           +RQ I ++I   +R
Sbjct: 326 IRQAITRSIADQAR 339

>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 = 63.2 bits (152), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 37/138 (26%), Positives = 75/138 (54%), Gaps = 1/138 (0%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           +R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF      +F++YA   
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
           +   I++   +   T+++  ++  + +K+ +AK    +    +P   ++A  +GI+ E +
Sbjct: 89  IIGEIQR-FLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 449 ERLIFITRMPLSMQQPVW 466
                  R+P S+ + V+
Sbjct: 148 VLAQEAVRLPTSIHETVY 165

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	488
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	1e-39
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	1e-39
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	5e-39
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	1e-38
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	4e-38
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	1e-25
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	2e-23
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-10
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	6e-07

>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 =  147 bits (373), Expect = 1e-39
 Identities = 75/258 (29%), Positives = 130/258 (50%), Gaps = 32/258 (12%)

Query: 248 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQ---------------------DLI 286
                 +DP+R +L       LLT +EE EL  +++                     +++
Sbjct: 72  IPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVV 131

Query: 287 RLEKEKSKL--QSQFGREPTLIEWAKAIGLSCRDLKSEL-------HSGNSSREKLINAN 337
           R +   S         +E    +  + I    + L  E          G ++R+ LI AN
Sbjct: 132 RAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEAN 191

Query: 338 LRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397
           LRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI
Sbjct: 192 LRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAI 251

Query: 398 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR--VGITVEKLERLIFIT 455
              +RTIR+P ++   ++K+    R   QE    P  E++A     G   +++E  + I 
Sbjct: 252 ADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIA 311

Query: 456 RMPLSMQQPVWADQDTTF 473
           + P+S++ P+  ++D+ +
Sbjct: 312 QEPVSLETPIGDEKDSFY 329

>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 =  142 bits (359), Expect = 1e-39
 Identities = 71/242 (29%), Positives = 122/242 (50%), Gaps = 36/242 (14%)

Query: 254 NDPLRLFLWGPETRK--LLTADEEFELIAQI------------------QDLIRLEKEKS 293
           +DP+R +L   E  +  LLT +EE +L  ++                  + +  + + K 
Sbjct: 6   SDPVRQYLH--EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKI 63

Query: 294 KLQSQFGREPTLIEWAKAIGLS------------CRDLKSELHSGNSSREKLINANLRLV 341
              ++  + P L E      +              +        G ++R+ LI ANLRLV
Sbjct: 64  LGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLV 123

Query: 342 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401
           V +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +
Sbjct: 124 VSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQA 183

Query: 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR--VGITVEKLERLIFITRMPL 459
           RTIR+P ++   ++K+    R   QE    P  E++A     G   +++E  + I + P+
Sbjct: 184 RTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV 243

Query: 460 SM 461
           S+
Sbjct: 244 SL 245

>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 =  146 bits (369), Expect = 5e-39
 Identities = 66/213 (30%), Positives = 113/213 (53%), Gaps = 6/213 (2%)

Query: 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322
           G +   +        L       I   KEK   ++    +  L    K +    +     
Sbjct: 136 GLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKEL----KRYLHI 191

Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
              G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F+
Sbjct: 192 AREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 251

Query: 383 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR-- 440
           +YA WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A    
Sbjct: 252 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMG 311

Query: 441 VGITVEKLERLIFITRMPLSMQQPVWADQDTTF 473
            G   +++E  + I + P+S++ P+  ++D+ +
Sbjct: 312 PGWDAKRVEETLKIAQEPVSLETPIGDEKDSFY 344

>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 =  139 bits (353), Expect = 1e-38
 Identities = 39/161 (24%), Positives = 82/161 (50%), Gaps = 2/161 (1%)

Query: 317 RDLKSELHSGNSS-REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 375
           ++L      G+   R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF  
Sbjct: 16  KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDL 75

Query: 376 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 435
               +F++YA   +   I++ +     T+++  ++  + +K+ +AK    +    +P   
Sbjct: 76  SYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVT 134

Query: 436 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQVM 476
           ++A  +GI+ E +       R+P S+ + V+ +      ++
Sbjct: 135 EIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLL 175

>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 =  146 bits (369), Expect = 4e-38
 Identities = 88/424 (20%), Positives = 177/424 (41%), Gaps = 37/424 (8%)

Query: 74  PLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM 133
            LL    E   ++   D  N    +     +    L +    +E +     DL       
Sbjct: 109 ELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDP 168

Query: 134 KRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTD 193
              ED + + T        E+  D E  D      +           + +P+L   +F +
Sbjct: 169 NAEEDLAPTATHVGSELSQEDLDDDEDED-----EEDGDDDSADDDNSIDPELAREKFAE 223

Query: 194 ISLTSSLGYPLEEVKQFSQPRFLERRSK----------KRKVSKPQVTNHETYNSRKASV 243
           +     +     + K  S     E   K            K     V +      R  + 
Sbjct: 224 LRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQ 283

Query: 244 KKKLSE------GFDRNDPLRLFL-------WGPETRKLLTADEEFELIAQIQDLIRLEK 290
           ++ + +         + + + LF        W      +     E  L    +++ R  +
Sbjct: 284 ERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEK-LHDVSEEVHRALQ 342

Query: 291 EKSKLQSQFGREPT-LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQ 349
           +  +++ + G     + +  + + +     +        ++++++ ANLRLV+ +AK+Y 
Sbjct: 343 KLQQIEEETGLTIEQVKDINRRMSIGEAKARR-------AKKEMVEANLRLVISIAKKYT 395

Query: 350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409
            RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I   +RTIR+P +
Sbjct: 396 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 455

Query: 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 469
           +   ++K+    R  +QE    P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+
Sbjct: 456 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDE 515

Query: 470 DTTF 473
           D+  
Sbjct: 516 DSHL 519

>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 =  103 bits (260), Expect = 1e-25
 Identities = 32/160 (20%), Positives = 70/160 (43%), Gaps = 10/160 (6%)

Query: 324 HSGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 8   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67

Query: 381 FASYAYWWVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLAR 439
             +Y    ++     AI+ + R++      +     ++ E      ++    P  E++A+
Sbjct: 68  AEAYIKLRIKG----AIYDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAK 123

Query: 440 RVGITVEKLERLIFITRMP--LSMQQPVWADQDTTFQVMP 477
            +GI+ E+L + +        LS+++          +++P
Sbjct: 124 ELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIP 163

>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 =   99 bits (249), Expect = 2e-23
 Identities = 40/123 (32%), Positives = 69/123 (56%), Gaps = 10/123 (8%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK-------LINANLR 339
           +L     ++     +   L +  +  GL+   +K      +    K       ++ ANLR
Sbjct: 220 KLHDVSEEVHRALQK---LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLR 276

Query: 340 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399
           LV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I  
Sbjct: 277 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 336

Query: 400 HSR 402
            +R
Sbjct: 337 QAR 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 = 62.9 bits (152), Expect = 2e-10
 Identities = 63/506 (12%), Positives = 142/506 (28%), Gaps = 134/506 (26%)

Query: 58  HFPTSVLLQEQRDEYRPLLHMFK------------EDKTSQATSD--------SRNIETE 97
           H        E + +Y+ +L +F+            +D      S         S++  + 
Sbjct: 6   HMDFET--GEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG 63

Query: 98  AFFV----EEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTM-----QSL 148
              +      K    + + V+++      +  L   SP       PS+   M       L
Sbjct: 64  TLRLFWTLLSKQEEMVQKFVEEVLRINYKF--LM--SPIKTEQRQPSMMTRMYIEQRDRL 119

Query: 149 SNDTEESVD-----AEPFDAVALARKALSASKEAASLAENPKLNG-AEFTDISLTSSLGY 202
            ND +          +P+  +   R+AL   + A ++     ++G        +   +  
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKL---RQALLELRPAKNVL----IDGVLGSGKTWVALDVCL 172

Query: 203 PLEEVKQFSQPRF---LERRSKKRKVSKPQVT-------NHETYNSRKASVKKKLSEGFD 252
             +   +     F   L+  +    V +           N  + +   +++K ++     
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 253 RNDPLRLFLWGPETRKLLTAD--------EEFE-----LI----AQIQDLIRLEKEK--- 292
                RL    P    LL             F      L+     Q+ D +         
Sbjct: 233 E--LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHIS 290

Query: 293 -SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGR 351
                     +       K +    +DL  E+ + N  R  +I  ++R  +     ++  
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK-- 348

Query: 352 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK-AIFQHSRTIRLPENI 410
               H    + +  +  S+   +P              R+   + ++F  S    +P  +
Sbjct: 349 ----HVNCDKLTTIIESSLNVLEPAE-----------YRKMFDRLSVFPPS--AHIPTIL 391

Query: 411 YTLL-----------------SKVLEAKR----------LYIQEGNHSPDKEDLARRVGI 443
            +L+                    L  K+          +Y++      ++  L R +  
Sbjct: 392 LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSI-- 449

Query: 444 TVEKLERLIFITRMPLSMQQPVWADQ 469
               ++              P + DQ
Sbjct: 450 ----VDHYNIPKTFDSDDLIPPYLDQ 471

>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 = 48.3 bits (115), Expect = 6e-07
 Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 352 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 411
           G    DL+QEG +GL+K+++ +       F+S+A+  +R+ +  AI + +    +  N  
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDET-KSSFSSFAFLCIRREMISAIRKANTQKHMVLNEA 59

Query: 412 TLLSKVLEAKRLYIQEGNHSPD 433
              + +LE    +  EG++  +
Sbjct: 60  LKTNAILEDSAYFDDEGHNINN 81

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	488
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	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	99.93
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.8
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.76
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.7
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.7
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.67
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.5
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.36
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.31
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	99.22
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	99.14
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	97.85
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	94.05
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	93.98
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	93.89
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	92.94
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	92.72
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	92.15
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	90.95
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	90.67
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	90.46
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	90.39
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	89.98
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	89.96
3c57_A	95	Two component transcriptional regulatory protein;	89.85
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	87.52
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	85.92
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	85.87
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	85.84
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	85.17
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	84.77
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	83.39
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	83.16
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	82.96
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	80.84
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	80.41

>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=2.5e-38  Score=333.54  Aligned_cols=234  Identities=32%  Similarity=0.536  Sum_probs=206.7

Q ss_pred             CCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHhhhCCCCcHHHHHH---
Q 011324          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAK---  310 (488)
Q Consensus       252 ~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~------------------~l~~~~Gr~Pt~~ewA~---  310 (488)
                      ...|+++.||++|+++|+||++||++|+++|+.++.++....                  ......|+.|+..+|+.   
T Consensus        91 ~~~d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (438)
T 1l9z_H           91 STSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT  170 (438)
T ss_pred             CCCChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchh
Confidence            356899999999999999999999999999999764433221                  12234567888888742   


Q ss_pred             ---------HhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCch
Q 011324          311 ---------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF  381 (488)
Q Consensus       311 ---------a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rF  381 (488)
                               +.+++..+|+..+++|..|+++||.+|+++|++||++|.++|.+++|||||||||||+|+++|||.+|++|
T Consensus       171 ~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rF  250 (438)
T 1l9z_H          171 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  250 (438)
T ss_pred             hhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCh
Confidence                     23566788999998888999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhC--CCHHHHHHHHHHhCCCc
Q 011324          382 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPL  459 (488)
Q Consensus       382 STYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LG--IS~etVk~~L~~ar~~l  459 (488)
                      +|||+|||||.|.++|+++.+.+++|.++.+.+++++++.+.+.+.+++.|+.+|||+.+|  +++++|..++..+...+
T Consensus       251 sTYA~~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~~~~~  330 (438)
T 1l9z_H          251 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV  330 (438)
T ss_pred             HHHHHHHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccccc
Confidence            9999999999999999999999999999999999999999999999999999999999999  99999999999999999


Q ss_pred             cccccCCCCCCCccccccCCCC-CCCC
Q 011324          460 SMQQPVWADQDTTFQVMPLLLS-HLPS  485 (488)
Q Consensus       460 SLD~~i~~d~~~tl~e~i~D~s-~~pe  485 (488)
                      |||.+++++++..+.|+++|.. .+|+
T Consensus       331 SLd~~~~~d~d~~l~d~l~d~~~~~pe  357 (438)
T 1l9z_H          331 SLETPIGDEKDSFYGDFIPDENLPSPV  357 (438)
T ss_pred             ccccccccccchhhhhhhcccccCCHH
Confidence            9999998777777888888753 3444

>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=6.1e-39  Score=314.75  Aligned_cols=209  Identities=33%  Similarity=0.577  Sum_probs=131.7

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHHH--h-----------------------hhCCCCcHH
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR-LEKEKSKLQ--S-----------------------QFGREPTLI  306 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~-le~~~~~l~--~-----------------------~~Gr~Pt~~  306 (488)
                      .+|++++||++|+++||||++||++|+++|+.++. .+.+.....  .                       ..+.+|+..
T Consensus         5 ~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~   84 (245)
T 3ugo_A            5 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTV   84 (245)
T ss_dssp             CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHH
T ss_pred             CCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhH
Confidence            47899999999999999999999999999999875 333322100  0                       024789999


Q ss_pred             HHHHHhcCCH----HHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchh
Q 011324          307 EWAKAIGLSC----RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA  382 (488)
Q Consensus       307 ewA~a~gm~e----eeLi~~l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFS  382 (488)
                      +||.+.+++.    .+|+..+++|+.|++.||+.|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+
T Consensus        85 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~  164 (245)
T 3ugo_A           85 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS  164 (245)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHH
T ss_pred             HHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHH
Confidence            9999988753    456677788889999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhC--CCHHHHHHHHHHhCCCcc
Q 011324          383 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLS  460 (488)
Q Consensus       383 TYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LG--IS~etVk~~L~~ar~~lS  460 (488)
                      ||++||||+.|.++++++.+.+++|.++.+.+.++.++.+.|...+++.||++|||+.||  ||+++|++++.+++.++|
T Consensus       165 tya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~ls  244 (245)
T 3ugo_A          165 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVS  244 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHTC------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccC
Confidence            999999999999999999999999999999999999999999999999999999999999  999999999999999998


Q ss_pred             c
Q 011324          461 M  461 (488)
Q Consensus       461 L  461 (488)
                      |
T Consensus       245 l  245 (245)
T 3ugo_A          245 L  245 (245)
T ss_dssp             -
T ss_pred             C
Confidence            6

>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=1.3e-38  Score=334.36  Aligned_cols=233  Identities=32%  Similarity=0.539  Sum_probs=203.2

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH------------------HHhhhCCCCcHHH-------
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK------------------LQSQFGREPTLIE-------  307 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~------------------l~~~~Gr~Pt~~e-------  307 (488)
                      ..|+++.||++|+++|+||++||++|+++|+.+..+......                  .....|+.|+..+       
T Consensus        77 ~~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (423)
T 2a6h_F           77 TSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTV  156 (423)
T ss_dssp             THHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHH
T ss_pred             CCcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhh
Confidence            468999999999999999999999999999987543322111                  1112234555433       


Q ss_pred             --HHH---HhcCCHHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchh
Q 011324          308 --WAK---AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA  382 (488)
Q Consensus       308 --wA~---a~gm~eeeLi~~l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFS  382 (488)
                        |+.   ++++++.+|+..+++|..|+++||.+|+++|+++|++|.++|.+++|||||||||||+|+++|||.+|++|+
T Consensus       157 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~Fs  236 (423)
T 2a6h_F          157 EEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS  236 (423)
T ss_dssp             HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCHH
T ss_pred             hhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHH
Confidence              332   346778889999998889999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhC--CCHHHHHHHHHHhCCCcc
Q 011324          383 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLS  460 (488)
Q Consensus       383 TYA~~wIRnaI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LG--IS~etVk~~L~~ar~~lS  460 (488)
                      |||+||||+.|.++|+++.+.+++|.++.+.++++.++.+.+.+.+++.|+.+|||+.||  +++++|..++..+...+|
T Consensus       237 tYa~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~~~S  316 (423)
T 2a6h_F          237 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVS  316 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSCCEE
T ss_pred             HHHHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccCCcc
Confidence            999999999999999999999999999999999999999999999999999999999999  999999999999999999


Q ss_pred             ccccCCCCCCCccccccCCCC-CCCC
Q 011324          461 MQQPVWADQDTTFQVMPLLLS-HLPS  485 (488)
Q Consensus       461 LD~~i~~d~~~tl~e~i~D~s-~~pe  485 (488)
                      ||.+++++++..+.|+++|.. .+|+
T Consensus       317 ld~~~~~~~~~~l~d~l~d~~~~~pe  342 (423)
T 2a6h_F          317 LETPIGDEKDSFYGDFIPDEHLPSPV  342 (423)
T ss_dssp             SSCBCSSSSSCBGGGSSCCSSSCCHH
T ss_pred             cccccCCCCccchhhhhccccCCCHH
Confidence            999998877778899988764 3443

>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=99.93  E-value=2.9e-27  Score=258.38  Aligned_cols=167  Identities=34%  Similarity=0.682  Sum_probs=158.6

Q ss_pred             CHHHHHHHhhhcH-HH---HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011324          315 SCRDLKSELHSGN-SS---REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (488)
Q Consensus       315 ~eeeLi~~l~~Gd-~A---rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIR  390 (488)
                      ...+|+.+++.|+ .|   ++.||..|+++|+++|++|++++.+++||+||||||||+++++||+.+|++|+||++||||
T Consensus       357 ~~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~ir  436 (613)
T 3iyd_F          357 QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR  436 (613)
T ss_dssp             THHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHH
Confidence            3567888999998 56   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCCCCC
Q 011324          391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD  470 (488)
Q Consensus       391 naI~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~  470 (488)
                      |.|.++++++.+.+++|.++.+.+++++++...+.+++|+.||.+|||+.||+++++|+.++..++.++||+.+++++++
T Consensus       437 n~i~~~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~~~~~~  516 (613)
T 3iyd_F          437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDED  516 (613)
T ss_dssp             HHHHHHTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCCSSSSS
T ss_pred             HHHHHHHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988877


Q ss_pred             CccccccCCCC
Q 011324          471 TTFQVMPLLLS  481 (488)
Q Consensus       471 ~tl~e~i~D~s  481 (488)
                      ..+.+++.|..
T Consensus       517 ~~l~d~i~d~~  527 (613)
T 3iyd_F          517 SHLGDFIEDTT  527 (613)
T ss_dssp             CCGGGSCCCSS
T ss_pred             ccHHHHhcCCC
Confidence            88889888765

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=99.80  E-value=2e-20  Score=175.75  Aligned_cols=153  Identities=25%  Similarity=0.458  Sum_probs=52.7

Q ss_pred             CCHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       314 m~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      +++.+|+..++.|+ .|++.|+..|.++|+++|++|.++..+++||+||||++||+++++||+.+|.+|.||+++||+|.
T Consensus        13 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~   92 (243)
T 1l0o_C           13 QEMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGE   92 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHH
Confidence            34567888888888 89999999999999999999999999999999999999999999999998889999999999999


Q ss_pred             HHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccccccCCC
Q 011324          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA  467 (488)
Q Consensus       393 I~~~IRk~sr~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~  467 (488)
                      |++++|++. .+++|..+.....+++++...+....++.++.++|++.+|++.+.+...+.......|++.++.+
T Consensus        93 ~~d~~r~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~  166 (243)
T 1l0o_C           93 IQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYE  166 (243)
T ss_dssp             -------CC-CCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC----------
T ss_pred             HHHHHHhcC-CccCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccc
Confidence            999999987 78999999999999999999999988889999999999999999999988877778889887644

>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=99.76  E-value=8e-18  Score=158.23  Aligned_cols=136  Identities=21%  Similarity=0.297  Sum_probs=122.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHcc---CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324          327 NSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (488)
Q Consensus       327 d~ArekLIesnlrLV~sIAkry~---~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~  403 (488)
                      +.|++.||..|.++|+.+|++|.   +++.+++||+||||++||+++++||+.+|.+|.||+++||+|.|++++|++.  
T Consensus        11 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~--   88 (239)
T 1rp3_A           11 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD--   88 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS--
T ss_pred             chHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC--
Confidence            36899999999999999999998   6789999999999999999999999999899999999999999999999876  


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccC
Q 011324          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPV  465 (488)
Q Consensus       404 irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i  465 (488)
                       +.|........++.++...+....++.|+.+|||+.+|++++++..++...  ...+|+|.++
T Consensus        89 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~  151 (239)
T 1rp3_A           89 -FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVF  151 (239)
T ss_dssp             -TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccc
Confidence             578888888899999999999999999999999999999999999887643  2345666554

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.70  E-value=3.4e-17  Score=166.27  Aligned_cols=85  Identities=41%  Similarity=0.907  Sum_probs=79.8

Q ss_pred             HHHHHHhhhcH----HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011324          317 RDLKSELHSGN----SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (488)
Q Consensus       317 eeLi~~l~~Gd----~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRna  392 (488)
                      ..|+.+++.|+    .|++.||..|+++|+++|++|++++.+++||+||||||||+++++|++.+|.+|+||++|||+|.
T Consensus       250 ~~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~  329 (339)
T 1sig_A          250 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA  329 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHH
Confidence            56788888887    59999999999999999999999999999999999999999999999998999999999999999


Q ss_pred             HHHHHHHhc
Q 011324          393 IRKAIFQHS  401 (488)
Q Consensus       393 I~~~IRk~s  401 (488)
                      |++++|++.
T Consensus       330 ~~~~lr~~~  338 (339)
T 1sig_A          330 ITRSIADQA  338 (339)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHhc
Confidence            999999875

>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=99.70  E-value=5.2e-17  Score=148.86  Aligned_cols=141  Identities=17%  Similarity=0.266  Sum_probs=111.5

Q ss_pred             CHHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (488)
Q Consensus       315 ~eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI  393 (488)
                      ++.+|+.+++.|+ .|++.|+..|.+.|+.+|++|.+ ..+++|++||+|+++|+++++|++..  .|.+|++.+++|.+
T Consensus         9 ~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~   85 (194)
T 1or7_A            9 TDQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTA   85 (194)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHH
Confidence            3567888888888 89999999999999999999999 99999999999999999999999864  59999999999999


Q ss_pred             HHHHHHhcCCccc----------------------chh----------HHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHH
Q 011324          394 RKAIFQHSRTIRL----------------------PEN----------IYTLLSKVLEAKRLY-IQEGNHSPDKEDLARR  440 (488)
Q Consensus       394 ~~~IRk~sr~irl----------------------P~~----------v~e~l~kI~ka~~~L-~~elgr~pS~eEIAe~  440 (488)
                      ++++|++.+....                      |..          +...+..+....+.+ ...+..+.|++|||+.
T Consensus        86 ~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~  165 (194)
T 1or7_A           86 KNYLVAQGRRPPSSDVDAIEAENFESGGALKEISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAI  165 (194)
T ss_dssp             HHHHHHHTTCCTHHHHHHHHHHSCCSSCC--------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHTTCCCHHHHHHH
T ss_pred             HHHHHHHhccCccccccccccccccccccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHHcCCCHHHHHHH
Confidence            9999987654321                      000          111222222222222 2234458899999999


Q ss_pred             hCCCHHHHHHHHHHhCCC
Q 011324          441 VGITVEKLERLIFITRMP  458 (488)
Q Consensus       441 LGIS~etVk~~L~~ar~~  458 (488)
                      ||||+++|+..+.+++..
T Consensus       166 lgis~~tV~~~l~ra~~~  183 (194)
T 1or7_A          166 MDCPVGTVRSRIFRAREA  183 (194)
T ss_dssp             TTSCHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHH
Confidence            999999999999988654

>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=99.50  E-value=3.2e-14  Score=125.79  Aligned_cols=106  Identities=18%  Similarity=0.291  Sum_probs=76.1

Q ss_pred             CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc------------------------
Q 011324          352 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP------------------------  407 (488)
Q Consensus       352 g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP------------------------  407 (488)
                      |.+++|++||||++||+++.+||+.+ .+|.||++++++|.+++++|++.+..+.+                        
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            67899999999999999999999987 78999999999999999999875432211                        


Q ss_pred             ----------hh----------HHHHHH-HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          408 ----------EN----------IYTLLS-KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       408 ----------~~----------v~e~l~-kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                                ..          +...+. .+....+.+...+..+.|++|||+.||||.++|+..+++++..
T Consensus        80 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~~L~~~~r~v~~~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~  151 (164)
T 3mzy_A           80 NNYKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRIRKK  151 (164)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             hhhcccCCCHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                      00          111222 2222222322244568899999999999999999999988654

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.36  E-value=1e-14  Score=131.74  Aligned_cols=128  Identities=9%  Similarity=0.061  Sum_probs=99.6

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc--
Q 011324          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP--  407 (488)
Q Consensus       330 rekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~irlP--  407 (488)
                      |+.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++++|++.  ..|.+|++.+++|.+++++|+.......+  
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~~~~~e~   80 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRD--VDPRLGLYRMFQGIWASANADGEAQTSQSDA   80 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCS--SCTTHHHHHHHHHHHHHHTTTTSCCCCCCSC
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCC--CcHHHHHHHHHHHHHHHHhhccCcccCCcch
Confidence            56789999999999999999999999999999999999999999975  36999999999999999998754211001  


Q ss_pred             ----hhHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          408 ----ENIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       408 ----~~v~e~l~kI~ka~~~L~-~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                          ..+...+..+....+.+. ..+..+.|++|||+.||||+++|+..+.+++..+
T Consensus        81 ~~~~~~l~~~l~~Lp~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~rar~~L  137 (157)
T 2lfw_A           81 EGTEAVARARLARMTPLSRQALLLTAMEGFSPEDAAYLIEVDTSEVETLVTEALAEI  137 (157)
T ss_dssp             SSSSSTTTTTTTTSCTTHHHHHTTTSSSCCCHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence                112223333333333322 2334578999999999999999999999887543

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.31  E-value=1.2e-12  Score=129.65  Aligned_cols=131  Identities=11%  Similarity=0.013  Sum_probs=103.1

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011324          325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (488)
Q Consensus       325 ~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~sr~  403 (488)
                      .|+ .+|+.|+..|.+.|+.+|++|+++..+++|++||.|+.+|+...+|++.  ..|.+|++++++|.+++++|+....
T Consensus        17 ~g~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~~~~   94 (286)
T 3n0r_A           17 RGSEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQLEVG   94 (286)
T ss_dssp             ---CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC----C
T ss_pred             CCCcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhccccccC
Confidence            344 6999999999999999999999999999999999999999999999874  4699999999999999999864321


Q ss_pred             cc----cchhHHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          404 IR----LPENIYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       404 ir----lP~~v~e~l~kI~ka~~~L-~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                      ..    ....+...+.++....+.+ ......+.+++|||+.||+++++|+..+.+++.
T Consensus        95 ~~~~~~~~~~l~~al~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~rA~~  153 (286)
T 3n0r_A           95 HDQGLHAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQA  153 (286)
T ss_dssp             CCCCCCTTSHHHHHHHHHSCHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCcccchHHHHHHHHHhCCHHHeeEEEEEeeCCCCHHHHHHHhCcCHHHHHHHHHHHHh
Confidence            11    1134666666665555543 333445799999999999999999999887653

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=99.22  E-value=1.4e-11  Score=104.62  Aligned_cols=84  Identities=18%  Similarity=0.156  Sum_probs=72.2

Q ss_pred             HHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHH
Q 011324          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  396 (488)
Q Consensus       318 eLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~  396 (488)
                      +|+..+..|+ .+++.|+..|.+.|+.+|.++ ++..+++|++||+|+.+|+.+.+|++.  ..|.+|++.+++|.++++
T Consensus        13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~   89 (112)
T 2o7g_A           13 ALALSAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADH   89 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHHH
Confidence            5777777777 899999999999999999999 888899999999999999999999964  369999999999999999


Q ss_pred             HHHhcCCc
Q 011324          397 IFQHSRTI  404 (488)
Q Consensus       397 IRk~sr~i  404 (488)
                      +|++.+..
T Consensus        90 ~R~~~~~~   97 (112)
T 2o7g_A           90 IRHVRSRP   97 (112)
T ss_dssp             TC------
T ss_pred             HHHhhccc
Confidence            99876543

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=99.14  E-value=3.2e-11  Score=97.96  Aligned_cols=77  Identities=14%  Similarity=0.124  Sum_probs=68.6

Q ss_pred             hhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011324          323 LHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (488)
Q Consensus       323 l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~s  401 (488)
                      +..|+ .+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+.+|++.  ..|.+|++.+++|.+++++|++.
T Consensus         6 ~~~g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~   83 (87)
T 1h3l_A            6 STAERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ   83 (87)
T ss_dssp             CHHHHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred             cCcccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence            34566 8999999999999999999999999999999999999999999999874  47999999999999999998765

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=97.85  E-value=2.8e-09  Score=103.72  Aligned_cols=142  Identities=6%  Similarity=-0.072  Sum_probs=104.2

Q ss_pred             HHHHHHHhhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHH----HHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011324          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLL----QEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (488)
Q Consensus       316 eeeLi~~l~~Gd-~ArekLIesnlrLV~sIAkry~~~g~d~EDLI----QEG~IGL~rAiekFDpskG~rFSTYA~~wIR  390 (488)
                      ++.|+.++..+| .+++.++..|.++++.+............|+.    ||.|+.+|+.+..|++..  .|.+|++.+++
T Consensus        84 ~~~ll~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~~--~~~~WL~~ia~  161 (258)
T 3clo_A           84 EDCIYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTP--AGNVWLIFCLY  161 (258)
T ss_dssp             CHHHHTTBCHHHHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECT--TSCEEEEEEEE
T ss_pred             HHHHHHhCChHHHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCCC--chHHHHHHHHH
Confidence            345777887777 78999999999999999988777777888886    999999999999998643  69999999999


Q ss_pred             HHHHHHHHHhcCCcc----------cchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          391 QTIRKAIFQHSRTIR----------LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       391 naI~~~IRk~sr~ir----------lP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      |.+.++.++......          .+..+...+..+....+++......+.|.+|||+.||||+++|+..+++++..+
T Consensus       162 n~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~erevl~L~~~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL  240 (258)
T 3clo_A          162 SLSADQRPEQGIYATITQMERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKL  240 (258)
T ss_dssp             EECSCCCCCSSCCCEEEETTTTEEEECCCHHHHTTSSCHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             HHHcchhhhhHHHHHHHhhcccccccchhhHHHHccCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            988877543211000          011223333334333333221123478999999999999999999999887654

>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=94.05  E-value=0.57  Score=42.95  Aligned_cols=30  Identities=10%  Similarity=0.101  Sum_probs=26.4

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      ..+.|.+|||+.||||.++|+.++++++..
T Consensus       201 ~~g~s~~EIA~~lgis~~~V~~~~~ra~~~  230 (239)
T 1rp3_A          201 YEELPAKEVAKILETSVSRVSQLKAKALER  230 (239)
T ss_dssp             TSCCCHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            458899999999999999999999887643

>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=93.98  E-value=0.017  Score=63.10  Aligned_cols=34  Identities=32%  Similarity=0.570  Sum_probs=13.5

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHH
Q 011324          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI  286 (488)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~  286 (488)
                      .+||+++||+++|..||||+++|++|+++|..+.
T Consensus        94 ~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~  127 (613)
T 3iyd_F           94 TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI  127 (613)
T ss_dssp             -----------C--------CSSSTTTHHHHHHH
T ss_pred             CCCcHHHHHHHhcccccCCchhHHHHHHHHHHhH
Confidence            5899999999999999999999999999999853

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=93.89  E-value=0.032  Score=45.44  Aligned_cols=31  Identities=10%  Similarity=0.078  Sum_probs=27.1

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          428 GNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      +..+.|++|||+.|||+..+|+..+++++..
T Consensus        50 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~   80 (92)
T 3hug_A           50 YYRGWSTAQIATDLGIAEGTVKSRLHYAVRA   80 (92)
T ss_dssp             HTSCCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            4457899999999999999999999988654

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=92.94  E-value=0.81  Score=48.20  Aligned_cols=30  Identities=17%  Similarity=0.225  Sum_probs=26.8

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .+.|++|||+.||||.++|+.++.+|...+
T Consensus       394 e~~TleEIAe~LgIS~erVRqi~~RAlkKL  423 (438)
T 1l9z_H          394 REHTLEEVGAYFGVTRERIRQIENKALRKL  423 (438)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            578999999999999999999998886554

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=92.72  E-value=0.12  Score=40.18  Aligned_cols=51  Identities=14%  Similarity=0.071  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCcc
Q 011324          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLS  460 (488)
Q Consensus       410 v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lS  460 (488)
                      +...+..+....+.+...+..+.+.+|||+.||++..+|+..+.+++..+-
T Consensus        10 l~~~l~~L~~~e~~vl~l~~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~   60 (79)
T 1x3u_A           10 IRARLQTLSERERQVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMAKMK   60 (79)
T ss_dssp             HHHHHHHHCHHHHHHHHHHTTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHc
Confidence            344455554544444433456899999999999999999999988765543

>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=92.15  E-value=0.15  Score=38.93  Aligned_cols=30  Identities=13%  Similarity=0.206  Sum_probs=27.0

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .+.|.+|||+.||+|.++|+..+.+++..+
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            589999999999999999999999886654

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=90.95  E-value=0.14  Score=47.04  Aligned_cols=32  Identities=19%  Similarity=0.232  Sum_probs=0.0

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          428 GNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      +..+.|++|||+.||||+++|+.++.+++..+
T Consensus       211 ~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~L  242 (243)
T 1l0o_C          211 YYKDQTQSEVASRLGISQVQMSRLEKKILQHI  242 (243)
T ss_dssp             --------------------------------
T ss_pred             HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence            34577999999999999999999999887654

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=90.67  E-value=0.18  Score=40.70  Aligned_cols=30  Identities=13%  Similarity=0.223  Sum_probs=26.7

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .+.|++|||+.||||.++|+.++.+++..+
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            589999999999999999999998876543

>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=90.46  E-value=0.063  Score=43.09  Aligned_cols=31  Identities=16%  Similarity=0.146  Sum_probs=27.0

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ..+.+.+|||+.|||+..+|+..+.+++..+
T Consensus        34 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL   64 (82)
T 1je8_A           34 AQGLPNKMIARRLDITESTVKVHVKHMLKKM   64 (82)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            4578999999999999999999998876554

>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=90.39  E-value=0.18  Score=42.43  Aligned_cols=30  Identities=13%  Similarity=0.206  Sum_probs=26.3

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .+.|++|||+.||||.++|+.++.+|...+
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~rAlkkL   67 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAKALRKL   67 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            578999999999999999999998876543

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=89.98  E-value=0.23  Score=37.43  Aligned_cols=31  Identities=19%  Similarity=0.099  Sum_probs=26.8

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ..+.|++|||+.+|+|..+|+..+++++..+
T Consensus        29 ~~g~s~~eIA~~lgis~~tv~~~~~ra~~~l   59 (70)
T 2o8x_A           29 LLGLSYADAAAVCGCPVGTIRSRVARARDAL   59 (70)
T ss_dssp             TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            4478999999999999999999998876543

>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=89.96  E-value=0.51  Score=36.44  Aligned_cols=30  Identities=17%  Similarity=0.225  Sum_probs=26.1

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .+.|.+|||+.||+|.++|+..+.++...+
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            578999999999999999999988775443

>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=89.85  E-value=0.082  Score=43.56  Aligned_cols=31  Identities=10%  Similarity=0.120  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCcc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPLS  460 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lS  460 (488)
                      .+.+++|||+.|||+..+|+..+.+++..+-
T Consensus        41 ~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~   71 (95)
T 3c57_A           41 EGLTNKQIADRMFLAEKTVKNYVSRLLAKLG   71 (95)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHc
Confidence            4789999999999999999999988765543

>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=87.52  E-value=0.29  Score=41.83  Aligned_cols=31  Identities=10%  Similarity=-0.088  Sum_probs=26.8

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          428 GNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      +..+.|++|||+.||+|+.+|+..+++++..
T Consensus        38 ~~~g~s~~EIA~~lgiS~~tV~~~l~ra~~k   68 (113)
T 1xsv_A           38 YLEDYSLSEIADTFNVSRQAVYDNIRRTGDL   68 (113)
T ss_dssp             HTSCCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            3457899999999999999999999887654

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=85.92  E-value=1.4  Score=35.50  Aligned_cols=26  Identities=12%  Similarity=0.234  Sum_probs=23.2

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFI  454 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~  454 (488)
                      |..||..|||+.+|+|..+|+.-|..
T Consensus        22 g~~psv~EIa~~lgvS~~TVrr~L~~   47 (77)
T 2jt1_A           22 GAPVKTRDIADAAGLSIYQVRLYLEQ   47 (77)
T ss_dssp             TSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            45899999999999999999988864

>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=85.87  E-value=1.1  Score=30.56  Aligned_cols=26  Identities=4%  Similarity=0.068  Sum_probs=22.9

Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324          431 SPDKEDLARRVGITVEKLERLIFITR  456 (488)
Q Consensus       431 ~pS~eEIAe~LGIS~etVk~~L~~ar  456 (488)
                      +.+..|||+.|||+..+|..++....
T Consensus        21 g~s~~~IA~~lgis~~Tv~~~~~~~~   46 (51)
T 1tc3_C           21 NVSLHEMSRKISRSRHCIRVYLKDPV   46 (51)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHCST
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHhhHH
Confidence            57999999999999999999987543

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=85.84  E-value=0.081  Score=42.97  Aligned_cols=31  Identities=13%  Similarity=0.156  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCcc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPLS  460 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lS  460 (488)
                      .+.+.+|||+.|||+..+|+..+.+++..+-
T Consensus        43 ~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~   73 (91)
T 2rnj_A           43 KGYSNQEIASASHITIKTVKTHVSNILSKLE   73 (91)
T ss_dssp             TTCCTTHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            3789999999999999999999988866543

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=85.17  E-value=0.72  Score=33.96  Aligned_cols=32  Identities=9%  Similarity=0.181  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM  461 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL  461 (488)
                      .+.+.+|||+.||+++.+|+..+.+++..+-.
T Consensus        12 ~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   43 (61)
T 2jpc_A           12 EGYTNHGISEKLHISIKTVETHRMNMMRKLQV   43 (61)
T ss_dssp             TSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTC
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCC
Confidence            36799999999999999999999887655433

>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=84.77  E-value=0.65  Score=38.03  Aligned_cols=32  Identities=9%  Similarity=0.121  Sum_probs=27.2

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM  461 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL  461 (488)
                      .+.+.+|||+.|||++.+|+..+..+...+-+
T Consensus        43 ~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv   74 (90)
T 3ulq_B           43 KGFTNQEIADALHLSKRSIEYSLTSIFNKLNV   74 (90)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            47899999999999999999999887655543

>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=83.39  E-value=3  Score=43.37  Aligned_cols=30  Identities=17%  Similarity=0.210  Sum_probs=22.3

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      .+.|++|||+.||||.++|+.++.+|...+
T Consensus       379 e~~Tl~EIA~~lgiS~erVrqi~~rAl~kL  408 (423)
T 2a6h_F          379 REHTLEEVGAFFGVTRERIRQIENKALRKL  408 (423)
T ss_dssp             -----CHHHHSSSSCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            578999999999999999999988876544

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=83.16  E-value=1.9  Score=32.56  Aligned_cols=31  Identities=13%  Similarity=0.111  Sum_probs=26.3

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ..+.+..|||+.||++..+|+..+.+++..+
T Consensus        24 ~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl   54 (74)
T 1fse_A           24 VQDKTTKEIASELFISEKTVRNHISNAMQKL   54 (74)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            3467999999999999999999998776544

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=82.96  E-value=1.3  Score=32.07  Aligned_cols=24  Identities=17%  Similarity=0.304  Sum_probs=21.4

Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHH
Q 011324          431 SPDKEDLARRVGITVEKLERLIFI  454 (488)
Q Consensus       431 ~pS~eEIAe~LGIS~etVk~~L~~  454 (488)
                      +.|..|||+.||++..+|...+..
T Consensus        31 g~s~~eIA~~lgis~~TV~~~l~~   54 (55)
T 2x48_A           31 GYTVQQIANALGVSERKVRRYLES   54 (55)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHh
Confidence            579999999999999999988753

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=80.84  E-value=0.73  Score=38.51  Aligned_cols=31  Identities=10%  Similarity=0.135  Sum_probs=26.9

Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324          431 SPDKEDLARRVGITVEKLERLIFITRMPLSM  461 (488)
Q Consensus       431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL  461 (488)
                      +.+.+|||+.|||++.+|+..+.++...+..
T Consensus        49 G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv   79 (99)
T 1p4w_A           49 GFLVTEIAKKLNRSIKTISSQKKSAMMKLGV   79 (99)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            6799999999999999999999887665544

>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=80.41  E-value=1.6  Score=37.28  Aligned_cols=29  Identities=14%  Similarity=0.092  Sum_probs=25.7

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      .+.|+.|||+.+|+|..+|+..+++++..
T Consensus        37 ~g~s~~EIA~~lgiS~~tV~~~l~ra~~k   65 (113)
T 1s7o_A           37 DDYSLAEIADEFGVSRQAVYDNIKRTEKI   65 (113)
T ss_dssp             TCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            46899999999999999999999887643

---

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	488
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	3e-29
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	5e-28
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	3e-20
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	4e-07
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	1e-06
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	7e-05

>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 =  111 bits (278), Expect = 3e-29
 Identities = 57/179 (31%), Positives = 92/179 (51%), Gaps = 30/179 (16%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIR------------------LEKEKSKLQ 296
           DP+R +L       LLT +EE +L  ++++ +                   + + K    
Sbjct: 2   DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGT 61

Query: 297 SQFGREPTLIEWAKAIGLSCRDLKSE------------LHSGNSSREKLINANLRLVVHV 344
           ++  + P L E      +   D K +               G ++R+ LI ANLRLVV +
Sbjct: 62  ARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSI 121

Query: 345 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403
           AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +RT
Sbjct: 122 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 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 =  111 bits (279), Expect = 5e-28
 Identities = 46/190 (24%), Positives = 84/190 (44%)

Query: 208 KQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETR 267
           + F Q R + ++      S   + +      R             + + + LF     + 
Sbjct: 142 EVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSD 201

Query: 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 327
               A          +     E+    LQ     E       + +    R +        
Sbjct: 202 TWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKAR 261

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 387
            ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA W
Sbjct: 262 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 321

Query: 388 WVRQTIRKAI 397
           W+RQ I ++I
Sbjct: 322 WIRQAITRSI 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 = 83.0 bits (205), Expect = 3e-20
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 324 HSGNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 6   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 65

Query: 381 FASYAYWWVRQTIRKAI 397
             +Y    ++  I   +
Sbjct: 66  AEAYIKLRIKGAIYDYL 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 = 44.7 bits (106), Expect = 4e-07
 Identities = 10/56 (17%), Positives = 27/56 (48%)

Query: 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM 457
            T+++  ++  + +K+ +AK    +    +P   ++A  +GI+ E +       R+
Sbjct: 2   GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRL 57

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 60

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]

 Score = 43.1 bits (102), Expect = 1e-06
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLSM 461
           IR+P ++   ++K+    R   QE    P  E++A  +G     +++E  + I + P+S+
Sbjct: 1   IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 60

>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 = 39.0 bits (91), Expect = 7e-05
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 9/76 (11%)

Query: 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MP 458
           SR +R          ++ E      ++    P  E++A+ +GI+ E+L + +        
Sbjct: 2   SRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI 55

Query: 459 LSMQQPVWADQDTTFQ 474
           LS+++  + D    + 
Sbjct: 56  LSLEEV-FRDFARDYS 70

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	488
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	100.0
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.84
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.78
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.44
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	98.89
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.87
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.71
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.55
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	96.49
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.57
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	94.14
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	93.25
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	92.95
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	92.01
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	90.01
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	89.91
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	87.92
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	85.59
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	83.95
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	81.86
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	80.52

>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=100.00  E-value=5.5e-34  Score=263.70  Aligned_cols=150  Identities=37%  Similarity=0.633  Sum_probs=122.2

Q ss_pred             CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------------hhhCCCCcHHHH-------
Q 011324          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ------------------SQFGREPTLIEW-------  308 (488)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~iq~l~~le~~~~~l~------------------~~~Gr~Pt~~ew-------  308 (488)
                      +||+++||++|+++||||+|||++|+++|+.++.+.....+..                  ...+..|...+|       
T Consensus         1 tDpVr~YLreig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~~   80 (180)
T d1ku2a2           1 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE   80 (180)
T ss_dssp             CHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTHH
T ss_pred             CCcHHHHHHHhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHHH
Confidence            5899999999999999999999999999998775544322221                  112223333222       


Q ss_pred             --HHHhcCC---HHHHHHHhhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhh
Q 011324          309 --AKAIGLS---CRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAS  383 (488)
Q Consensus       309 --A~a~gm~---eeeLi~~l~~Gd~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFST  383 (488)
                        .......   ...+......|+.|+++||.+|++||++||++|.+.|++++||||||+|||++|+++|||++|++|+|
T Consensus        81 ~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f~t  160 (180)
T d1ku2a2          81 EVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST  160 (180)
T ss_dssp             HHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCHHH
Confidence              2222111   24466777888999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhcCC
Q 011324          384 YAYWWVRQTIRKAIFQHSRT  403 (488)
Q Consensus       384 YA~~wIRnaI~~~IRk~sr~  403 (488)
                      ||+|||+++|.++|++++|+
T Consensus       161 ya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         161 YATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHhCCC
Confidence            99999999999999998864

>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=99.84  E-value=1.5e-21  Score=193.84  Aligned_cols=83  Identities=42%  Similarity=0.913  Sum_probs=77.0

Q ss_pred             HHHHHhhhcH----HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011324          318 DLKSELHSGN----SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (488)
Q Consensus       318 eLi~~l~~Gd----~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI  393 (488)
                      .+...+..|.    .|+++||+.|++||.+||++|.++|++++||||+|++|||+|+++|||.+|++|+|||+||||++|
T Consensus       248 ~i~~~i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~  327 (334)
T d1siga_         248 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI  327 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHH
Confidence            3445566665    699999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHh
Q 011324          394 RKAIFQH  400 (488)
Q Consensus       394 ~~~IRk~  400 (488)
                      .++|+++
T Consensus       328 ~~~~~~~  334 (334)
T d1siga_         328 TRSIADQ  334 (334)
T ss_dssp             HHHHHHC
T ss_pred             HHHHhCC
Confidence            9999875

>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=99.78  E-value=1.7e-19  Score=149.07  Aligned_cols=74  Identities=24%  Similarity=0.379  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCC---CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011324          328 SSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~---g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IRk~s  401 (488)
                      ..+++||..|++||.++|++|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|+++||+..
T Consensus        10 ~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~d   86 (87)
T d1rp3a3          10 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD   86 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            468999999999999999998654   78999999999999999999999999999999999999999999999864

>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=98.89  E-value=1.3e-09  Score=83.25  Aligned_cols=58  Identities=26%  Similarity=0.461  Sum_probs=55.2

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhC--CCHHHHHHHHHHhCCCccc
Q 011324          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLSM  461 (488)
Q Consensus       404 irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LG--IS~etVk~~L~~ar~~lSL  461 (488)
                      ||+|.|+.+.++++.++.++|.+++||+||.+|||+.||  +++++|+.++..++.++||
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            689999999999999999999999999999999999998  5588999999999999997

>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=98.87  E-value=8e-10  Score=86.70  Aligned_cols=69  Identities=16%  Similarity=0.135  Sum_probs=64.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011324          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  398 (488)
Q Consensus       328 ~ArekLIesnlrLV~sIAkry~~~g~d~EDLIQEG~IGL~rAiekFDpskG~rFSTYA~~wIRnaI~~~IR  398 (488)
                      .+|++++..|.+.|+.+|++++++..+++|++||.|+.+|+..++|++.  .+|.+|++.+++|.+++++|
T Consensus         7 ~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   75 (75)
T d1h3la_           7 ARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYR   75 (75)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHhC
Confidence            6799999999999999999999999999999999999999999999864  47999999999999998753

>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=98.71  E-value=1.1e-08  Score=77.12  Aligned_cols=55  Identities=18%  Similarity=0.268  Sum_probs=51.9

Q ss_pred             CCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhC
Q 011324          402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR  456 (488)
Q Consensus       402 r~irlP~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar  456 (488)
                      +.|++|+++.+.++++.++.+.|.+++||.||.+|||+.||+++++|..++..++
T Consensus         2 g~IrvPr~~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~r   56 (57)
T d1l0oc_           2 GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR   56 (57)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCEeCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHhc
Confidence            4789999999999999999999999999999999999999999999999987653

>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=98.55  E-value=4.6e-09  Score=83.29  Aligned_cols=72  Identities=14%  Similarity=0.169  Sum_probs=61.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHh--CCCccccccCCCCCCCccccccCCC
Q 011324          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQVMPLLL  480 (488)
Q Consensus       408 ~~v~e~l~kI~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~~tl~e~i~D~  480 (488)
                      +.+.+.+++|.++...|.+++||.||.+|||+.|||++++|+.++...  ...+|||.++.+ ++..+.|++++.
T Consensus         3 Rs~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~d-~~~~~~e~lpss   76 (77)
T d1rp3a1           3 RQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRD-FARDYSELIPSS   76 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHTTTGGGS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCccC-CCCchhccCCCC
Confidence            456688899999999999999999999999999999999999998754  467999997654 445788888875

>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=96.49  E-value=0.0029  Score=46.59  Aligned_cols=40  Identities=30%  Similarity=0.439  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHhhhc
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG  326 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l~~G  326 (488)
                      ++.++..+|...+||+||.+|.|+++|++.+++...+..+
T Consensus        16 ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_          16 KIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            6677889999999999999999999999999987766543

>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=95.57  E-value=0.012  Score=45.14  Aligned_cols=37  Identities=41%  Similarity=0.591  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHh
Q 011324          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL  323 (488)
Q Consensus       287 ~le~~~~~l~~~~Gr~Pt~~ewA~a~gm~eeeLi~~l  323 (488)
                      +++++...|+..+||+||.+|.|..+||+.+++...+
T Consensus        11 ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l   47 (77)
T d1rp3a1          11 RIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTL   47 (77)
T ss_dssp             HHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence            6788999999999999999999999999998876554

>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=94.14  E-value=0.016  Score=43.29  Aligned_cols=32  Identities=19%  Similarity=0.163  Sum_probs=27.7

Q ss_pred             HhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          426 QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       426 ~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                      ..+..+.+++|||+.||+|+++|+..+++|+.
T Consensus        29 l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~   60 (68)
T d1or7a1          29 LRELDGLSYEEIAAIMDCPVGTVRSRIFRARE   60 (68)
T ss_dssp             HHHTTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34455899999999999999999999998864

>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=93.25  E-value=0.12  Score=38.03  Aligned_cols=37  Identities=30%  Similarity=0.561  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHhhhCCCCcHHHHHHHhc--CCHHHHHHH
Q 011324          286 IRLEKEKSKLQSQFGREPTLIEWAKAIG--LSCRDLKSE  322 (488)
Q Consensus       286 ~~le~~~~~l~~~~Gr~Pt~~ewA~a~g--m~eeeLi~~  322 (488)
                      -++.++..+|...+||+||.+|.|+++|  ++.+.+...
T Consensus        12 ~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~   50 (60)
T d1ku2a1          12 NKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEET   50 (60)
T ss_dssp             HHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHH
Confidence            3567788999999999999999999997  455555443

>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=92.95  E-value=0.033  Score=41.32  Aligned_cols=30  Identities=10%  Similarity=0.053  Sum_probs=26.6

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHhCC
Q 011324          428 GNHSPDKEDLARRVGITVEKLERLIFITRM  457 (488)
Q Consensus       428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (488)
                      +..+.|++|||+.||+|..+|+..+++++.
T Consensus        34 ~~~~~s~~eIA~~lgis~~tv~~~~~ra~~   63 (71)
T d1rp3a2          34 FYEELPAKEVAKILETSVSRVSQLKAKALE   63 (71)
T ss_dssp             HTSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HhHhCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            445889999999999999999999998764

>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=92.01  E-value=0.17  Score=38.26  Aligned_cols=42  Identities=19%  Similarity=0.309  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCC-CHHHHHHHHHH
Q 011324          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFI  454 (488)
Q Consensus       413 ~l~kI~ka~~~L~~elgr~pS~eEIAe~LGI-S~etVk~~L~~  454 (488)
                      ...+|-+.+..+..+.|..||++|||+.+|+ |..+|...+..
T Consensus         6 rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~   48 (71)
T d1jhfa1           6 RQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   48 (71)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            3456667777788888889999999999999 89999998864

>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=90.01  E-value=0.076  Score=43.52  Aligned_cols=31  Identities=13%  Similarity=0.040  Sum_probs=27.1

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          428 GNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       428 lgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      +..+.|++|||+.||||.++|+..+++|+..
T Consensus        29 y~~~ls~~EIA~~lgiS~~aV~~~l~RA~~~   59 (106)
T d1s7oa_          29 YADDYSLAEIADEFGVSRQAVYDNIKRTEKI   59 (106)
T ss_dssp             HHTCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            3447899999999999999999999988754

>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=89.91  E-value=0.099  Score=42.82  Aligned_cols=34  Identities=9%  Similarity=-0.160  Sum_probs=28.6

Q ss_pred             HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCC
Q 011324          425 IQEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (488)
Q Consensus       425 ~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (488)
                      ...+..+.|+.|||+.||||.++|+..+++|+..
T Consensus        28 ~L~~~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~   61 (106)
T d1xsva_          28 ELFYLEDYSLSEIADTFNVSRQAVYDNIRRTGDL   61 (106)
T ss_dssp             HHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCcHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            3344558999999999999999999999988754

>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=87.92  E-value=0.21  Score=37.44  Aligned_cols=45  Identities=11%  Similarity=0.053  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCccc
Q 011324          417 VLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM  461 (488)
Q Consensus       417 I~ka~~~L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL  461 (488)
                      +-....++...+..+.+..|||+.|||++.+|+..+..+...+-.
T Consensus        13 LT~rE~~vl~~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   57 (70)
T d1yioa1          13 LTGREQQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQKLNV   57 (70)
T ss_dssp             SCHHHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            333444445555568899999999999999999998876555433

>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=85.59  E-value=0.33  Score=35.64  Aligned_cols=36  Identities=11%  Similarity=0.095  Sum_probs=28.8

Q ss_pred             HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       424 L~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      +......+.|.+|||+.||+++.+|+..+......+
T Consensus        12 vl~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl   47 (65)
T d1l3la1          12 YLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRF   47 (65)
T ss_dssp             HHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence            344455588999999999999999999988765444

>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=83.95  E-value=0.8  Score=33.50  Aligned_cols=35  Identities=11%  Similarity=0.056  Sum_probs=28.1

Q ss_pred             HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          425 IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       425 ~~elgr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ......+.+.+|||+.||+++.+|+..+......+
T Consensus        13 l~l~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl   47 (67)
T d1fsea_          13 FELLVQDKTTKEIASELFISEKTVRNHISNAMQKL   47 (67)
T ss_dssp             HHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence            33445588999999999999999999988665443

>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=81.86  E-value=1.2  Score=32.49  Aligned_cols=27  Identities=15%  Similarity=0.261  Sum_probs=23.9

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHh
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFIT  455 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~a  455 (488)
                      +.+.|.+|||+.||||.+.|+.+...|
T Consensus        26 ~~~~tl~eIa~~lgiS~erVrqi~~~a   52 (61)
T d1ku3a_          26 GREHTLEEVGAYFGVTRERIRQIENKA   52 (61)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            457799999999999999999987765

>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=80.52  E-value=0.98  Score=33.07  Aligned_cols=31  Identities=16%  Similarity=0.146  Sum_probs=25.7

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHhCCCc
Q 011324          429 NHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (488)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (488)
                      ..+.+..|||+.|||++.+|+..+......+
T Consensus        19 ~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl   49 (67)
T d1a04a1          19 AQGLPNKMIARRLDITESTVKVHVKHMLKKM   49 (67)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence            3478999999999999999999987655443