Citrus Sinensis ID: 011577

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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--
Protein Sequence
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccccccHHHHHHHHccccccccccccccHHHHHHHcccccHHHHHHcccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHcccHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHccEEEEEHHccccccccHHHHHHcccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHcccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHccccccccccccccccccccccccccccEEEccccccccEEccccccHHHccccccEcccccccHccHHHHHHHcccccccEEcccEEccEEEEccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccHHHHHHHHcHcccccccccccccccccccHHHHccccccccHHHHHHcccccccccccccccccHHHHHHHHccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHcccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHcccccEEcccccccccccHHHHHccccc
Coil and Loop (DISEMBL)
meagrnllssppsfpsrtrvkhslsssasssssssVLMHneqsapavasvptssvarhfptsvllqeqrdeyrpllhmfkedktsqatsdsrnIETEAFFveeknsgdlDQLVQDLEHqflhwpdlwnlsppmkrgedpsvsltmqslsndteesvdaepfDAVALARKALSASKEAAslaenpklngaeftdisltsslgypleevkqfsqprflerrskkrkvskpqvtnhetynSRKASVKKKLsegfdrndplrlflwgpetrklltaDEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRdlkselhsgnssREKLINANLRLVVHVAKQYqgrgislhdLLQEGSMGLMKSVEkfkpqagcrfasYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIqegnhspdkedlaRRVGITVEKLERLIFITrmplsmqqpvwadqdttFQSTFLDAAG
Flexible Loop (DISEMBL)
meagrnllssppsfpsrtrVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMfkedktsqatsdsrNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAslaenpklngaeFTDISLTSslgypleevkqfsqprflerrskkrkvskpqvtnhetynsrkasvkkklsegfdrndplrlfLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLqsqfgreptLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFqhsrtirlpeNIYTLLSKVLEAKRLYIqegnhspdkedlarRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG
Low Complexity Region (SEG)
MEAGRNLLSSPPSFPSRTRVKHslsssasssssssVLMHNEQsapavasvptssvaRHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDavalarkalsaskeaaslaeNPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG
Disordered region (IsUnstruct)
**************************************************************************************************FFV******DLDQLVQDLEHQFLHWPDLWNL******************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE*********FGREPTLIEWAKAIGLSCRDL************KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG********LARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT**********
Disordered Region (DISOPRED)
**********PPSF**************************EQS***********VARHFPTSVLLQEQ********************************************VQDLEHQFLHWP**********************************************************************************************************************************DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS*************EWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK*************EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLD***
Disordered Region (DISEMBL)
******************************************************VARHFPTSVLLQEQRDEYRPLLHMFKED*********RNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQS**********AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLE*************TNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK********SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG
Disordered Region (DISPRO)
*********************************SSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM***********************DAEPFDAVALARKALSASKE**SL*EN*******************************************************************FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFExxxxxxxxxxxxxxxxxxxxxFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG
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	482	2.2.26 [Sep-21-2011]
Q9LD95	547	RNA polymerase sigma fact	yes	no	0.935	0.824	0.521	1e-128
O22056	572	RNA polymerase sigma fact	no	no	0.531	0.447	0.366	1e-46
P26683	390	RNA polymerase sigma fact	yes	no	0.545	0.674	0.361	1e-46
P38023	399	RNA polymerase sigma fact	yes	no	0.470	0.568	0.394	4e-44
Q31ME3	320	RNA polymerase sigma fact	no	no	0.466	0.703	0.4	2e-41
P74565	425	RNA polymerase sigma fact	N/A	no	0.493	0.56	0.325	8e-38
Q31QG5	320	RNA polymerase sigma fact	no	no	0.456	0.687	0.398	1e-37
P52322	416	RNA polymerase sigma fact	no	no	0.470	0.545	0.325	1e-36
Q59996	404	Probable RNA polymerase s	N/A	no	0.456	0.544	0.343	2e-35
Q03066	416	RNA polymerase sigma-C fa	no	no	0.456	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 =  458 bits (1179), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 255/489 (52%), Positives = 330/489 (67%), Gaps = 38/489 (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 FQSTFLDAA 481
           FQ    D+ 
Sbjct: 451 FQEITPDSG 459

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 =  187 bits (476), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 100/277 (36%), Positives = 168/277 (60%), Gaps = 14/277 (5%)

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 EKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG 482
           EKL  +    ++P+S++ P+  ++D+     F+++ G
Sbjct: 271 EKLRFIAKSAQLPISLETPIGKEEDSRL-GDFIESDG 306

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 =  179 bits (454), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 90/228 (39%), Positives = 146/228 (64%), Gaps = 1/228 (0%)

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 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG 482
           E++A R+ +T+EKL  +    ++P+S++ P+  ++D+     F++A G
Sbjct: 269 EEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRL-GDFIEADG 315

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 =  170 bits (430), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 90/225 (40%), Positives = 136/225 (60%)

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 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLD 479
            +LA  + + +E++   I + R P+S+   V   QDT  Q    D
Sbjct: 191 SELAEVLELPLEQVREYIQMNRQPVSLDVKVGDSQDTELQELLED 235

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

 Score =  158 bits (400), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 94/289 (32%), Positives = 158/289 (54%), Gaps = 51/289 (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 KEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG 482
           +E++A ++ +T+EKL  +    ++P+S++ P+  ++D+     F++A G
Sbjct: 294 EEEIAEKMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRL-GDFIEADG 341

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

 Score =  154 bits (390), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 148/267 (55%), Gaps = 40/267 (14%)

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

Query: 291 ----EKSK-------LQSQFGRE----PTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 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 RMPLSMQQPVWADQDTTFQSTFLDAAG 482
           ++P+S++ P+  ++D+     F++A G
Sbjct: 307 QLPISLETPIGKEEDSRL-GDFIEADG 332

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

 Score =  150 bits (380), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 90/262 (34%), Positives = 136/262 (51%), Gaps = 42/262 (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 IFITRMPLSMQQPVWADQDTTF 473
           +      +S++  V  D+DT  
Sbjct: 288 LTQVPRSVSLELKVGQDKDTEL 309

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

 Score =  149 bits (377), 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	482
297741628	561	unnamed protein product [Vitis vinifera]	0.968	0.832	0.613	1e-164
359481391	572	PREDICTED: RNA polymerase sigma factor r	0.987	0.832	0.609	1e-163
224068757	535	predicted protein [Populus trichocarpa]	0.923	0.831	0.601	1e-161
255556952	548	RNA polymerase sigma factor rpoD, putati	0.948	0.833	0.6	1e-159
356536959	571	PREDICTED: RNA polymerase sigma factor r	0.981	0.828	0.568	1e-142
356548319	574	PREDICTED: RNA polymerase sigma factor r	0.983	0.825	0.548	1e-140
449451030	562	PREDICTED: RNA polymerase sigma factor s	0.966	0.829	0.537	1e-132
312282671	547	unnamed protein product [Thellungiella h	0.935	0.824	0.531	1e-130
297827203	546	RNA polymerase sigma-70 factor [Arabidop	0.933	0.824	0.527	1e-129
18404292	547	RNApolymerase sigma-subunit F [Arabidops	0.935	0.824	0.521	1e-126

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

 Score =  584 bits (1505), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 299/487 (61%), Positives = 364/487 (74%), Gaps = 20/487 (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

Query: 475 STFLDAA 481
               D  
Sbjct: 467 EVTADTG 473

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 =  579 bits (1493), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 298/489 (60%), Positives = 364/489 (74%), Gaps = 13/489 (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 FQSTFLDAA 481
           FQ    D  
Sbjct: 476 FQEVTADTG 484

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 =  576 bits (1484), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 288/479 (60%), Positives = 358/479 (74%), Gaps = 34/479 (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 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLD 479
           KR YIQEGNH P  E++ARRVGI ++KLE+L+  TR PLSMQQ VW+DQ+TTFQ    D
Sbjct: 387 KRSYIQEGNHQPTAEEIARRVGIAIDKLEKLLCFTRTPLSMQQTVWSDQNTTFQEITAD 445

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 =  567 bits (1460), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 288/480 (60%), Positives = 353/480 (73%), Gaps = 23/480 (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 AKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLD 479
           AKR YI EGNH+P KE+LA+R+GIT  +LERL+++ RMPLSMQQ VWADQ+TTFQ    D
Sbjct: 399 AKRSYIMEGNHNPTKEELAKRIGITTVRLERLLYMARMPLSMQQTVWADQETTFQEITAD 458

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 =  510 bits (1313), Expect = e-142,   Method: Compositional matrix adjust.
 Identities = 277/487 (56%), Positives = 352/487 (72%), Gaps = 14/487 (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 FQSTFLD 479
           FQ    D
Sbjct: 475 FQEITAD 481

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 =  505 bits (1300), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 268/489 (54%), Positives = 345/489 (70%), Gaps = 15/489 (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 TTFQSTFLD 479
           TTFQ    D
Sbjct: 476 TTFQEITAD 484

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 =  479 bits (1234), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 262/487 (53%), Positives = 335/487 (68%), Gaps = 21/487 (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 QSTFLDA 480
           Q    D+
Sbjct: 467 QEITADS 473

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 =  471 bits (1211), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 260/489 (53%), Positives = 328/489 (67%), Gaps = 38/489 (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 FQSTFLDAA 481
           FQ    D+ 
Sbjct: 451 FQEVTPDSG 459

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 =  467 bits (1201), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 258/489 (52%), Positives = 332/489 (67%), Gaps = 39/489 (7%)

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 FQSTFLDAA 481
           FQ    D+ 
Sbjct: 450 FQEITPDSG 458

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 =  458 bits (1179), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 255/489 (52%), Positives = 330/489 (67%), Gaps = 38/489 (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 FQSTFLDAA 481
           FQ    D+ 
Sbjct: 451 FQEITPDSG 459

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	482
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.792	0.698	0.504	6.1e-94
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.539	0.454	0.479	2e-63
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.531	0.447	0.366	3e-46
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.309	0.237	0.409	2.4e-34
TIGR_CMR|GSU_1525	328	GSU_1525 "RNA polymerase sigma	0.342	0.503	0.361	2.4e-33
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.595	0.497	0.299	3e-32
TIGR_CMR|CJE_1081	622	CJE_1081 "RNA polymerase sigma	0.400	0.310	0.321	6.4e-31
TIGR_CMR|CPS_4334	616	CPS_4334 "RNA polymerase sigma	0.319	0.25	0.370	9.2e-31
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.400	0.521	0.358	1.4e-30
UNIPROTKB|P00579	613	rpoD [Escherichia coli K-12 (t	0.360	0.283	0.368	5.2e-30

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

 Score = 935 (334.2 bits), Expect = 6.1e-94, P = 6.1e-94
 Identities = 203/402 (50%), Positives = 263/402 (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 RRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA 480
               VG++ EKL++L++ TR PLSMQQP+W+DQDTTFQ    D+
Sbjct:   417 GHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDS 458

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 = 313 (115.2 bits), Expect = 2.4e-33, Sum P(2) = 2.4e-33
 Identities = 60/166 (36%), Positives = 106/166 (63%)

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 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAA 481
             ++A  + +    + RL+ + +   S+++P+  + D     T  D +
Sbjct:   199 EVATEMKVNSAYVRRLMVLLKKTYSIERPMGENSDYFLIDTIEDTS 244

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 = 357 (130.7 bits), Expect = 3.0e-32, P = 3.0e-32
 Identities = 91/304 (29%), Positives = 167/304 (54%)

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 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFL 478
                R  +QE    P  E++A R+ + ++K+ +++ I + P+S++ P+  ++D+     F+
Sbjct:   430 RTSRQLVQEIGREPSPEEIAERMNLPLDKVRKVLKIAKEPISLETPIGEEEDSHL-GDFI 488

Query:   479 DAAG 482
             +  G
Sbjct:   489 EDKG 492

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|CJE_1081 CJE_1081 "RNA polymerase sigma factor RpoD" [Campylobacter jejuni RM1221 (taxid:195099)]

 Score = 320 (117.7 bits), Expect = 6.4e-31, Sum P(2) = 6.4e-31
 Identities = 64/199 (32%), Positives = 123/199 (61%)

Query:   275 EFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334
             E  +++   ++ +L + K   +  F  E + +   K I      +K      + ++ ++ 
Sbjct:   333 ETTMVSTYMEIKKLFQTKEASEKSFDLEKSRL---KEI---LEQIKRGKKISDEAKGRMA 386

Query:   335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 394
              +NLRLVV +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I 
Sbjct:   387 KSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAIS 446

Query:   395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 454
             +AI   +RTIR+P ++   ++++ +  R ++Q+    PD   +A+ VG++V+K++++I I
Sbjct:   447 RAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVGLSVDKVKQVIKI 506

Query:   455 TRMPLSMQQPVWADQDTTF 473
             T+ P+S++ P+  + D  F
Sbjct:   507 TKEPISLEAPIGNEDDGKF 525

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|CPS_4334 CPS_4334 "RNA polymerase sigma-70 factor" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 323 (118.8 bits), Expect = 9.2e-31, Sum P(2) = 9.2e-31
 Identities = 57/154 (37%), Positives = 103/154 (66%)

Query:   329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
             ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW
Sbjct:   377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query:   389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
             +RQ I ++I   +RTIR+P ++   ++K+    R  +QE    P  E+LA R+ +  +K+
Sbjct:   437 IRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPTPEELAERMVMPEDKI 496

Query:   449 ERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG 482
              +++ I + P+SM+ P+  D+D+       D +G
Sbjct:   497 RKVLKIAKEPISMETPIGDDEDSHLGDFIEDGSG 530

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

UNIPROTKB|P00579 rpoD [Escherichia coli K-12 (taxid:83333)]

 Score = 318 (117.0 bits), Expect = 5.2e-30, Sum P(2) = 5.2e-30
 Identities = 66/179 (36%), Positives = 112/179 (62%)

Query:   294 KLQSQFGREPTL-IEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
             KLQ Q   E  L IE  K I    R +         ++++++ ANLRLV+ +AK+Y  RG
Sbjct:   343 KLQ-QIEEETGLTIEQVKDIN---RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRG 398

Query:   353 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 412
             +   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I   +RTIR+P ++  
Sbjct:   399 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIE 458

Query:   413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
              ++K+    R  +QE    P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+D+
Sbjct:   459 TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517

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

GO:0009408 "response to heat" evidence=IEP

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

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

GO:0005515 "protein binding" evidence=IPI

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

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

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	0.5214	0.9356	0.8244	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	482
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	2e-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	5e-50
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	5e-49
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	1e-45
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	1e-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	6e-33
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	2e-28
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	3e-19
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	3e-19
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	2e-18
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	2e-17
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	3e-17
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	2e-16
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	6e-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	1e-09
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	2e-09
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	2e-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	7e-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 = 2e-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 = 5e-50
 Identities = 84/211 (39%), Positives = 130/211 (61%)

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 ERLIFITRMPLSMQQPVWADQDTTFQSTFLD 479
              + + R P+S+   V  +QDT       D
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELSELLED 242

Length = 327

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

 Score =  170 bits (434), 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 = 1e-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 = 1e-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 (357), 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 = 76/225 (33%), Positives = 121/225 (53%), Gaps = 42/225 (18%)

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 EGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
           E    P  E++A  + +  EK+  ++ I + P+S++ P+  + D+
Sbjct: 228 ELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDS 272

Length = 367

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

 Score =  130 bits (329), Expect = 6e-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 = 66/195 (33%), Positives = 116/195 (59%), Gaps = 16/195 (8%)

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 RMPLSMQQPVWADQD 470
           + P+S++ P+  D+D
Sbjct: 508 KEPISLETPIGDDED 522

Length = 619

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

 Score = 81.5 bits (202), Expect = 3e-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 = 86.6 bits (215), Expect = 3e-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 = 2e-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 = 80.3 bits (199), Expect = 3e-17
 Identities = 36/117 (30%), Positives = 68/117 (58%)

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 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 446
              I++     +  +R+P  +  L  K+ +A     Q    SP   ++A R+G++ E
Sbjct: 65  MGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEE 121

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 = 78.8 bits (195), Expect = 2e-16
 Identities = 45/153 (29%), Positives = 88/153 (57%), Gaps = 2/153 (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 DLARRVGITVEKLERLIFITRMPLSMQQPVWAD 468
           ++A+ + +  E++   +   + P+S+ +P++ D
Sbjct: 144 EIAKELEVPREEVVFALDAIQDPVSLFEPIYHD 176

Length = 258

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

 Score = 77.2 bits (190), Expect = 6e-16
 Identities = 46/153 (30%), Positives = 88/153 (57%), Gaps = 2/153 (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 DLARRVGITVEKLERLIFITRMPLSMQQPVWAD 468
           ++A+ + +  E++   +   + P+S+ +P++ D
Sbjct: 141 EIAKELKVPQEEVVFALDAIQDPVSLFEPIYND 173

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 = 70.1 bits (172), 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 = 54.5 bits (132), Expect = 1e-09
 Identities = 21/67 (31%), Positives = 35/67 (52%)

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 FQSTFLD 479
                 D
Sbjct: 62  LGDLLED 68

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 = 2e-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 = 7e-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 = 40.4 bits (95), Expect = 0.001
 Identities = 45/159 (28%), Positives = 78/159 (49%), Gaps = 13/159 (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-----PLSMQQPVWADQDTTFQSTFLDAAG 482
           E +     M      LS+   + AD D +   T LD  G
Sbjct: 151 EAM----EMGKSYQALSVDHSIEADSDGS-TVTLLDIVG 184

Length = 257

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	482
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	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	99.98
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	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
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	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	99.94
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
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	99.93
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	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	99.86
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.85
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.78
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.78
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.76
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.76
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.75
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.75
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.73
PRK12513	194	RNA polymerase sigma factor; Provisional	99.72
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.71
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.71
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.7
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.7
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.69
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.69
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.69
PRK12537	182	RNA polymerase sigma factor; Provisional	99.69
PRK12524	196	RNA polymerase sigma factor; Provisional	99.68
PRK12514	179	RNA polymerase sigma factor; Provisional	99.68
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.68
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.67
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.66
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.66
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.66
PRK12538	233	RNA polymerase sigma factor; Provisional	99.66
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.66
PRK12534	187	RNA polymerase sigma factor; Provisional	99.66
PRK12526	206	RNA polymerase sigma factor; Provisional	99.65
PRK12531	194	RNA polymerase sigma factor; Provisional	99.65
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.65
PRK12519	194	RNA polymerase sigma factor; Provisional	99.65
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.64
PRK11922	231	RNA polymerase sigma factor; Provisional	99.64
PRK12539	184	RNA polymerase sigma factor; Provisional	99.63
PRK12536	181	RNA polymerase sigma factor; Provisional	99.63
PRK12515	189	RNA polymerase sigma factor; Provisional	99.63
PRK12542	185	RNA polymerase sigma factor; Provisional	99.62
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.61
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.6
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.59
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.59
PRK11924	179	RNA polymerase sigma factor; Provisional	99.59
PRK12512	184	RNA polymerase sigma factor; Provisional	99.58
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.58
PRK12522	173	RNA polymerase sigma factor; Provisional	99.57
PRK12543	179	RNA polymerase sigma factor; Provisional	99.57
PRK12520	191	RNA polymerase sigma factor; Provisional	99.56
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.56
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.55
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.55
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.55
PRK12518	175	RNA polymerase sigma factor; Provisional	99.55
PRK12516	187	RNA polymerase sigma factor; Provisional	99.54
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.53
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.53
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.53
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.52
PRK12529	178	RNA polymerase sigma factor; Provisional	99.52
PRK12547	164	RNA polymerase sigma factor; Provisional	99.51
PRK12541	161	RNA polymerase sigma factor; Provisional	99.51
PRK12535	196	RNA polymerase sigma factor; Provisional	99.51
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.5
PRK12533	216	RNA polymerase sigma factor; Provisional	99.5
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.49
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.49
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.49
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.46
PRK12545	201	RNA polymerase sigma factor; Provisional	99.46
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.46
PRK12540	182	RNA polymerase sigma factor; Provisional	99.46
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.45
PRK12528	161	RNA polymerase sigma factor; Provisional	99.45
PRK12532	195	RNA polymerase sigma factor; Provisional	99.44
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.43
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.43
PRK12544	206	RNA polymerase sigma factor; Provisional	99.43
PRK12517	188	RNA polymerase sigma factor; Provisional	99.43
PRK12530	189	RNA polymerase sigma factor; Provisional	99.43
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.42
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.41
PRK12546	188	RNA polymerase sigma factor; Provisional	99.41
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.4
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.36
PRK12511	182	RNA polymerase sigma factor; Provisional	99.36
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.31
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.31
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.3
PRK12525	168	RNA polymerase sigma factor; Provisional	99.29
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.25
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.18
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.17
PRK09191	261	two-component response regulator; Provisional	99.17
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.1
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.07
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	99.04
PF07638	185	Sigma70_ECF: ECF sigma factor	98.78
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	97.94
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	97.27
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	96.23
PRK07670	251	RNA polymerase sigma factor SigD; Validated	96.15
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	96.09
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	96.08
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	96.03
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	95.98
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	95.86
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	95.73
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	95.62
PRK05949	327	RNA polymerase sigma factor; Validated	95.59
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	95.58
PRK05901	509	RNA polymerase sigma factor; Provisional	95.26
PRK07598	415	RNA polymerase sigma factor SigC; Validated	95.18
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	94.95
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	94.83
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	94.73
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	94.62
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	94.43
PRK07405	317	RNA polymerase sigma factor SigD; Validated	94.42
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	94.33
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	94.08
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	93.97
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	93.76
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	93.72
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	92.86
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	92.83
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	92.57
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	92.23
PRK08215	258	sporulation sigma factor SigG; Reviewed	92.12
PRK08583	257	RNA polymerase sigma factor SigB; Validated	91.87
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	91.63
PRK05572	252	sporulation sigma factor SigF; Validated	91.61
PHA02547	179	55 RNA polymerase sigma factor; Provisional	91.33
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	90.3
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	88.99
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	86.85
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	86.0
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	85.77
PF10668	60	Phage_terminase: Phage terminase small subunit; In	84.44
PF06971	50	Put_DNA-bind_N: Putative DNA-binding protein N-ter	84.0
PRK06930	170	positive control sigma-like factor; Validated	83.97
COG4941	415	Predicted RNA polymerase sigma factor containing a	83.41
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	82.1
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	81.5
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	81.15
PRK00118	104	putative DNA-binding protein; Validated	80.58
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	80.5

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=1.4e-47  Score=400.96  Aligned_cols=228  Identities=39%  Similarity=0.646  Sum_probs=218.0

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhhCCCCcHHHHHH--
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAK--  310 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~--------------------le~~~~~l~~~~g~~pt~~ewA~--  310 (482)
                      .+|+++.||++|++.||||++||++|+++||.+++                    |++++..|++++|++||..|||.  
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            47999999999999999999999999999999999                    89999999999999999999994  


Q ss_pred             --------------------HhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhH
Q 011577          311 --------------------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV  370 (482)
Q Consensus       311 --------------------a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAi  370 (482)
                                          ++||++++|+..++.|..|+++||.+|+++|+++|++|.++|++++||||||+||||+|+
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                                455677778888899999999999999999999999999999999999999999999999


Q ss_pred             HhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHH
Q 011577          371 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER  450 (482)
Q Consensus       371 ekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~  450 (482)
                      ++|||.+|++|+||++||||++|.+++++++++|++|.++.+.+++++++.+.|...+|+.|+.+|||+.|||++++|+.
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             HHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577          451 LIFITRMPLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       451 ~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      ++..++.++|||.+++++++..+.|+++|+
T Consensus       298 ~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~  327 (415)
T PRK07598        298 VLLRVPRSVSLETKVGKDKDTELGDLLETD  327 (415)
T ss_pred             HHHHccCCcccccccCCCccccHHHhccCC
Confidence            999999999999999988888888888764

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

Probab=100.00  E-value=6.4e-45  Score=366.57  Aligned_cols=226  Identities=43%  Similarity=0.726  Sum_probs=216.9

Q ss_pred             cHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHH
Q 011577          255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  334 (482)
Q Consensus       255 d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI  334 (482)
                      |++..||++++++|+||++||.+|+++++.++++++++..|+++.|++|+..+||+++|+++.+|+.+++.|..|+++||
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 011577          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  414 (482)
Q Consensus       335 ~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l  414 (482)
                      .+|+++|+++|++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.++.+.+++|.++...+
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             HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577          415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       415 ~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      ++++++...+...+|+.|+.+|||+.+|+++++|..++..+...+|||.+++++++.++.++++|+
T Consensus       161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~  226 (298)
T TIGR02997       161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD  226 (298)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC
Confidence            999999999999999999999999999999999999999999999999999876666777777653

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=8e-45  Score=371.20  Aligned_cols=228  Identities=38%  Similarity=0.653  Sum_probs=221.1

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHH
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~  332 (482)
                      .+|++..||++|+++|+||++||++|+++|+.++.+++.+..|+..+|++|+..+||.+++|++.+|+..++.|+.|++.
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 011577          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (482)
Q Consensus       333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e  412 (482)
                      ||..|+++|+++|++|.+++.+++|||||||||||+++++|||++|++|+|||+||||++|.++|+++++.|++|.++..
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             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       413 ~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      .++++.++.+.+...+|+.|+.+|||+.+||++++|..++..++.++|||.|++++++.++.|+++|+
T Consensus       176 ~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~  243 (327)
T PRK05949        176 KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDE  243 (327)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCC
Confidence            99999999999999999999999999999999999999999999999999999887777888888775

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.4e-44  Score=375.00  Aligned_cols=227  Identities=37%  Similarity=0.703  Sum_probs=220.6

Q ss_pred             CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHH
Q 011577          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (482)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~L  333 (482)
                      .|++..||++|+++|+||++||++|+++|++++.+++++.+|+...|++|+..+||.++|++..+|..++..|..|++.|
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 011577          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL  413 (482)
Q Consensus       334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~  413 (482)
                      |.+|+++|+++|++|.++|.+++||+||||||||+|+++||+.+|++|+|||+||||++|.++|+++++.|++|.++...
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             HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577          414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       414 l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      ++++.++...|.+.+|+.||.+|||+.||+++++|..++..+..++|||.|++++++.++.|+++|+
T Consensus       222 ~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~  288 (373)
T PRK07406        222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD  288 (373)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCC
Confidence            9999999999999999999999999999999999999999888999999999887777888988874

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=1.4e-43  Score=360.44  Aligned_cols=227  Identities=40%  Similarity=0.644  Sum_probs=220.1

Q ss_pred             CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHH
Q 011577          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (482)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~L  333 (482)
                      +|++..||++|+++|+||++||.+|+++|++++.+++++..|++++|++|+..+||.++++++.+|+..++.|+.|++.|
T Consensus         7 ~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L   86 (317)
T PRK07405          7 TDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKM   86 (317)
T ss_pred             CcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHH
Q 011577          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL  413 (482)
Q Consensus       334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~  413 (482)
                      |..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|.++++.+++|.++...
T Consensus        87 ~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~  166 (317)
T PRK07405         87 VEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK  166 (317)
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577          414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       414 l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      +++++++...+...+|+.|+.+|||+.+|+++++|..++...+..+|||.|++++++.++.++++|+
T Consensus       167 ~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~  233 (317)
T PRK07405        167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT  233 (317)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCC
Confidence            9999999999999999999999999999999999999999889999999999887777888888764

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

Probab=100.00  E-value=9.5e-41  Score=340.57  Aligned_cols=228  Identities=36%  Similarity=0.626  Sum_probs=211.0

Q ss_pred             CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hhCCCCcHH---------------HHHHHhcCCH-
Q 011577          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC-  316 (482)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~-~~g~~pt~~---------------ewA~a~gmdd-  316 (482)
                      .|.+..|+.+++..++++.++|.++.+.++....+......+.. ..|..|+..               +|+..+..++ 
T Consensus         8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee   87 (342)
T COG0568           8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE   87 (342)
T ss_pred             hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence            57899999999999999999999999999887777667777777 677888876               6665555554 


Q ss_pred             HHHHHHHhhc--H-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577          317 RDLKSELHSG--N-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (482)
Q Consensus       317 ~eLi~~l~~G--d-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI  393 (482)
                      ..|..++..|  + .|..+||.+|++||++||++|.|+|+.+.||||||+||||+|++||||++|++|+|||+||||++|
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             HHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcc
Q 011577          394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  473 (482)
Q Consensus       394 ~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l  473 (482)
                      .++|.++.|+|++|.|+.+.++++.+..+.+.+.++++|+.+|||+.||++.++|+.++.++..++|||.|+|++++..+
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             cccccCCC
Q 011577          474 QSTFLDAA  481 (482)
Q Consensus       474 ~d~i~D~~  481 (482)
                      +|+++|..
T Consensus       248 ~d~leD~~  255 (342)
T COG0568         248 GDFLEDDK  255 (342)
T ss_pred             HHHhhcCC
Confidence            99999975

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=1e-40  Score=356.81  Aligned_cols=216  Identities=36%  Similarity=0.579  Sum_probs=195.1

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHH
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~  332 (482)
                      ..|+++.||++|+++|+||++||++|+++|+.+..++..   +.       ....|+.   ....+|...+..|..|+++
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            468999999999999999999999999999886433321   11       1122432   2456788888899999999


Q ss_pred             HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011577          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (482)
Q Consensus       333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e  412 (482)
                      ||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.+++|.++.+
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             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCC
Q 011577          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAA  481 (482)
Q Consensus       413 ~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~  481 (482)
                      .++++.++.+.|...+|+.||.+|||+.|||++++|..++...+.++|||.+++++++.++.|+++|+.
T Consensus       356 ~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~  424 (509)
T PRK05901        356 TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSE  424 (509)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCC
Confidence            999999999999999999999999999999999999999999999999999998887778999998864

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=1.3e-39  Score=332.66  Aligned_cols=214  Identities=36%  Similarity=0.596  Sum_probs=194.4

Q ss_pred             CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHH
Q 011577          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (482)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~L  333 (482)
                      +|++..||++++++|+||++||.+|+++|+.+..++..           |+..+|+...  ...+|...++.|..|+++|
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           1122232111  3467888999999999999


Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHH
Q 011577          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL  413 (482)
Q Consensus       334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~  413 (482)
                      |..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.+++|.++.+.
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             HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577          414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       414 l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      ++++.++...|...+|+.||.+|||+.||+++++|..++..+...+|||.|++++++.++.|+++|+
T Consensus       172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~  238 (324)
T PRK07921        172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDS  238 (324)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCC
Confidence            9999999999999999999999999999999999999998888999999999877777889999875

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2.7e-36  Score=312.71  Aligned_cols=192  Identities=39%  Similarity=0.707  Sum_probs=180.3

Q ss_pred             CCCCCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHH
Q 011577          250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS  329 (482)
Q Consensus       250 ~~~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~A  329 (482)
                      +...+|+++.||++|+++|+||++||.+|+++++.                                        ++..|
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            33457899999999999999999999999987764                                        12389


Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011577          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (482)
Q Consensus       330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~  409 (482)
                      ++.||..|+++|+++|++|.+++.+++||+||||||||+|+++|||.+|++|+|||+||||++|.++|+++.+.+++|.+
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             HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCC
Q 011577          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAA  481 (482)
Q Consensus       410 v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~  481 (482)
                      +.+.++++.++.+.|...+|+.||.+|||+.|||++++|+.++..++.++|||.|++++++..+.|+++|+.
T Consensus       211 ~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~  282 (367)
T PRK09210        211 MVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQD  282 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCC
Confidence            999999999999999999999999999999999999999999999989999999999877788999998864

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=4.7e-34  Score=313.48  Aligned_cols=154  Identities=36%  Similarity=0.737  Sum_probs=149.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP  407 (482)
                      .|+++||.+|++||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|+++.++|++|
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             hhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCC
Q 011577          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAA  481 (482)
Q Consensus       408 ~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~  481 (482)
                      .++.+.++++.++.+.+.+++|+.||.+|||+.||+++++|+.++..+..++|||.|++++++.++.|+++|+.
T Consensus       460 ~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~  533 (619)
T PRK05658        460 VHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKN  533 (619)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999888888999998863

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=99.98  E-value=2.3e-31  Score=267.67  Aligned_cols=188  Identities=22%  Similarity=0.413  Sum_probs=159.4

Q ss_pred             CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHH
Q 011577          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (482)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~L  333 (482)
                      .+..+.||+++.++|+||+++|.+|+++++.                                       .++..|+++|
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            3567889999999999999999999997643                                       1234899999


Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH-
Q 011577          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT-  412 (482)
Q Consensus       334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e-  412 (482)
                      |..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|+|||+||||++|.++|+++.+.+++|.+... 
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            9999999999999999999999999999999999999999999999999999999999999999999999999987544 


Q ss_pred             ----HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH-HcCCCccCcccCCCCCCC--cccccccCC
Q 011577          413 ----LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQSTFLDA  480 (482)
Q Consensus       413 ----~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~-~ar~~lSLD~~i~~d~~~--~l~d~i~D~  480 (482)
                          .+.++..........+++.|+.+|||+.||+++++|..+.. .....+|||.+++++++.  ++.|+++|+
T Consensus       126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~  200 (289)
T PRK07500        126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDD  200 (289)
T ss_pred             HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCC
Confidence                33333333333334678899999999999999999988754 345789999999765543  678888775

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.97  E-value=1.9e-30  Score=260.40  Aligned_cols=186  Identities=27%  Similarity=0.489  Sum_probs=156.7

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcH-HHHH
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN-SSRE  331 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd-~Are  331 (482)
                      +.+++..|++++++.|+||.++|.+|+..++.                                        .|+ .|++
T Consensus        12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~----------------------------------------~Gd~~a~~   51 (284)
T PRK06596         12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE----------------------------------------HGDLEAAK   51 (284)
T ss_pred             CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH----------------------------------------cCCHHHHH
Confidence            45789999999999999999999999886432                                        234 8999


Q ss_pred             HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHH
Q 011577          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  411 (482)
Q Consensus       332 ~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~  411 (482)
                      .||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++|+++.+.+++|.+..
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            99999999999999999999999999999999999999999999999999999999999999999999887889998653


Q ss_pred             H--HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc-CCCccCcccCCCCC--CCcccccccCC
Q 011577          412 T--LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQ--DTTFQSTFLDA  480 (482)
Q Consensus       412 e--~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a-r~~lSLD~~i~~d~--~~~l~d~i~D~  480 (482)
                      .  ...++.+...++.  .++.|+.+|||+.||+++++|..++... ...+|||.++++++  +.++.++++|+
T Consensus       132 ~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~  203 (284)
T PRK06596        132 QRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDK  203 (284)
T ss_pred             HHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCC
Confidence            2  2333444444442  3478999999999999999999987643 46899999987553  24577888775

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=99.97  E-value=9.5e-31  Score=260.03  Aligned_cols=153  Identities=23%  Similarity=0.384  Sum_probs=141.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP  407 (482)
                      .++++||..|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|+++.+.+++|
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--cCCCccCcccCCCCCC--CcccccccCC
Q 011577          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQD--TTFQSTFLDA  480 (482)
Q Consensus       408 ~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~--ar~~lSLD~~i~~d~~--~~l~d~i~D~  480 (482)
                      .++.+.+.+++++...|.+.+|+.||.+|||+.||+++++|.+++..  ...++|||.+++++++  ..+.|.++|+
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  4568999999875433  3566777665

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

Probab=99.97  E-value=1.2e-30  Score=254.40  Aligned_cols=153  Identities=40%  Similarity=0.757  Sum_probs=145.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccch
Q 011577          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (482)
Q Consensus       329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~  408 (482)
                      |+++||..|+++|+++|++|.+++.+++||+|||+|||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
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             hHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCC
Q 011577          409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAA  481 (482)
Q Consensus       409 ~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~  481 (482)
                      ++...++++.++...+...+|+.||.+|||+.||+++++|..++......+|||.+++++++.++.|+++|++
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~  153 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTS  153 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCC
Confidence            9999999999999999999999999999999999999999999988888999999998777767888888764

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.

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.97  E-value=3.6e-30  Score=256.05  Aligned_cols=184  Identities=26%  Similarity=0.516  Sum_probs=151.4

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHH
Q 011577          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (482)
Q Consensus       256 ~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~  335 (482)
                      ++..||++++++|+|++++|.+|+.++..                                       .++..|++.||.
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 011577          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL  413 (482)
Q Consensus       336 snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~--e~  413 (482)
                      .|+++|+++|++|.+++.+++||+||||+||++|+++|||++|++|+|||+|||+++|.++|+++.+.+++|.+..  ..
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            9999999999999999999999999999999999999999999999999999999999999999877789886543  33


Q ss_pred             HHHHHHHHHHHHHhcCCCC-cHHHHHHHhCCCHHHHHHHHHHcC-CCccCcccCCCCCC--CcccccccCC
Q 011577          414 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFITR-MPLSMQQPVWADQD--TTFQSTFLDA  480 (482)
Q Consensus       414 l~kI~ka~~eL~~e~gr~p-S~eEIAe~LGIS~etVk~~L~~ar-~~lSLD~~i~~d~~--~~l~d~i~D~  480 (482)
                      ..++.+....+.  ..+.| +.+|||+.||+++++|..++.... ..+|||.+++++++  .++.|.++|.
T Consensus       123 ~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~  191 (270)
T TIGR02392       123 FFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDK  191 (270)
T ss_pred             HHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCC
Confidence            344444444332  21345 699999999999999999876443 47999999876543  3566777664

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.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=99.97  E-value=2.1e-29  Score=257.55  Aligned_cols=188  Identities=36%  Similarity=0.630  Sum_probs=173.5

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHH
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~  332 (482)
                      ..|.++.||++|+..|+||+++|..|+.+++.                                        ++..|++.
T Consensus        51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~   90 (325)
T PRK05657         51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR   90 (325)
T ss_pred             cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence            46789999999999999999999999887653                                        22389999


Q ss_pred             HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHH
Q 011577          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (482)
Q Consensus       333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e  412 (482)
                      ||..|.++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+||++||||..|.++++++.+.+++|.++..
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            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       413 ~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      .++.+.++...|...+++.|+.+|||+.||++++.|+.++.......|||.++..+...++.|.++|+
T Consensus       171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~  238 (325)
T PRK05657        171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADE  238 (325)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCC
Confidence            88888888888988899999999999999999999999998877889999998877777788888765

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=99.97  E-value=1.4e-29  Score=250.22  Aligned_cols=157  Identities=28%  Similarity=0.505  Sum_probs=142.6

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccCC-CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011577          325 SGN-SSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (482)
Q Consensus       325 ~Gd-~Are~LI~snlrLV~sIAkrY~~~-g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r  402 (482)
                      +|+ .|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+|+|++++|++..
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            455 899999999999999999999876 667999999999999999999999999999999999999999999999999


Q ss_pred             CcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH--HcCCCccCcccCCCCCC--Cccccccc
Q 011577          403 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQD--TTFQSTFL  478 (482)
Q Consensus       403 ~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~--~ar~~lSLD~~i~~d~~--~~l~d~i~  478 (482)
                      .+++|+++...++++.++...|.+.+|+.|+.+|||+.||+++++|..++.  .....+|||.+++++++  .++.+.++
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  35777777


Q ss_pred             CCC
Q 011577          479 DAA  481 (482)
Q Consensus       479 D~~  481 (482)
                      |+.
T Consensus       181 d~~  183 (256)
T PRK07408        181 DPR  183 (256)
T ss_pred             Ccc
Confidence            763

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=99.96  E-value=1.4e-28  Score=242.34  Aligned_cols=176  Identities=27%  Similarity=0.469  Sum_probs=158.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 011577          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (482)
Q Consensus       264 i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~s  343 (482)
                      ..++|+||++||.+|+..++.                                        ++..|++.||..|.++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence            467899999999888876553                                        2237999999999999999


Q ss_pred             HHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHH
Q 011577          344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  423 (482)
Q Consensus       344 IAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~e  423 (482)
                      +|++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|++++|++. .+++|.++.....++.++...
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             HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCC--CcccccccCC
Q 011577          424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQSTFLDA  480 (482)
Q Consensus       424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~~l~d~i~D~  480 (482)
                      +..++++.|+.+|||+.||+++++|..++.....++|||.++.++++  .++.+.+.|+
T Consensus       129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~  187 (254)
T TIGR02850       129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDE  187 (254)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCc
Confidence            99999999999999999999999999999988889999999864443  3467777664

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=1.7e-27  Score=234.86  Aligned_cols=176  Identities=27%  Similarity=0.486  Sum_probs=157.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 011577          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (482)
Q Consensus       264 i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~s  343 (482)
                      ..++|+|+++|+..|+.+++.                                        ++..|++.||..|.++|++
T Consensus        13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~   52 (258)
T PRK08215         13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS   52 (258)
T ss_pred             CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence            466789999999888876553                                        2348999999999999999


Q ss_pred             HHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHH
Q 011577          344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  423 (482)
Q Consensus       344 IAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~e  423 (482)
                      +|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|.|.+++++.. .+++|+++.....++.++...
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             HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCC--CcccccccCC
Q 011577          424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQSTFLDA  480 (482)
Q Consensus       424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~~l~d~i~D~  480 (482)
                      +...+++.|+.+|||+.|||++++|...+.....++|||.+++++++  .++.|.++|+
T Consensus       132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~  190 (258)
T PRK08215        132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDE  190 (258)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCc
Confidence            99999999999999999999999999999887888999999865543  2456777665

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=99.95  E-value=2.8e-26  Score=229.72  Aligned_cols=191  Identities=36%  Similarity=0.597  Sum_probs=171.0

Q ss_pred             CCCCCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHH
Q 011577          250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS  329 (482)
Q Consensus       250 ~~~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~A  329 (482)
                      .....|.+++||++|..+|.||.++|.+|+..++.                                        ++..|
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~a   47 (285)
T TIGR02394         8 ETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFEA   47 (285)
T ss_pred             ccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHHH
Confidence            34457899999999999999999999999887654                                        22489


Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011577          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (482)
Q Consensus       330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~  409 (482)
                      ++.||..|.++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+||+.|||+.++.++++++.+.+++|..
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             HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCC
Q 011577          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       410 v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      +...++.+.+..+.+....++.|+..|+|+.||+++..|..++..+...+|+|.++..++..++.+.+.++
T Consensus       128 ~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~  198 (285)
T TIGR02394       128 VIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADE  198 (285)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCC
Confidence            99999888887777777788899999999999999999999999888899999988766555555555543

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=99.94  E-value=2.4e-26  Score=227.54  Aligned_cols=153  Identities=23%  Similarity=0.373  Sum_probs=135.8

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHcc---CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011577          325 SGN-SSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (482)
Q Consensus       325 ~Gd-~Are~LI~snlrLV~sIAkrY~---~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq  400 (482)
                      .|+ .|+++||..|+++|+++|++|.   ..+.+++||+|||+||||+|+++|||++|++|+|||+||||++|.+++|++
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            455 8999999999999999999985   235689999999999999999999999999999999999999999999998


Q ss_pred             cCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcC--CCccCcccCCC--CC--CCccc
Q 011577          401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--DQ--DTTFQ  474 (482)
Q Consensus       401 ~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i~~--d~--~~~l~  474 (482)
                      .   ++|+++.+.++++.++...|...+|+.|+.+|||+.||+++++|..++..++  ..+|||.++..  ++  +.++.
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  46899998643  21  34577


Q ss_pred             ccccCC
Q 011577          475 STFLDA  480 (482)
Q Consensus       475 d~i~D~  480 (482)
                      |.++|+
T Consensus       176 ~~l~d~  181 (257)
T PRK05911        176 ERIADE  181 (257)
T ss_pred             hhccCC
Confidence            888775

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=99.94  E-value=4.9e-26  Score=220.28  Aligned_cols=158  Identities=27%  Similarity=0.432  Sum_probs=144.2

Q ss_pred             HHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011577          322 ELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (482)
Q Consensus       322 ~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq  400 (482)
                      +++.|+ .|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.+++|++
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            344556 8999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCC--Cccccccc
Q 011577          401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQSTFL  478 (482)
Q Consensus       401 ~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~~l~d~i~  478 (482)
                      . .+++|+++.....++.++...+...+++.||.+|||+.||+++++|..++..+....|||.+++++++  .++.|.+.
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  24667776


Q ss_pred             CC
Q 011577          479 DA  480 (482)
Q Consensus       479 D~  480 (482)
                      |+
T Consensus       163 ~~  164 (231)
T TIGR02885       163 DK  164 (231)
T ss_pred             CC
Confidence            65

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=8.2e-26  Score=222.99  Aligned_cols=160  Identities=27%  Similarity=0.484  Sum_probs=142.5

Q ss_pred             HHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC-CHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (482)
Q Consensus       318 eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~-d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~  395 (482)
                      .+....+.|+ +++ .||+.|+|||.++|++|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||..+|+++|++
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            3455556677 788 9999999999999999998887 999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcC--CCccCcccCCCCCCCcc
Q 011577          396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTF  473 (482)
Q Consensus       396 ~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i~~d~~~~l  473 (482)
                      ++|++. .+++|+.+.+..+++..+..+|..+++|+||..|||+.|||+.++|...+....  ..+|+|..+..+++...
T Consensus        92 ~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~~  170 (247)
T COG1191          92 YLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDV  170 (247)
T ss_pred             HHHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccch
Confidence            999999 999999999999999999999999999999999999999999999999998664  68999887664443334


Q ss_pred             cccccC
Q 011577          474 QSTFLD  479 (482)
Q Consensus       474 ~d~i~D  479 (482)
                      .+.+.+
T Consensus       171 ~~~~~~  176 (247)
T COG1191         171 DDQIEN  176 (247)
T ss_pred             hhcccc
Confidence            444433

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=99.93  E-value=8.9e-25  Score=216.92  Aligned_cols=175  Identities=21%  Similarity=0.334  Sum_probs=150.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 011577          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (482)
Q Consensus       264 i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~s  343 (482)
                      .+++|+||.++|.+|+..++.                                       .++..|++.|+..|.++|+.
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            378999999999999987654                                       12337999999999999999


Q ss_pred             HHHHcc-C--CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHH
Q 011577          344 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA  420 (482)
Q Consensus       344 IAkrY~-~--~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka  420 (482)
                      +|++|. +  .+.+++||+||||+|||+++++||+.+|++|+||+++||||.|.+++|+..   ++|+++.....++.++
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   6899999989999999


Q ss_pred             HHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCCC---CCcccccccCC
Q 011577          421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQSTFLDA  480 (482)
Q Consensus       421 ~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~---~~~l~d~i~D~  480 (482)
                      ...|...+++.||.+|||+.+|++.+.|..++...  ...+|||.++..++   ..++.+.++|+
T Consensus       124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~  188 (268)
T PRK06288        124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESP  188 (268)
T ss_pred             HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCC
Confidence            99999999999999999999999999999998754  45799999874222   23566666554

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

Probab=99.93  E-value=9.6e-25  Score=210.53  Aligned_cols=154  Identities=27%  Similarity=0.465  Sum_probs=140.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (482)
Q Consensus       327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl  406 (482)
                      ..|++.||..|.++|+++|++|.+++.+++||+|||++|||+|+++||+.+|.+|+||+++||+|.|.++++++...+++
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            36999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC--CccCcccCCCCC--CCcccccccCC
Q 011577          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQ--DTTFQSTFLDA  480 (482)
Q Consensus       407 P~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~--~lSLD~~i~~d~--~~~l~d~i~D~  480 (482)
                      |.++.....+++++...+...+++.|+.+|||+.||+++++|..++.....  .+|||.++.+++  +.++.|.++++
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~~  159 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDE  159 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCCc
Confidence            999999999999999999999999999999999999999999998886654  899999986332  23466666654

This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=99.93  E-value=3.1e-24  Score=211.06  Aligned_cols=144  Identities=23%  Similarity=0.364  Sum_probs=134.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (482)
Q Consensus       327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl  406 (482)
                      ..|+++||..|.++|+.+|++|.+++.+++||+||||+|||+++++||++.|.+|.||+++||+|.|.+++++....+++
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            38999999999999999999999999999999999999999999999999999999999999999999999999888999


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCCCC
Q 011577          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQD  470 (482)
Q Consensus       407 P~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~  470 (482)
                      |.++.....++.++...+...+++.|+.+|||+.||++.+.+..++...  ...+|||.+++.+++
T Consensus       108 ~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~  173 (255)
T TIGR02941       108 PRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSD  173 (255)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCC
Confidence            9999999999999999999999999999999999999999999887654  467999999875543

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

>PRK05572 sporulation sigma factor SigF; Validated

Probab=99.92  E-value=2e-23  Score=205.37  Aligned_cols=177  Identities=27%  Similarity=0.425  Sum_probs=154.8

Q ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHH
Q 011577          263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV  342 (482)
Q Consensus       263 ~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~  342 (482)
                      .-+..|.||.+++.+|+..++.                                        ++..|++.||..|.++|+
T Consensus         7 ~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v~   46 (252)
T PRK05572          7 NKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLVW   46 (252)
T ss_pred             cCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHH
Confidence            3467799999988888765432                                        224899999999999999


Q ss_pred             HHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHH
Q 011577          343 HVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKR  422 (482)
Q Consensus       343 sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~  422 (482)
                      .+|++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||+|.|.+++|+.. .+++|+.+.....++.++..
T Consensus        47 ~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~~  125 (252)
T PRK05572         47 SVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKD  125 (252)
T ss_pred             HHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999988889999999999999999999885 78999999999999999999


Q ss_pred             HHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCC--CcccccccCC
Q 011577          423 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQSTFLDA  480 (482)
Q Consensus       423 eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~--~~l~d~i~D~  480 (482)
                      .+...+++.|+..|||+.||++++.|..++.......||+.++.+++.  .++.|.++++
T Consensus       126 ~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~  185 (252)
T PRK05572        126 ELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQ  185 (252)
T ss_pred             HHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCC
Confidence            998888899999999999999999999998887888999998865443  2345555554

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=99.91  E-value=1.8e-23  Score=205.49  Aligned_cols=152  Identities=22%  Similarity=0.310  Sum_probs=135.8

Q ss_pred             HHHHHHH-HhhcH-HHHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011577          316 CRDLKSE-LHSGN-SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (482)
Q Consensus       316 d~eLi~~-l~~Gd-~Are~LI~snlrLV~sIAkrY~~---~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR  390 (482)
                      +.+|+.+ ..+|+ .|++.||..|.++|+.+|++|.+   ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+
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            4556666 34456 89999999999999999999965   6889999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHH--HcCCCccCcccCCCC
Q 011577          391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWAD  468 (482)
Q Consensus       391 naI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~--~ar~~lSLD~~i~~d  468 (482)
                      |.|++++|++.   ++|..+.+.+.+++++...+.+.+++.|+.+|||+.||+++++|+.++.  .....+|||.++.++
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  345789999998654


Q ss_pred             CC
Q 011577          469 QD  470 (482)
Q Consensus       469 ~~  470 (482)
                      ++
T Consensus       165 ~~  166 (251)
T PRK07670        165 DD  166 (251)
T ss_pred             CC
Confidence            43

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=99.91  E-value=6e-23  Score=202.13  Aligned_cols=143  Identities=24%  Similarity=0.375  Sum_probs=132.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (482)
Q Consensus       327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl  406 (482)
                      ..|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|.+|.||+++||+|.|.+++|++...+++
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            38999999999999999999999999999999999999999999999999888999999999999999999999989999


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCCC
Q 011577          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ  469 (482)
Q Consensus       407 P~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~  469 (482)
                      |+++....+++..+...+...+++.|+.+|+|+.+|++.+.|...+...  ...+|+|.+++.++
T Consensus       108 ~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~  172 (257)
T PRK08583        108 PRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADS  172 (257)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCC
Confidence            9999999999999999998888899999999999999999998887654  35789999886544

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=99.90  E-value=1.5e-22  Score=197.61  Aligned_cols=138  Identities=22%  Similarity=0.310  Sum_probs=123.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011577          329 SREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (482)
Q Consensus       329 Are~LI~snlrLV~sIAkrY~~---~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir  405 (482)
                      -...|+..|+++|.++|++|.+   .+.+.+||+|||+||||+|+++||+.+| +|+||++|||||+|.++|++..   +
T Consensus        16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~---~   91 (231)
T PRK12427         16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD---W   91 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC---C
Confidence            4457899999999999999874   4679999999999999999999998665 8999999999999999999865   5


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH--cCCCccCcccCCCCCC
Q 011577          406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQD  470 (482)
Q Consensus       406 lP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~--ar~~lSLD~~i~~d~~  470 (482)
                      .|+.+.....+++++...+.+.+|+.|+.+|||+.||+++++|..++..  +...+|||.+++++++
T Consensus        92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~  158 (231)
T PRK12427         92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAH  158 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCc
Confidence            7999999999999999999999999999999999999999999998764  4568999999876554

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

Probab=99.89  E-value=2.7e-22  Score=193.52  Aligned_cols=143  Identities=20%  Similarity=0.362  Sum_probs=126.6

Q ss_pred             HHHHHHHHHHHHHHHccC---CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011577          333 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (482)
Q Consensus       333 LI~snlrLV~sIAkrY~~---~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~  409 (482)
                      ||..|.++|+++|++|.+   ++.+++||+||||+|||+++++||+.+|++|+||+++||+|.|++++|+..   ++|..
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             HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCC-CCCccccccc
Q 011577          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWAD-QDTTFQSTFL  478 (482)
Q Consensus       410 v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d-~~~~l~d~i~  478 (482)
                      +...++++.++...+...+++.|+.+|||+.||++++.|..++..+  ...+|+|.++.++ +..++.+.++
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~  149 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIE  149 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhcc
Confidence            9999999999999999999999999999999999999999998644  4568898876543 2334555554

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=99.86  E-value=1e-20  Score=184.10  Aligned_cols=143  Identities=21%  Similarity=0.389  Sum_probs=127.8

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHcc---CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011577          325 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (482)
Q Consensus       325 ~Gd~Are~LI~snlrLV~sIAkrY~---~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~  401 (482)
                      .|.-++++||..|.++|+.+|++|.   +++.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|.+++|++.
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            4667999999999999999999997   6789999999999999999999999998999999999999999999999976


Q ss_pred             CCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCCCC
Q 011577          402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQD  470 (482)
Q Consensus       402 r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~  470 (482)
                         ++|..+.....++.++...+...+++.|+.+|||+.||+++++|..++...  ...+|++.+++++++
T Consensus        85 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~  152 (236)
T PRK06986         85 ---WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGD  152 (236)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCc
Confidence               368888888788888888888889999999999999999999999988743  356789988765443

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.85  E-value=1.7e-20  Score=182.45  Aligned_cols=162  Identities=22%  Similarity=0.345  Sum_probs=127.2

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHH
Q 011577          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (482)
Q Consensus       256 ~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~  335 (482)
                      .|..|+.+++..|+||+++|..|+..++.                                        ++..|++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence            57789999999999999999888775543                                        23489999999


Q ss_pred             HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---cc------
Q 011577          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI---RL------  406 (482)
Q Consensus       336 snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i---rl------  406 (482)
                      .|.++|+++|.+|.+++.+++||+|||||++|+++++||+++|.+|.||+++|++|.+++++|+..+..   .+      
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             -------------------chhH-H--HHHHHHHHHHHHHH--------Hhc----CCCCcHHHHHHHhCCCHHHHHHHH
Q 011577          407 -------------------PENI-Y--TLLSKVLEAKRLYI--------QEG----NHSPDKEDLARRVGITVEKLERLI  452 (482)
Q Consensus       407 -------------------P~~v-~--e~l~kI~ka~~eL~--------~e~----gr~pS~eEIAe~LGIS~etVk~~L  452 (482)
                                         |... .  .....+.++...|.        ..+    ..+.|++|||+.||+|.++|+..+
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                               0000 0  11112333332221        112    356799999999999999999998


Q ss_pred             HHcCC
Q 011577          453 FITRM  457 (482)
Q Consensus       453 ~~ar~  457 (482)
                      ++++.
T Consensus       217 ~rA~~  221 (233)
T PRK05803        217 KRALK  221 (233)
T ss_pred             HHHHH
Confidence            88764

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.78  E-value=4.3e-18  Score=165.23  Aligned_cols=141  Identities=25%  Similarity=0.392  Sum_probs=108.5

Q ss_pred             HHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHH
Q 011577          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  396 (482)
Q Consensus       318 eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~  396 (482)
                      .|+.+++.|+ .|++.|+..|.++|+.+|++|.+++.+++||+||+|+++|+++++|++..+++|.||++++++|.|+++
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            3444444556 899999999999999999999999999999999999999999999999888899999999999999999


Q ss_pred             HHHhcCCcc---c--c--------------------h---hHH---HHHHHHHHHHHHHHH--------hc----CCCCc
Q 011577          397 IFQHSRTIR---L--P--------------------E---NIY---TLLSKVLEAKRLYIQ--------EG----NHSPD  433 (482)
Q Consensus       397 Lrkq~r~ir---l--P--------------------~---~v~---e~l~kI~ka~~eL~~--------e~----gr~pS  433 (482)
                      +|++.+...   +  +                    .   ...   .....+.++...|+.        .+    ..+.|
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            997654211   0  0                    0   000   011123334333321        12    35889


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          434 KEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       434 ~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      ++|||+.||+|+++|+..+++++..
T Consensus       201 ~~EIA~~lgis~~tVk~~~~rA~~~  225 (234)
T PRK08301        201 QKEVADMLGISQSYISRLEKRIIKR  225 (234)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999988653

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.78  E-value=5.2e-18  Score=164.60  Aligned_cols=134  Identities=25%  Similarity=0.436  Sum_probs=104.5

Q ss_pred             hhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011577          324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (482)
Q Consensus       324 ~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r  402 (482)
                      +.|+ .|++.|+..|.++|+++|.+|.++..+++||+||+|+++|+++++|+++++.+|.||+++|++|.|++++|+..+
T Consensus        43 ~~gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r  122 (227)
T TIGR02846        43 KEGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKK  122 (227)
T ss_pred             HcCCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhc
Confidence            3455 899999999999999999999999999999999999999999999999888899999999999999999998754


Q ss_pred             Ccc-c----------------------c-----hh---HHHHHHHHHHHHHHHH--------Hhc----CCCCcHHHHHH
Q 011577          403 TIR-L----------------------P-----EN---IYTLLSKVLEAKRLYI--------QEG----NHSPDKEDLAR  439 (482)
Q Consensus       403 ~ir-l----------------------P-----~~---v~e~l~kI~ka~~eL~--------~e~----gr~pS~eEIAe  439 (482)
                      ... .                      +     ..   .......+.+++..|.        ..+    ..+.|++|||+
T Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe  202 (227)
T TIGR02846       123 TKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAK  202 (227)
T ss_pred             cccceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHH
Confidence            211 0                      0     00   0011122333333222        112    25789999999


Q ss_pred             HhCCCHHHHHHHHHHcCC
Q 011577          440 RVGITVEKLERLIFITRM  457 (482)
Q Consensus       440 ~LGIS~etVk~~L~~ar~  457 (482)
                      +||+++++|+.++++++.
T Consensus       203 ~lgis~~tV~~~~~rAl~  220 (227)
T TIGR02846       203 ILGISRSYVSRIEKRALM  220 (227)
T ss_pred             HHCCCHHHHHHHHHHHHH
Confidence            999999999999988764

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.

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.76  E-value=1.1e-17  Score=158.28  Aligned_cols=146  Identities=22%  Similarity=0.286  Sum_probs=113.4

Q ss_pred             cCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (482)
Q Consensus       313 gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn  391 (482)
                      .+++..|+..++.|+ .|++.|+..|.++|+.+|++|.++..+++||+||+|++||+++.+||+.+|.+|.||++.+++|
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 8999999999999999999999999999999999999999999999998878999999999999


Q ss_pred             HHHHHHHHhcCCccc--------------------------------chh-H--HHHH--------HHHHHHHHHHHHhc
Q 011577          392 TIRKAIFQHSRTIRL--------------------------------PEN-I--YTLL--------SKVLEAKRLYIQEG  428 (482)
Q Consensus       392 aI~~~Lrkq~r~irl--------------------------------P~~-v--~e~l--------~kI~ka~~eL~~e~  428 (482)
                      .+.+++++..+..+.                                |.. +  ....        ..+....+.+...+
T Consensus        88 ~~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l~  167 (208)
T PRK08295         88 QIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELY  167 (208)
T ss_pred             HHHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            999999864332111                                000 0  0011        11111112221114


Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      ..+.+++|||+.||+|+++|+..+++++..
T Consensus       168 ~e~~s~~EIA~~lgis~~tV~~~l~rar~~  197 (208)
T PRK08295        168 LDGKSYQEIAEELNRHVKSIDNALQRVKRK  197 (208)
T ss_pred             HccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            457899999999999999999999988754

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.76  E-value=1.1e-17  Score=156.74  Aligned_cols=145  Identities=22%  Similarity=0.288  Sum_probs=112.8

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      |++.+|+..++.|+ .|++.||..|.+.|+.+|+++.++..+++||+||+|+++|+++.+|++..+..|.||++.+|++.
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            56788999999988 89999999999999999999999999999999999999999999999987779999999999999


Q ss_pred             HHHHHHHhcCCcc--------------------------------cchhH---HHHHHHHHHHHHH--------HHHhcC
Q 011577          393 IRKAIFQHSRTIR--------------------------------LPENI---YTLLSKVLEAKRL--------YIQEGN  429 (482)
Q Consensus       393 I~~~Lrkq~r~ir--------------------------------lP~~v---~e~l~kI~ka~~e--------L~~e~g  429 (482)
                      |++++++..+..+                                -|...   .+....+.++...        +...+-
T Consensus        84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~  163 (198)
T TIGR02859        84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL  163 (198)
T ss_pred             HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            9888874311100                                01110   0111112223322        222233


Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .+.|++|||+.||+|+++|+..+++++..
T Consensus       164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~  192 (198)
T TIGR02859       164 DGKSYQEIACDLNRHVKSIDNALQRVKRK  192 (198)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            47899999999999999999999988754

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.

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.75  E-value=1.5e-17  Score=161.92  Aligned_cols=128  Identities=19%  Similarity=0.281  Sum_probs=109.0

Q ss_pred             HHhhcHHHHHHHHHHHHHHHHHHHHHccCCC--CCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011577          322 ELHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ  399 (482)
Q Consensus       322 ~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g--~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrk  399 (482)
                      .++.|+..+++||..|.|+|.++|++|.++.  .+.+|++|+|+||||+|+++||+++|.+|.|||.+||+++|++++|+
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             hcC---CcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHH------hCCCHHHHH
Q 011577          400 HSR---TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR------VGITVEKLE  449 (482)
Q Consensus       400 q~r---~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~------LGIS~etVk  449 (482)
                      ..+   .+++|+...+...++..+..++....++.++.+||+..      .||+.+.+-
T Consensus        83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv  141 (218)
T TIGR02895        83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELV  141 (218)
T ss_pred             cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHh
Confidence            873   45788766665667777777888888889999999864      377766553

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=99.75  E-value=2.1e-17  Score=161.02  Aligned_cols=143  Identities=24%  Similarity=0.371  Sum_probs=112.8

Q ss_pred             CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (482)
Q Consensus       315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI  393 (482)
                      .+.+|+..+..|+ .|++.|+..|.+.|+.+|++|.+++.+++||+||+|+++|+++++|++..+++|.||++++++|.+
T Consensus        38 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~  117 (234)
T TIGR02835        38 EEEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEI  117 (234)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence            3566777888877 899999999999999999999999999999999999999999999998877889999999999999


Q ss_pred             HHHHHHhcCCcc-cc----------------------h-----hH---HHHHHHHHHHHHHHHH--------hc----CC
Q 011577          394 RKAIFQHSRTIR-LP----------------------E-----NI---YTLLSKVLEAKRLYIQ--------EG----NH  430 (482)
Q Consensus       394 ~~~Lrkq~r~ir-lP----------------------~-----~v---~e~l~kI~ka~~eL~~--------e~----gr  430 (482)
                      ++++|+..+... .+                      .     ..   ......+.+++..|..        .+    ..
T Consensus       118 ~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~e  197 (234)
T TIGR02835       118 LMYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGT  197 (234)
T ss_pred             HHHHHHhccccCcccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCC
Confidence            999998664211 00                      0     00   0011224444433321        12    25


Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          431 SPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       431 ~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      +.|++|||+.||+|+++|+..+++++.
T Consensus       198 g~s~~EIA~~Lgis~~tV~~~l~ra~~  224 (234)
T TIGR02835       198 EKTQKEVADMLGISQSYISRLEKRILK  224 (234)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            789999999999999999999988754

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.

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.73  E-value=3.4e-17  Score=152.89  Aligned_cols=145  Identities=17%  Similarity=0.178  Sum_probs=114.5

Q ss_pred             cCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (482)
Q Consensus       313 gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn  391 (482)
                      .++++.|+..++.|+ .|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +..|.+|++.+++|
T Consensus         4 ~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n   82 (186)
T PRK05602          4 ADPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLN   82 (186)
T ss_pred             cccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHH
Confidence            356788999988888 8999999999999999999999999999999999999999999999975 45899999999999


Q ss_pred             HHHHHHHHhcCCcc--c---------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHH
Q 011577          392 TIRKAIFQHSRTIR--L---------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLE  449 (482)
Q Consensus       392 aI~~~Lrkq~r~ir--l---------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk  449 (482)
                      .+.+++|++.....  +         |...   .+....+.++...|.        ..+..+.+++|||+.||+|.++|+
T Consensus        83 ~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~  162 (186)
T PRK05602         83 LCYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALE  162 (186)
T ss_pred             HHHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHH
Confidence            99999997754211  0         1110   011122333333222        223347899999999999999999


Q ss_pred             HHHHHcCCC
Q 011577          450 RLIFITRMP  458 (482)
Q Consensus       450 ~~L~~ar~~  458 (482)
                      ..+++++..
T Consensus       163 ~~l~Rar~~  171 (186)
T PRK05602        163 SLLARGRRA  171 (186)
T ss_pred             HHHHHHHHH
Confidence            999998754

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=9.3e-17  Score=150.91  Aligned_cols=143  Identities=15%  Similarity=0.188  Sum_probs=114.1

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      +++..|+..++.|+ .|++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++++|++.  ..|.+|++++++|.
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            56788999999888 8999999999999999999999999999999999999999999999974  46999999999999


Q ss_pred             HHHHHHHhcCCcccc-----------------hhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCC
Q 011577          393 IRKAIFQHSRTIRLP-----------------ENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGIT  444 (482)
Q Consensus       393 I~~~Lrkq~r~irlP-----------------~~v---~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS  444 (482)
                      +++++|+..+....+                 ...   ......+.++...|...        +..+.+++|||+.||+|
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   01112244444443322        23467999999999999


Q ss_pred             HHHHHHHHHHcCCC
Q 011577          445 VEKLERLIFITRMP  458 (482)
Q Consensus       445 ~etVk~~L~~ar~~  458 (482)
                      +++|+..+++++..
T Consensus       169 ~~tV~~~l~ra~~~  182 (194)
T PRK12513        169 EETVKSRLRYALQK  182 (194)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999988754

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.71  E-value=9.3e-17  Score=151.51  Aligned_cols=143  Identities=8%  Similarity=0.067  Sum_probs=111.8

Q ss_pred             CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (482)
Q Consensus       315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI  393 (482)
                      ++.+|+..+..|+ .|++.|+..|.++|+.+|.+|.++..+++|++||+|+++|+++++||+.+| .|.+|++.+++|.+
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            4567888888888 899999999999999999999999999999999999999999999998655 79999999999999


Q ss_pred             HHHHHHhcCCccc---------------chh-H--HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011577          394 RKAIFQHSRTIRL---------------PEN-I--YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK  447 (482)
Q Consensus       394 ~~~Lrkq~r~irl---------------P~~-v--~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~et  447 (482)
                      ++++|++.+..+.               +.. +  .+....+.+++..|.        ..+..+.+++|||+.||+++++
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               000 0  011122333333221        2233478999999999999999


Q ss_pred             HHHHHHHcCCC
Q 011577          448 LERLIFITRMP  458 (482)
Q Consensus       448 Vk~~L~~ar~~  458 (482)
                      |+..+++++..
T Consensus       175 Vk~~l~ra~~~  185 (194)
T PRK09646        175 VKTRMRDGLIR  185 (194)
T ss_pred             HHHHHHHHHHH
Confidence            99999988754

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.71  E-value=1.2e-16  Score=150.29  Aligned_cols=143  Identities=15%  Similarity=0.229  Sum_probs=111.2

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCC---CCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV  389 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g---~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wI  389 (482)
                      ++++.|+..+..|+ .|++.|+..|.++|+.++.++.+++   .+++|++||+++++|+++++|++..+ .|.||++.++
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   57999999999999999999987544 7999999999


Q ss_pred             HHHHHHHHHHhcCCcccc-------------hh----------HHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCH
Q 011577          390 RQTIRKAIFQHSRTIRLP-------------EN----------IYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITV  445 (482)
Q Consensus       390 RnaI~~~Lrkq~r~irlP-------------~~----------v~e~l~kI~ka~~eL~-~e~gr~pS~eEIAe~LGIS~  445 (482)
                      +|.+++++|++.+.....             ..          +...+.++....+.+. ..+..+.+++|||+.||+|.
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             00          1111222222222221 12334789999999999999


Q ss_pred             HHHHHHHHHcCC
Q 011577          446 EKLERLIFITRM  457 (482)
Q Consensus       446 etVk~~L~~ar~  457 (482)
                      .+|+..+++++.
T Consensus       162 ~~V~~~l~Ra~~  173 (189)
T PRK06811        162 SAIDNRLSRGRK  173 (189)
T ss_pred             HHHHHHHHHHHH
Confidence            999999998864

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

Probab=99.70  E-value=1.8e-16  Score=145.62  Aligned_cols=143  Identities=14%  Similarity=0.161  Sum_probs=113.2

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      |++++|+..+..|+ .|++.|+..|.+.|++++.++.++..+++|++||+|+.+|+.+++|++.  ..|.+|++.+++|.
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            45778888888888 8999999999999999999999999999999999999999999999875  36999999999999


Q ss_pred             HHHHHHHhcCCcccch-----------------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577          393 IRKAIFQHSRTIRLPE-----------------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFI  454 (482)
Q Consensus       393 I~~~Lrkq~r~irlP~-----------------~v~e~l~kI~ka~~eL~-~e~gr~pS~eEIAe~LGIS~etVk~~L~~  454 (482)
                      +++++|+..+...++.                 .+...+.++....+++. ..+..+.+++|||+.||+|+++|+..+.+
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            9999998765432211                 01122222222222221 22334789999999999999999999998


Q ss_pred             cCCC
Q 011577          455 TRMP  458 (482)
Q Consensus       455 ar~~  458 (482)
                      ++..
T Consensus       159 a~~~  162 (169)
T TIGR02954       159 ALKK  162 (169)
T ss_pred             HHHH
Confidence            8654

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.

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.70  E-value=2e-16  Score=147.36  Aligned_cols=144  Identities=14%  Similarity=0.118  Sum_probs=112.4

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      +++.+|+..++.|+ .|++.|+..|.+.|+.++++|.+++.+++|++||+|+++|+++++|++.. ..|.+|++++++|.
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            46788888888888 89999999999999999999999999999999999999999999998754 36999999999999


Q ss_pred             HHHHHHHhcCCcc-c------------c-----hhHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011577          393 IRKAIFQHSRTIR-L------------P-----ENIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE  446 (482)
Q Consensus       393 I~~~Lrkq~r~ir-l------------P-----~~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~e  446 (482)
                      +++++|+..+... +            +     .........+.++...|.        ..+..+.+++|||+.||++++
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     000011112333333322        223347899999999999999


Q ss_pred             HHHHHHHHcCCC
Q 011577          447 KLERLIFITRMP  458 (482)
Q Consensus       447 tVk~~L~~ar~~  458 (482)
                      +|+..+++++..
T Consensus       167 ~V~~~l~ra~~~  178 (186)
T PRK13919        167 TLKTRARRALSR  178 (186)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988754

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.69  E-value=1.7e-16  Score=147.13  Aligned_cols=141  Identities=12%  Similarity=0.189  Sum_probs=109.6

Q ss_pred             HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHH
Q 011577          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  394 (482)
Q Consensus       316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~  394 (482)
                      +++|+..++.|+ .|+++|+..|.++|+.+|.+|.+++.+++|++||+|+++|+++.+|++..  .|.+|++.+++|.++
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            456777888888 89999999999999999999999999999999999999999999999864  699999999999999


Q ss_pred             HHHHHhcCCccc----------------------chhH-H--HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHh
Q 011577          395 KAIFQHSRTIRL----------------------PENI-Y--TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRV  441 (482)
Q Consensus       395 ~~Lrkq~r~irl----------------------P~~v-~--e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~L  441 (482)
                      +++|+..+....                      |... .  +....+.++...|.        ..+..+.+++|||+.|
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            999986542110                      0000 0  01112333333221        1133467999999999


Q ss_pred             CCCHHHHHHHHHHcCCC
Q 011577          442 GITVEKLERLIFITRMP  458 (482)
Q Consensus       442 GIS~etVk~~L~~ar~~  458 (482)
                      |+++++|+..+++++..
T Consensus       163 gis~~~v~~~l~Rar~~  179 (187)
T TIGR02948       163 DLPVGTVKTRIHRGREA  179 (187)
T ss_pred             CCCHHHHHHHHHHHHHH
Confidence            99999999999988754

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

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.69  E-value=3e-16  Score=147.20  Aligned_cols=145  Identities=13%  Similarity=0.081  Sum_probs=114.2

Q ss_pred             hcCCHHHHHHHHhh---cH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHH
Q 011577          312 IGLSCRDLKSELHS---GN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW  387 (482)
Q Consensus       312 ~gmdd~eLi~~l~~---Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~  387 (482)
                      ..+++++|+..++.   |+ .|++.|+..|.+.|+.+|.+|.++..+++|++||+|++||+++++|++.  ..|.+|+++
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            45778889988885   35 8999999999999999999999999999999999999999999999863  479999999


Q ss_pred             HHHHHHHHHHHHhcCCcccc-h-----------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCC
Q 011577          388 WVRQTIRKAIFQHSRTIRLP-E-----------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGIT  444 (482)
Q Consensus       388 wIRnaI~~~Lrkq~r~irlP-~-----------~---v~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS  444 (482)
                      +++|.+++++|+..+..... .           .   ..+....+.++...|...        +..+.+++|||+.||||
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            99999999999765322211 0           0   011123344444444332        22367999999999999


Q ss_pred             HHHHHHHHHHcCCC
Q 011577          445 VEKLERLIFITRMP  458 (482)
Q Consensus       445 ~etVk~~L~~ar~~  458 (482)
                      .++|+..+++++..
T Consensus       164 ~~tV~~~l~Ra~~~  177 (188)
T PRK09640        164 LSATKMRYKRALDK  177 (188)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999988653

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.69  E-value=3.5e-16  Score=146.48  Aligned_cols=141  Identities=18%  Similarity=0.213  Sum_probs=108.3

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCC----CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (482)
Q Consensus       317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~----g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn  391 (482)
                      ..|+..+..|+ .|++.|+..|.+.|+.+|.++.++    +.+++|++||+|++||+++.+|++. +..|.+|++.+++|
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            45778888888 899999999999999999998765    4689999999999999999999864 45799999999999


Q ss_pred             HHHHHHHHhcCCcccc--------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011577          392 TIRKAIFQHSRTIRLP--------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE  446 (482)
Q Consensus       392 aI~~~Lrkq~r~irlP--------------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~e  446 (482)
                      .+++++|++.+....+              ...   .+....+.+++..|.        ..+..+.+++|||+.||++++
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              000   111112333333222        223347899999999999999


Q ss_pred             HHHHHHHHcCCC
Q 011577          447 KLERLIFITRMP  458 (482)
Q Consensus       447 tVk~~L~~ar~~  458 (482)
                      +|+..+++++..
T Consensus       171 tV~~~l~Ra~~~  182 (189)
T PRK09648        171 AVRVAQHRALAR  182 (189)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988643

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.69  E-value=2.2e-16  Score=147.42  Aligned_cols=144  Identities=11%  Similarity=0.150  Sum_probs=113.4

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      +++.+|+..+..|+ .|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++.+++|.
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            45677888888888 89999999999999999999999999999999999999999999998643 47999999999999


Q ss_pred             HHHHHHHhcCCcccc-------------hh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011577          393 IRKAIFQHSRTIRLP-------------EN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL  448 (482)
Q Consensus       393 I~~~Lrkq~r~irlP-------------~~---v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etV  448 (482)
                      +++++|+..+.....             ..   ..+....+.++...|.        ..+..+.+++|||+.||||+++|
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            999999886532211             00   0011222333333322        22334789999999999999999


Q ss_pred             HHHHHHcCCC
Q 011577          449 ERLIFITRMP  458 (482)
Q Consensus       449 k~~L~~ar~~  458 (482)
                      +..+++++..
T Consensus       167 ~~~l~ra~~~  176 (182)
T PRK12537        167 KAWIKRSLKA  176 (182)
T ss_pred             HHHHHHHHHH
Confidence            9999988653

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.68  E-value=3.4e-16  Score=147.90  Aligned_cols=146  Identities=17%  Similarity=0.155  Sum_probs=114.2

Q ss_pred             cCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (482)
Q Consensus       313 gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn  391 (482)
                      .+++..|+.++..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++. ...|.||++.+++|
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------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHH
Q 011577          392 TIRKAIFQHSRTI-RL------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEK  447 (482)
Q Consensus       392 aI~~~Lrkq~r~i-rl------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~et  447 (482)
                      .+++++|++.+.. .+            |...   .+....+.++...|.        ..+..+.+++|||+.||+|+++
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            9999999755421 10            0110   011122333333222        2233578999999999999999


Q ss_pred             HHHHHHHcCCCc
Q 011577          448 LERLIFITRMPL  459 (482)
Q Consensus       448 Vk~~L~~ar~~l  459 (482)
                      |+..+++++..+
T Consensus       169 V~~~l~Ra~~~L  180 (196)
T PRK12524        169 VESLTARGKRAL  180 (196)
T ss_pred             HHHHHHHHHHHH
Confidence            999999997654

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.68  E-value=3.3e-16  Score=145.19  Aligned_cols=144  Identities=9%  Similarity=0.051  Sum_probs=111.0

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      ++...|+..+..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++.+++|.
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            34566777777787 89999999999999999999999999999999999999999999998653 46999999999999


Q ss_pred             HHHHHHHhcCCcc-c------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011577          393 IRKAIFQHSRTIR-L------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL  448 (482)
Q Consensus       393 I~~~Lrkq~r~ir-l------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etV  448 (482)
                      +++++|+..+... +            |...   .+....+..+...|.        ..+..+.+++|||+.||+|+++|
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            1110   011112333333222        22334789999999999999999


Q ss_pred             HHHHHHcCCC
Q 011577          449 ERLIFITRMP  458 (482)
Q Consensus       449 k~~L~~ar~~  458 (482)
                      +..+++++..
T Consensus       163 ~~~l~Rar~~  172 (179)
T PRK12514        163 RTWLRRSLLK  172 (179)
T ss_pred             HHHHHHHHHH
Confidence            9999988754

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

Probab=99.68  E-value=4.1e-16  Score=142.28  Aligned_cols=138  Identities=15%  Similarity=0.149  Sum_probs=106.8

Q ss_pred             HHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011577          320 KSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  398 (482)
Q Consensus       320 i~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lr  398 (482)
                      +.++++|+ .|++.|+..|.+.++.++.++.++..+++|++||+|+++|+++++|+...+ .|.+|++.+++|.+++++|
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 899999999999999999999998999999999999999999999987544 8999999999999999999


Q ss_pred             HhcCCcccc--------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577          399 QHSRTIRLP--------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIF  453 (482)
Q Consensus       399 kq~r~irlP--------------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~  453 (482)
                      ++.+....+              ...   .+....+.++...|.        ..+..+.+++|||+.||||+++|+..++
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            876433211              000   011122333333222        2234578999999999999999999999


Q ss_pred             HcCCC
Q 011577          454 ITRMP  458 (482)
Q Consensus       454 ~ar~~  458 (482)
                      +++..
T Consensus       161 ra~~~  165 (170)
T TIGR02952       161 RAIKK  165 (170)
T ss_pred             HHHHH
Confidence            88643

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.

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.67  E-value=5.7e-16  Score=139.64  Aligned_cols=129  Identities=16%  Similarity=0.151  Sum_probs=99.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC----
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT----  403 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~----  403 (482)
                      .||+.|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.+|++.+++|.+++++|++.+.    
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 56689999999999999999999997666 799999999999999999987421    


Q ss_pred             --cccchh---HHHHHHHHHHHH-------HHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          404 --IRLPEN---IYTLLSKVLEAK-------RLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       404 --irlP~~---v~e~l~kI~ka~-------~eL-~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                        ...|..   ..+....+..+.       +.+ ...+..+.|++|||+.||+|+++|+..+++++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~  149 (154)
T PRK06759         82 VCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEK  149 (154)
T ss_pred             cccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence              111211   111122233333       222 2334457899999999999999999999988653

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.66  E-value=9.7e-16  Score=144.69  Aligned_cols=144  Identities=16%  Similarity=0.120  Sum_probs=113.6

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      +++++++..+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|+..  ..|.+|++.+++|.
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            56778888888888 8999999999999999999999999999999999999999999999975  36999999999999


Q ss_pred             HHHHHHHhcCCcccc-----------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHH
Q 011577          393 IRKAIFQHSRTIRLP-----------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLER  450 (482)
Q Consensus       393 I~~~Lrkq~r~irlP-----------~~---v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~  450 (482)
                      +++++|+..+....+           ..   ..+....+..+...|+.        .+..+.+++|||+.||++.++|+.
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            999999765432211           00   01112223333333221        233478999999999999999999


Q ss_pred             HHHHcCCCc
Q 011577          451 LIFITRMPL  459 (482)
Q Consensus       451 ~L~~ar~~l  459 (482)
                      .+++++..+
T Consensus       170 rl~rar~~L  178 (192)
T PRK09643        170 RCARGRARL  178 (192)
T ss_pred             HHHHHHHHH
Confidence            999987643

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.66  E-value=7.5e-16  Score=142.89  Aligned_cols=142  Identities=13%  Similarity=0.176  Sum_probs=110.4

Q ss_pred             CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (482)
Q Consensus       315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI  393 (482)
                      ..+.|+..++.|+ .|++.|+..|.++|+++|+++.++..+++|++||+|++||+++++|++..  .|.+|++.+++|.+
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            3456788888888 89999999999999999999999999999999999999999999999753  79999999999999


Q ss_pred             HHHHHHhcCCccc----------------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHH
Q 011577          394 RKAIFQHSRTIRL----------------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARR  440 (482)
Q Consensus       394 ~~~Lrkq~r~irl----------------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~  440 (482)
                      ++++|+..+....                      |...   .+....+..+...|.        ..+..+.+++|||+.
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                      1000   011112333333222        122347799999999


Q ss_pred             hCCCHHHHHHHHHHcCCC
Q 011577          441 VGITVEKLERLIFITRMP  458 (482)
Q Consensus       441 LGIS~etVk~~L~~ar~~  458 (482)
                      ||||+++|+..+++++..
T Consensus       162 lgis~~~v~~~l~Rar~~  179 (187)
T PRK09641        162 LDLPVGTVKTRIHRGREA  179 (187)
T ss_pred             HCCCHHHHHHHHHHHHHH
Confidence            999999999999988753

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.66  E-value=9.6e-16  Score=141.31  Aligned_cols=143  Identities=12%  Similarity=0.133  Sum_probs=112.7

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      |++..|+..+..|+ .|++.|+..|.+.|+.+|++|.++..+++|++||+|+++|++++.|++.  .+|.+|++.+++|.
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            55777888888888 8999999999999999999999999999999999999999999999874  47999999999999


Q ss_pred             HHHHHHHhcCCcccch------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011577          393 IRKAIFQHSRTIRLPE------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE  449 (482)
Q Consensus       393 I~~~Lrkq~r~irlP~------------~---v~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk  449 (482)
                      +++++|+..+......            .   .......+.+....|...        +..+.+++|||+.||+++.+|+
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            9999998754322110            0   001222233333333222        2246799999999999999999


Q ss_pred             HHHHHcCCC
Q 011577          450 RLIFITRMP  458 (482)
Q Consensus       450 ~~L~~ar~~  458 (482)
                      ..+++++..
T Consensus       161 ~~l~ra~~~  169 (176)
T PRK09638        161 SRVHHGIKQ  169 (176)
T ss_pred             HHHHHHHHH
Confidence            999988653

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=8e-16  Score=150.62  Aligned_cols=144  Identities=14%  Similarity=0.158  Sum_probs=112.6

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      .++.+|+..++.|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+++|+.+++|++..+ .|.+|++.+++|.
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            46778888888888 899999999999999999999999999999999999999999999986443 7999999999999


Q ss_pred             HHHHHHHhcCCcc---------cch--h-H--HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHH
Q 011577          393 IRKAIFQHSRTIR---------LPE--N-I--YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLER  450 (482)
Q Consensus       393 I~~~Lrkq~r~ir---------lP~--~-v--~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~  450 (482)
                      +++++|++.+...         .+.  . +  .+....+..+...|.        ..+..+.+++|||+.||+|+++|+.
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  011122333333332        2233478999999999999999999


Q ss_pred             HHHHcCCC
Q 011577          451 LIFITRMP  458 (482)
Q Consensus       451 ~L~~ar~~  458 (482)
                      .+++++..
T Consensus       207 ~l~RAr~k  214 (233)
T PRK12538        207 LLKRGRQQ  214 (233)
T ss_pred             HHHHHHHH
Confidence            99998754

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.66  E-value=1.1e-15  Score=142.08  Aligned_cols=143  Identities=19%  Similarity=0.256  Sum_probs=111.3

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      .++..|+..+..|+ .|++.|+..|.+.|+.+|+++.++..+++||+||+|+++|+++++|++.  ..|.+|++.+++|.
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            45677888888888 8999999999999999999999999999999999999999999999875  46999999999999


Q ss_pred             HHHHHHHhcCCccc----------------------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHH
Q 011577          393 IRKAIFQHSRTIRL----------------------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLAR  439 (482)
Q Consensus       393 I~~~Lrkq~r~irl----------------------P~~v---~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe  439 (482)
                      +++++++..+....                      |...   .+....+..+...|..        .+..+.+++|||+
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        2234679999999


Q ss_pred             HhCCCHHHHHHHHHHcCCC
Q 011577          440 RVGITVEKLERLIFITRMP  458 (482)
Q Consensus       440 ~LGIS~etVk~~L~~ar~~  458 (482)
                      .||+++++|+..+++++..
T Consensus       163 ~lgis~~tv~~~l~rar~~  181 (190)
T TIGR02939       163 IMDCPVGTVRSRIFRAREA  181 (190)
T ss_pred             HHCcCHHHHHHHHHHHHHH
Confidence            9999999999999988754

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.

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=6.8e-16  Score=144.04  Aligned_cols=142  Identities=13%  Similarity=0.065  Sum_probs=110.2

Q ss_pred             HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHH
Q 011577          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  394 (482)
Q Consensus       316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~  394 (482)
                      ...++..+..|+ .+++.|+..|.++|+.+|++|.++..+++|++||+|+++|+++++|++.++ .|.||++.+++|.++
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 899999999999999999999999999999999999999999999998644 689999999999999


Q ss_pred             HHHHHhcCCcc------c---------chh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHH
Q 011577          395 KAIFQHSRTIR------L---------PEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKL  448 (482)
Q Consensus       395 ~~Lrkq~r~ir------l---------P~~---v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etV  448 (482)
                      +++|+..+...      .         |..   ..+....+..++..|.        ..+..+.+++|||+.||+|+++|
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   0111223333433332        12334789999999999999999


Q ss_pred             HHHHHHcCCC
Q 011577          449 ERLIFITRMP  458 (482)
Q Consensus       449 k~~L~~ar~~  458 (482)
                      +..+++++..
T Consensus       171 ~~~l~Rar~~  180 (187)
T PRK12534        171 KSWIRRGLAK  180 (187)
T ss_pred             HHHHHHHHHH
Confidence            9999998754

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=1.3e-15  Score=145.50  Aligned_cols=140  Identities=12%  Similarity=0.125  Sum_probs=106.8

Q ss_pred             HHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011577          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  397 (482)
Q Consensus       319 Li~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~L  397 (482)
                      |...+..|+ .|++.|+..|.+.|+.++.++.++..+++|++||+|+++|+++++|++.++ .|.||++++++|.+++++
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            445556666 899999999999999999999999999999999999999999999997654 599999999999999999


Q ss_pred             HHhcCCccc-------c------------hhHHH--HHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHH
Q 011577          398 FQHSRTIRL-------P------------ENIYT--LLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKL  448 (482)
Q Consensus       398 rkq~r~irl-------P------------~~v~e--~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etV  448 (482)
                      |+..+....       +            .....  ....+.+++..|        ...+..+.+++|||+.||+|+++|
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  011233333222        222444789999999999999999


Q ss_pred             HHHHHHcCCCc
Q 011577          449 ERLIFITRMPL  459 (482)
Q Consensus       449 k~~L~~ar~~l  459 (482)
                      +..+++++..+
T Consensus       187 ~~~l~Ra~~~L  197 (206)
T PRK12526        187 KSRLRLALAKL  197 (206)
T ss_pred             HHHHHHHHHHH
Confidence            99999887543

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=9.2e-16  Score=144.74  Aligned_cols=141  Identities=10%  Similarity=0.075  Sum_probs=108.6

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (482)
Q Consensus       317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~  395 (482)
                      .+|+..+..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++.+++|.+++
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            34777788888 899999999999999999999999999999999999999999999987543 7999999999999999


Q ss_pred             HHHHhcCCcc-c------ch-----------hHH--HHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHH
Q 011577          396 AIFQHSRTIR-L------PE-----------NIY--TLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEK  447 (482)
Q Consensus       396 ~Lrkq~r~ir-l------P~-----------~v~--e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~et  447 (482)
                      ++|+..+... .      +.           ...  .....+.++...|..        .+-.+.+++|||+.||||+++
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            9998653211 0      00           000  011223333332221        233467999999999999999


Q ss_pred             HHHHHHHcCCC
Q 011577          448 LERLIFITRMP  458 (482)
Q Consensus       448 Vk~~L~~ar~~  458 (482)
                      |+..+++++..
T Consensus       174 Vk~rl~ra~~~  184 (194)
T PRK12531        174 VKSRLRLAVEK  184 (194)
T ss_pred             HHHHHHHHHHH
Confidence            99999988654

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.65  E-value=8.8e-16  Score=140.59  Aligned_cols=134  Identities=19%  Similarity=0.242  Sum_probs=103.5

Q ss_pred             HhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011577          323 LHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (482)
Q Consensus       323 l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~  401 (482)
                      ++.|+ .|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+  .+.+|.+|++.+++|.+.+++++..
T Consensus         4 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~   81 (182)
T PRK09652          4 VQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQG   81 (182)
T ss_pred             hhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHccc
Confidence            45566 89999999999999999999999999999999999999999999999  3568999999999999999999865


Q ss_pred             CCcccc----------------------hhHH---HHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHH
Q 011577          402 RTIRLP----------------------ENIY---TLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKL  448 (482)
Q Consensus       402 r~irlP----------------------~~v~---e~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etV  448 (482)
                      +....+                      ....   .....+..+...|        ...+..+.+++|||+.||+|+.+|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV  161 (182)
T PRK09652         82 RRPPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTV  161 (182)
T ss_pred             CCCCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHH
Confidence            432211                      0000   1122233222222        122334789999999999999999


Q ss_pred             HHHHHHcCCC
Q 011577          449 ERLIFITRMP  458 (482)
Q Consensus       449 k~~L~~ar~~  458 (482)
                      +..+++++..
T Consensus       162 ~~~l~ra~~~  171 (182)
T PRK09652        162 RSRIFRAREA  171 (182)
T ss_pred             HHHHHHHHHH
Confidence            9999988653

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=1.2e-15  Score=143.15  Aligned_cols=143  Identities=20%  Similarity=0.203  Sum_probs=109.9

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      .++.+|+..++.|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++..+ .|.||++++++|.
T Consensus        14 ~~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~   91 (194)
T PRK12519         14 RSDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSR   91 (194)
T ss_pred             ccHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHH
Confidence            35677888888888 899999999999999999999999999999999999999976 67887554 7999999999999


Q ss_pred             HHHHHHHhcCCcccc----------------h-hH--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCH
Q 011577          393 IRKAIFQHSRTIRLP----------------E-NI--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITV  445 (482)
Q Consensus       393 I~~~Lrkq~r~irlP----------------~-~v--~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~  445 (482)
                      +++++|++.+.....                . .+  .+....+..+...|..        .+..+.+++|||+.||+|+
T Consensus        92 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~  171 (194)
T PRK12519         92 AIDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPL  171 (194)
T ss_pred             HHHHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCH
Confidence            999999865421110                0 00  0111223333333322        2334779999999999999


Q ss_pred             HHHHHHHHHcCCC
Q 011577          446 EKLERLIFITRMP  458 (482)
Q Consensus       446 etVk~~L~~ar~~  458 (482)
                      .+|+..+++++..
T Consensus       172 ~tV~~~l~Ra~~~  184 (194)
T PRK12519        172 GTVKARARQGLLK  184 (194)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999988653

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.64  E-value=2e-15  Score=141.64  Aligned_cols=142  Identities=15%  Similarity=0.206  Sum_probs=109.9

Q ss_pred             CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (482)
Q Consensus       315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI  393 (482)
                      +++.|+..++.|+ .|++.|+..|.+.|+.+++++.++..+++|++||+|+++|+++.+|++..  .|.+|++++++|.+
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            4567888888888 89999999999999999999999999999999999999999999999864  59999999999999


Q ss_pred             HHHHHHhcCCcc---c-------------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHH
Q 011577          394 RKAIFQHSRTIR---L-------------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARR  440 (482)
Q Consensus       394 ~~~Lrkq~r~ir---l-------------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~  440 (482)
                      ++++|++.+...   .                   |...   .+....+.++...|.        ..+-.+.+++|||+.
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                   1000   001112223332222        113346799999999


Q ss_pred             hCCCHHHHHHHHHHcCCC
Q 011577          441 VGITVEKLERLIFITRMP  458 (482)
Q Consensus       441 LGIS~etVk~~L~~ar~~  458 (482)
                      ||+++++|+..+++++..
T Consensus       164 lgis~~tv~~~l~Rar~~  181 (193)
T PRK11923        164 MQCPVGTVRSRIFRAREA  181 (193)
T ss_pred             HCCCHHHHHHHHHHHHHH
Confidence            999999999999988753

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=1.9e-15  Score=146.98  Aligned_cols=143  Identities=15%  Similarity=0.193  Sum_probs=113.0

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      +++..|+..+..|+ .|++.|+..|.+.|+++++++.+++.+++||+||+|++||+++++|++.  ..|.+|++++++|.
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            45677888888777 8999999999999999999999999999999999999999999999985  47999999999999


Q ss_pred             HHHHHHHhcCCcccch-----------------------h---HHHHHHHHHHHHHHHHHh--------cCCCCcHHHHH
Q 011577          393 IRKAIFQHSRTIRLPE-----------------------N---IYTLLSKVLEAKRLYIQE--------GNHSPDKEDLA  438 (482)
Q Consensus       393 I~~~Lrkq~r~irlP~-----------------------~---v~e~l~kI~ka~~eL~~e--------~gr~pS~eEIA  438 (482)
                      +++++|+..+......                       .   ..+....+.+++..|...        +..+.+++|||
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   001122244444433222        23467999999


Q ss_pred             HHhCCCHHHHHHHHHHcCCC
Q 011577          439 RRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       439 e~LGIS~etVk~~L~~ar~~  458 (482)
                      +.||+|.++|+..+++++..
T Consensus       173 e~lgis~~tVk~~l~Rar~k  192 (231)
T PRK11922        173 QALGLPEETVKTRLHRARRL  192 (231)
T ss_pred             HHHCcCHHHHHHHHHHHHHH
Confidence            99999999999999988753

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=3.7e-15  Score=139.38  Aligned_cols=141  Identities=11%  Similarity=0.104  Sum_probs=108.2

Q ss_pred             HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHH----HccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011577          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAK----QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (482)
Q Consensus       316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAk----rY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR  390 (482)
                      +.+|+..+..|+ .||+.|+..|.+.|+.+|+    +|.++..+++|++||+|+.+|+.++.|++.  ..|.+|++.+++
T Consensus         8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~--~~f~~wl~~i~~   85 (184)
T PRK12539          8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPE--QPLTPWVYAIAR   85 (184)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCC--CChHHHHHHHHH
Confidence            566777888888 8999999999999999986    455788999999999999999999999875  369999999999


Q ss_pred             HHHHHHHHHhcCC-cccc---------h---hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHH
Q 011577          391 QTIRKAIFQHSRT-IRLP---------E---NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLE  449 (482)
Q Consensus       391 naI~~~Lrkq~r~-irlP---------~---~v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk  449 (482)
                      |.+++++|+..+. ...+         .   ...+....+..+...|..        .+..+.+++|||+.||+|+++|+
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            9999999986542 1111         0   011122233333333321        13347899999999999999999


Q ss_pred             HHHHHcCCC
Q 011577          450 RLIFITRMP  458 (482)
Q Consensus       450 ~~L~~ar~~  458 (482)
                      ..+++++..
T Consensus       166 ~~l~ra~~~  174 (184)
T PRK12539        166 VSVHRGLKA  174 (184)
T ss_pred             HHHHHHHHH
Confidence            999988653

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=3.8e-15  Score=138.95  Aligned_cols=141  Identities=9%  Similarity=0.037  Sum_probs=107.4

Q ss_pred             HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccC-CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (482)
Q Consensus       316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~-~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI  393 (482)
                      ...++..+..|+ .|++.|+..|.+.|+.++.++.+ ...+++|++||+|++||+.++.|++.  ..|.+|++.+++|.+
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            345667777777 89999999999999999988764 57899999999999999999999974  469999999999999


Q ss_pred             HHHHHHhcCCcccc--------------hhHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577          394 RKAIFQHSRTIRLP--------------ENIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERL  451 (482)
Q Consensus       394 ~~~Lrkq~r~irlP--------------~~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~  451 (482)
                      ++++|+..+.....              .........+.++...|.        ..+-.+.+++|||+.||+|+++|+..
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            99999864422100              011112222333333321        22234789999999999999999999


Q ss_pred             HHHcCCC
Q 011577          452 IFITRMP  458 (482)
Q Consensus       452 L~~ar~~  458 (482)
                      +++++..
T Consensus       166 l~rar~~  172 (181)
T PRK12536        166 IHRGLKA  172 (181)
T ss_pred             HHHHHHH
Confidence            9988654

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=3.6e-15  Score=139.82  Aligned_cols=144  Identities=13%  Similarity=0.126  Sum_probs=112.3

Q ss_pred             cCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (482)
Q Consensus       313 gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn  391 (482)
                      .+++.+|+..+..|+ .|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+++++|++.  ..|.+|++.+++|
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 8999999999999999999999999999999999999999999999964  4799999999999


Q ss_pred             HHHHHHHHhcCCccc-------------chhHH---HHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHH
Q 011577          392 TIRKAIFQHSRTIRL-------------PENIY---TLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEK  447 (482)
Q Consensus       392 aI~~~Lrkq~r~irl-------------P~~v~---e~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~et  447 (482)
                      .+++++++..+....             |....   +....+.++...|        ...+..+.+++|||+.||+|+++
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            999999976432110             01100   0111122222222        12233478999999999999999


Q ss_pred             HHHHHHHcCCC
Q 011577          448 LERLIFITRMP  458 (482)
Q Consensus       448 Vk~~L~~ar~~  458 (482)
                      |+..+++++..
T Consensus       164 V~~~l~Rar~~  174 (189)
T PRK12515        164 VKTRMFYARKK  174 (189)
T ss_pred             HHHHHHHHHHH
Confidence            99999998754

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.62  E-value=1.6e-15  Score=141.73  Aligned_cols=135  Identities=16%  Similarity=0.095  Sum_probs=104.5

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577          325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (482)
Q Consensus       325 ~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~  403 (482)
                      +|+ .|++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+++++|+...+..|.||++.+++|.+++++|++.+.
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 8999999999999999999999999999999999999999999999865445799999999999999999987543


Q ss_pred             cccc------------hhH------HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          404 IRLP------------ENI------YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       404 irlP------------~~v------~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ....            ...      ......+.++...|.        ..+..+.+++|||+.||+|+++|+..+++++.
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      001122333333322        12334689999999999999999999998876


Q ss_pred             Cc
Q 011577          458 PL  459 (482)
Q Consensus       458 ~l  459 (482)
                      .+
T Consensus       165 ~L  166 (185)
T PRK12542        165 RV  166 (185)
T ss_pred             HH
Confidence            43

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

Probab=99.61  E-value=6.6e-15  Score=145.33  Aligned_cols=144  Identities=12%  Similarity=0.046  Sum_probs=113.1

Q ss_pred             hcCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHH-------hHHhhCCCCCCchhh
Q 011577          312 IGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFAS  383 (482)
Q Consensus       312 ~gmdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLir-------AiekFDp~kG~rFST  383 (482)
                      ++.++..|+..+++|+ .||+.|+..|.+.|+.++.++.++..+++|++||+|+.+|.       .+.+|++.  ..|.|
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            4567788999999998 89999999999999999999999999999999999999994       78889864  47999


Q ss_pred             HHHHHHHHHHHHHHHHhcCCccc---------------chhH-H------HHHHHHHHHHHHHHHh--------cCCCCc
Q 011577          384 YAYWWVRQTIRKAIFQHSRTIRL---------------PENI-Y------TLLSKVLEAKRLYIQE--------GNHSPD  433 (482)
Q Consensus       384 YA~~wIRnaI~~~Lrkq~r~irl---------------P~~v-~------e~l~kI~ka~~eL~~e--------~gr~pS  433 (482)
                      |++.+++|.+++++|++.+...+               |... .      .....+.+++.+|...        +..+.|
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               1100 0      0112244444443322        234679


Q ss_pred             HHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          434 KEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       434 ~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ++|||+.|||++++|+..+++++.
T Consensus       180 ~~EIA~~Lgis~~TVk~rl~RAr~  203 (244)
T TIGR03001       180 MDRIGAMYQVHRSTVSRWVAQARE  203 (244)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHH
Confidence            999999999999999999998865

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.

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

Probab=99.60  E-value=5.3e-15  Score=137.17  Aligned_cols=141  Identities=17%  Similarity=0.194  Sum_probs=106.3

Q ss_pred             HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC-----CHhHHHHHHHHHHHH-hHHhhCCCCCCchhhHHHHH
Q 011577          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWW  388 (482)
Q Consensus       316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~-----d~EDLIQEG~IGLir-AiekFDp~kG~rFSTYA~~w  388 (482)
                      ..+|+..++.|+ .|++.|+..|.+.|+.+|++|.++..     +++|++||+|+.+|+ ...+|++.  ..|.+|++.+
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 89999999999999999999998887     899999999999998 78889754  3699999999


Q ss_pred             HHHHHHHHHHHhcCCcc------c------c---hhHHHH---HHH-------HHHHHHH-HHHhcCCCCcHHHHHHHhC
Q 011577          389 VRQTIRKAIFQHSRTIR------L------P---ENIYTL---LSK-------VLEAKRL-YIQEGNHSPDKEDLARRVG  442 (482)
Q Consensus       389 IRnaI~~~Lrkq~r~ir------l------P---~~v~e~---l~k-------I~ka~~e-L~~e~gr~pS~eEIAe~LG  442 (482)
                      ++|.+++++|+..+..+      .      +   ......   +..       +....+. +...+..+.|++|||+.||
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            99999999987532111      0      0   011111   111       1111122 1222334789999999999


Q ss_pred             CCHHHHHHHHHHcCCC
Q 011577          443 ITVEKLERLIFITRMP  458 (482)
Q Consensus       443 IS~etVk~~L~~ar~~  458 (482)
                      ||+++|+..+++++..
T Consensus       162 is~~tVk~~l~Rar~~  177 (183)
T TIGR02999       162 VSVRTVERDWRFARAW  177 (183)
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            9999999999998753

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.

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.59  E-value=8.2e-15  Score=137.62  Aligned_cols=141  Identities=19%  Similarity=0.150  Sum_probs=108.7

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (482)
Q Consensus       317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~  395 (482)
                      ..|+.++..|+ .|++.|+..|.+.|+.++. +.++..+++|++||+|+.+|+.+++|++.  ..|.+|++.+++|.+++
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            45777778888 8999999999999999995 67888999999999999999999999864  47999999999999999


Q ss_pred             HHHHhcCCccc-----chh---------HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHH
Q 011577          396 AIFQHSRTIRL-----PEN---------IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIF  453 (482)
Q Consensus       396 ~Lrkq~r~irl-----P~~---------v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~  453 (482)
                      ++|+..+....     +..         ..+....+.+++..|..        .+..+.+++|||+.||+|+++|+..++
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            99976432211     100         01112233444433322        233467999999999999999999999


Q ss_pred             HcCCCcc
Q 011577          454 ITRMPLS  460 (482)
Q Consensus       454 ~ar~~lS  460 (482)
                      +++..+-
T Consensus       169 Rar~~Lr  175 (185)
T PRK09649        169 RARDALL  175 (185)
T ss_pred             HHHHHHH
Confidence            9986554

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

Probab=99.59  E-value=1.1e-14  Score=131.67  Aligned_cols=130  Identities=15%  Similarity=0.162  Sum_probs=101.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-  406 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl-  406 (482)
                      +|++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++..  .|.+|++++++|.+++++|++.+.... 
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  699999999999999999987654221 


Q ss_pred             chhH----------------HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          407 PENI----------------YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       407 P~~v----------------~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      -...                .+....+.+++..|..        ....+.+++|||+.||||.++|+..+++++..+
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            0000                0111223333333321        133478999999999999999999999887543

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).

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=1.5e-14  Score=132.09  Aligned_cols=138  Identities=14%  Similarity=0.128  Sum_probs=105.7

Q ss_pred             HHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHH
Q 011577          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  397 (482)
Q Consensus       319 Li~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~L  397 (482)
                      |...+..|+ .|++.|+..|.+.|+.+|+++.++..+++|++||+|++||+++++|+  .+..|.+|++.+++|.+.+++
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            455666677 89999999999999999999999999999999999999999999998  345899999999999999999


Q ss_pred             HHhcCCcccc----------------hh----------HHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHH
Q 011577          398 FQHSRTIRLP----------------EN----------IYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLER  450 (482)
Q Consensus       398 rkq~r~irlP----------------~~----------v~e~l~kI~ka~~eL-~~e~gr~pS~eEIAe~LGIS~etVk~  450 (482)
                      ++..+.....                ..          +...+.++....+.+ ...+..+.+++|||+.||+|..+|+.
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            9765432211                00          111122222222221 12233477999999999999999999


Q ss_pred             HHHHcCCC
Q 011577          451 LIFITRMP  458 (482)
Q Consensus       451 ~L~~ar~~  458 (482)
                      .+++++..
T Consensus       161 ~~~ra~~~  168 (179)
T PRK11924        161 RLRRARQL  168 (179)
T ss_pred             HHHHHHHH
Confidence            99988653

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.58  E-value=2.2e-14  Score=133.51  Aligned_cols=139  Identities=12%  Similarity=0.138  Sum_probs=105.6

Q ss_pred             HHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccC----CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       318 eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~----~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      .|+..+..|+ .|++.|+..|.+.|+.+|.++++    ...+++|++||+|+.+|...++|+..  ..|.+|++.+++|.
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            3566666666 89999999999999999999875    34689999999999999999999863  47999999999999


Q ss_pred             HHHHHHHhcCCcccc---------h-h--HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHH
Q 011577          393 IRKAIFQHSRTIRLP---------E-N--IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLI  452 (482)
Q Consensus       393 I~~~Lrkq~r~irlP---------~-~--v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L  452 (482)
                      +.+++|++.+....+         . .  -......+.++...|..        .+-.+.+++|||+.||+|..+|+..+
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  01112233333333221        12347799999999999999999999


Q ss_pred             HHcCCC
Q 011577          453 FITRMP  458 (482)
Q Consensus       453 ~~ar~~  458 (482)
                      ++++..
T Consensus       169 ~ra~~~  174 (184)
T PRK12512        169 HRGLAA  174 (184)
T ss_pred             HHHHHH
Confidence            988654

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

Probab=99.58  E-value=2.5e-14  Score=133.76  Aligned_cols=132  Identities=16%  Similarity=0.186  Sum_probs=105.3

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011577          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (482)
Q Consensus       325 ~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i  404 (482)
                      ++..+++.++..|.+.++.++++++++..+++||+||+|+.+|+++..| .. +..|.||++++++|.+++++|+..+..
T Consensus        12 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~r~~   89 (182)
T COG1595          12 GDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRKRRR   89 (182)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhcccc
Confidence            3448999999999999999999999998899999999999999999999 33 457999999999999999999876543


Q ss_pred             cc-c-------------hhH-----HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          405 RL-P-------------ENI-----YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       405 rl-P-------------~~v-----~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      .. +             ...     .+....+.++...|+..        ...+.|++|||+.|||++++|+..+++++.
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~  169 (182)
T COG1595          90 ARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARK  169 (182)
T ss_pred             cccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            21 0             101     22333455555444332        334789999999999999999999999875


Q ss_pred             C
Q 011577          458 P  458 (482)
Q Consensus       458 ~  458 (482)
                      .
T Consensus       170 ~  170 (182)
T COG1595         170 K  170 (182)
T ss_pred             H
Confidence            4

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.57  E-value=2.1e-14  Score=132.58  Aligned_cols=129  Identities=10%  Similarity=0.061  Sum_probs=100.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-  406 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl-  406 (482)
                      ..+++|+..|.++|+.+|++|.++..+++|++||+|+.||+++++|++.  .+|.+|++.+++|.+++++|++.+.... 
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~Rk~~~~~~~~   80 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYV--ENYKKWITTICVRTFYDFYRKKKRWKDRI   80 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCc--cchHHHHHHHHHHHHHHHHHHhccccccc
Confidence            4689999999999999999999999999999999999999999999975  3799999999999999999986543210 


Q ss_pred             --------------------chhH--HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577          407 --------------------PENI--YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITR  456 (482)
Q Consensus       407 --------------------P~~v--~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar  456 (482)
                                          +...  .+....+.+++..|..        .+..+.+++|||+.||+++++|+..+.+++
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                                0110  0111223333333322        233477999999999999999999999887


Q ss_pred             CC
Q 011577          457 MP  458 (482)
Q Consensus       457 ~~  458 (482)
                      ..
T Consensus       161 ~~  162 (173)
T PRK12522        161 KQ  162 (173)
T ss_pred             HH
Confidence            54

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.57  E-value=2e-14  Score=133.78  Aligned_cols=132  Identities=15%  Similarity=0.182  Sum_probs=102.4

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577          325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (482)
Q Consensus       325 ~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~  403 (482)
                      .|+ .|++.|+..|.+.|+.++++|.++..+++|++||+|+.+|+++.+|++..  .|.+|++.+++|.+.+++++..+.
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  699999999999999998765421


Q ss_pred             cc---------------cchhHH--HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          404 IR---------------LPENIY--TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       404 ir---------------lP~~v~--e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .+               .|..+.  +....+.++...|+        ..+..+.+++|||+.||||+++|+..+++++..
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               111111  11223333333322        123347799999999999999999999988654

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.56  E-value=1.8e-14  Score=135.23  Aligned_cols=129  Identities=16%  Similarity=0.176  Sum_probs=100.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccch
Q 011577          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (482)
Q Consensus       329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~  408 (482)
                      +|+.|+..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|++.  .+|.||++.+++|.+++++|++.+......
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            789999999999999999999999999999999999999999999864  369999999999999999998765322110


Q ss_pred             ------------------------------hH------HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCC
Q 011577          409 ------------------------------NI------YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGIT  444 (482)
Q Consensus       409 ------------------------------~v------~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS  444 (482)
                                                    ..      .+....+..++..|..        .+..+.|++|||+.||+|
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        233467999999999999


Q ss_pred             HHHHHHHHHHcCCCc
Q 011577          445 VEKLERLIFITRMPL  459 (482)
Q Consensus       445 ~etVk~~L~~ar~~l  459 (482)
                      +++|+..+++++..+
T Consensus       161 ~~tV~~~l~Rar~~L  175 (191)
T PRK12520        161 ATNAWVLLYRARMRL  175 (191)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999987643

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

Probab=99.56  E-value=3e-14  Score=124.62  Aligned_cols=126  Identities=25%  Similarity=0.397  Sum_probs=100.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc---
Q 011577          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR---  405 (482)
Q Consensus       329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir---  405 (482)
                      |++.|+..|.++|+++++++.+++.+.+|++|||+++|+++++.|++.  ..|.+|+++++++.+.++++++.+ .+   
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  689999999999999999998864 11   


Q ss_pred             -----------cch----------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          406 -----------LPE----------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       406 -----------lP~----------~v~e~l~kI~ka~~eL~-~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                                 .|.          .+...+..+....+.+. ..+..+.+..|||+.+|+|+.+|+..+.+++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~  152 (158)
T TIGR02937        79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK  152 (158)
T ss_pred             hhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                       011          01122222322233332 22234789999999999999999999988754

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.

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

Probab=99.55  E-value=1.8e-14  Score=135.47  Aligned_cols=129  Identities=16%  Similarity=0.148  Sum_probs=102.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP  407 (482)
                      .+|+.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+.+|++.  ..|.+|++.+++|.+++++|++.+.....
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  46999999999999999999875432110


Q ss_pred             --hhH--------------------H-----HHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHH
Q 011577          408 --ENI--------------------Y-----TLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLI  452 (482)
Q Consensus       408 --~~v--------------------~-----e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L  452 (482)
                        ...                    .     .....+..++..|+..        +..+.+++|||+.||||+++|+..+
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     0112344444444332        2246799999999999999999999


Q ss_pred             HHcCCC
Q 011577          453 FITRMP  458 (482)
Q Consensus       453 ~~ar~~  458 (482)
                      ++++..
T Consensus       169 ~Rar~~  174 (193)
T TIGR02947       169 HRGRKQ  174 (193)
T ss_pred             HHHHHH
Confidence            998764

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.

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.55  E-value=3.9e-14  Score=130.48  Aligned_cols=132  Identities=11%  Similarity=0.079  Sum_probs=101.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011577          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (482)
Q Consensus       326 Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir  405 (482)
                      +..+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++. ...|.+|++.+++|.+++++|++.+...
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            348999999999999999999999999999999999999999999999743 2479999999999999999997653211


Q ss_pred             --------c-----chhHHH--HHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          406 --------L-----PENIYT--LLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       406 --------l-----P~~v~e--~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                              .     +..+..  ....+..+...|        ...+..+.+++|||+.||+|+++|+..+++++..
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                    0     111110  111233333322        2223347899999999999999999999988653

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.55  E-value=4.1e-14  Score=131.95  Aligned_cols=129  Identities=12%  Similarity=0.069  Sum_probs=100.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-  406 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl-  406 (482)
                      .|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+++++|++.  ..|.+|++.+++|.+++++|+..+.... 
T Consensus        16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~~   93 (179)
T PRK09415         16 DLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVIV   93 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccccc
Confidence            7999999999999999999999999999999999999999999999874  3699999999999999999975332111 


Q ss_pred             --------------chh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 --------------PEN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 --------------P~~---v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                                    |..   ..+....+.++...|..        .+..+.+++|||+.||||+++|+..+++++..
T Consensus        94 ~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~  170 (179)
T PRK09415         94 TEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKEL  170 (179)
T ss_pred             cccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                          100   01112223333333221        22346799999999999999999999998754

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.55  E-value=5e-14  Score=129.80  Aligned_cols=135  Identities=18%  Similarity=0.184  Sum_probs=101.9

Q ss_pred             HHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011577          321 SELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ  399 (482)
Q Consensus       321 ~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrk  399 (482)
                      ..++.|+ .|++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++.  ..|.+|++.+++|.+++++|+
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            4456666 89999999999999999999875 4789999999999999999999974  479999999999999999997


Q ss_pred             hcCCcc----cc-----------hhHH--HHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577          400 HSRTIR----LP-----------ENIY--TLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFI  454 (482)
Q Consensus       400 q~r~ir----lP-----------~~v~--e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L~~  454 (482)
                      ..+...    .+           ....  +....+.++...|...        +..+.+++|||+.||+|+++|+..+++
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  0111233333333322        224669999999999999999999998


Q ss_pred             cCCC
Q 011577          455 TRMP  458 (482)
Q Consensus       455 ar~~  458 (482)
                      ++..
T Consensus       160 ar~~  163 (175)
T PRK12518        160 ARRQ  163 (175)
T ss_pred             HHHH
Confidence            8754

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.54  E-value=5.6e-14  Score=132.62  Aligned_cols=130  Identities=15%  Similarity=0.114  Sum_probs=102.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (482)
Q Consensus       327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl  406 (482)
                      ..+|+.|+..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|+..  ..|.+|++++++|.+++++|++.+....
T Consensus         9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~~   86 (187)
T PRK12516          9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQD   86 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCccc
Confidence            48999999999999999999999999999999999999999999999864  3699999999999999999987653211


Q ss_pred             c------------h-hHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 P------------E-NIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 P------------~-~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .            . ........+..++..|.        .....+.+++|||+.||+|+++|+..+++++..
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~  159 (187)
T PRK12516         87 TDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQR  159 (187)
T ss_pred             cccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            0            0 00111222333333332        223347899999999999999999999988754

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

Probab=99.53  E-value=4.2e-14  Score=126.80  Aligned_cols=129  Identities=17%  Similarity=0.177  Sum_probs=98.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-  406 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl-  406 (482)
                      +|++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+.+.+|++.  .+|.+|++.++++.+.+++++..+.... 
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            3789999999999999999999999999999999999999999999874  4799999999999999999876532110 


Q ss_pred             ---------------chh---HHHHHHHHHHHH-------HHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 ---------------PEN---IYTLLSKVLEAK-------RLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 ---------------P~~---v~e~l~kI~ka~-------~eL~-~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                                     |..   ..+....+..+.       +++. ..+..+.+.+|||+.||+|..+|+..+++++..
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                           100   011111222222       2221 213347799999999999999999999988643

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.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.53  E-value=1.2e-13  Score=141.01  Aligned_cols=141  Identities=13%  Similarity=0.155  Sum_probs=109.4

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (482)
Q Consensus       317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~  395 (482)
                      .+|+.+++.|+ .++++|+..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++
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  47999999999999999


Q ss_pred             HHHHhcCCcc---c----------------------------------chhHH---HHH-HHHHHHHHHHHHh-------
Q 011577          396 AIFQHSRTIR---L----------------------------------PENIY---TLL-SKVLEAKRLYIQE-------  427 (482)
Q Consensus       396 ~Lrkq~r~ir---l----------------------------------P~~v~---e~l-~kI~ka~~eL~~e-------  427 (482)
                      ++|++.+...   .                                  |....   +.+ ..+.+++..|...       
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                                  00000   001 1233333333222       


Q ss_pred             -cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          428 -GNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       428 -~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                       +..+.+++|||+.||+|+++|+..+++++..+
T Consensus       165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~L  197 (339)
T PRK08241        165 RDVLGWSAAEVAELLDTSVAAVNSALQRARATL  197 (339)
T ss_pred             HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence             23467999999999999999999999887543

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

Probab=99.53  E-value=5.8e-14  Score=130.27  Aligned_cols=134  Identities=15%  Similarity=0.191  Sum_probs=100.2

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHcc----CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHH
Q 011577          325 SGN-SSREKLINANLRLVVHVAKQYQ----GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ  399 (482)
Q Consensus       325 ~Gd-~Are~LI~snlrLV~sIAkrY~----~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrk  399 (482)
                      .|+ .|++.|+..|.+.|+.+|++|.    ++..+++|++||+|+.+|+++.+|+...+..|.+|++.+++|.+++++++
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            455 8999999999999999999875    35678999999999999999999987656689999999999999999986


Q ss_pred             hc----CCc----c-----------------------cchhH---HHHHHHHHHHHHHH--------HHhcCCCCcHHHH
Q 011577          400 HS----RTI----R-----------------------LPENI---YTLLSKVLEAKRLY--------IQEGNHSPDKEDL  437 (482)
Q Consensus       400 q~----r~i----r-----------------------lP~~v---~e~l~kI~ka~~eL--------~~e~gr~pS~eEI  437 (482)
                      ..    +..    .                       -|...   .+....+.++...|        ...+..+.+++||
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    0                       01000   11112233333222        1223357899999


Q ss_pred             HHHhCCCHHHHHHHHHHcCCC
Q 011577          438 ARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       438 Ae~LGIS~etVk~~L~~ar~~  458 (482)
                      |+.||||+++|+..+++++..
T Consensus       163 A~~lgis~~~v~~~l~Ra~~~  183 (189)
T TIGR02984       163 AERMDRSEGAVSMLWVRGLAR  183 (189)
T ss_pred             HHHHCcCHHHHHHHHHHHHHH
Confidence            999999999999999988643

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).

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

Probab=99.52  E-value=1.1e-13  Score=125.98  Aligned_cols=131  Identities=13%  Similarity=0.115  Sum_probs=100.7

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc
Q 011577          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (482)
Q Consensus       326 Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir  405 (482)
                      +..+++.|+..|.+.|+.++.+++++..+++|++||+|+.+|+.+++|+.  ...|.+|++.+++|.+++++|+..+...
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            34899999999999999999999999999999999999999999999964  3479999999999999999998654110


Q ss_pred             ----cc-----h---------hHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          406 ----LP-----E---------NIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       406 ----lP-----~---------~v~e~l~kI~ka~~eL~-~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                          .+     .         .+...+.++....+.+. ..+-.+.+++|||+.||+|+++|+..+.+++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~  153 (162)
T TIGR02983        82 PTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALAR  153 (162)
T ss_pred             cccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence                00     0         01122222222222221 222346799999999999999999999988754

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.

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.52  E-value=8.9e-14  Score=129.71  Aligned_cols=134  Identities=12%  Similarity=0.041  Sum_probs=99.9

Q ss_pred             hhcH-HHHHHHHHHHHHHHHHHHHHccC--CCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011577          324 HSGN-SSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (482)
Q Consensus       324 ~~Gd-~Are~LI~snlrLV~sIAkrY~~--~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq  400 (482)
                      ..|+ .+|+.|+..|.+.|+.++.++.+  +..+++|++||.|+.+|+.+++|+......|.||++++++|.+++++|++
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            3455 89999999999999998766555  46789999999999999999999754345799999999999999999976


Q ss_pred             cCCcc--------------cchhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577          401 SRTIR--------------LPENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFIT  455 (482)
Q Consensus       401 ~r~ir--------------lP~~v---~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L~~a  455 (482)
                      .+...              -|...   .+....+.+++..|+.+        .-.+.+++|||+.||+|+++|+..++++
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              11111   11223344444443322        2236799999999999999999999987


Q ss_pred             CC
Q 011577          456 RM  457 (482)
Q Consensus       456 r~  457 (482)
                      ..
T Consensus       168 l~  169 (178)
T PRK12529        168 YV  169 (178)
T ss_pred             HH
Confidence            54

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.51  E-value=1.5e-13  Score=126.28  Aligned_cols=130  Identities=15%  Similarity=0.128  Sum_probs=100.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc
Q 011577          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (482)
Q Consensus       327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl  406 (482)
                      +..|..|+..|.+.|+.+|+++.++..+++|++||+|+.+|+.+++|+..  ..|.+|++.+++|.+++++|+..+....
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  3699999999999999999976543211


Q ss_pred             ------------ch-hHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 ------------PE-NIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 ------------P~-~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                                  +. ........+..++..|.        ..+..+.+++|||+.|||++++|+..+++++..
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                        00 00011122333333322        223347899999999999999999999988753

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.51  E-value=1.4e-13  Score=125.55  Aligned_cols=128  Identities=12%  Similarity=0.135  Sum_probs=99.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP  407 (482)
                      .|++.++..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++.   .|.||++.+++|.+++++|+..+.....
T Consensus         5 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~~   81 (161)
T PRK12541          5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTTT   81 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccccc
Confidence            7999999999999999999999999999999999999999999999863   5999999999999999999865422110


Q ss_pred             ------------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          408 ------------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       408 ------------~~---v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                                  ..   .......+..+...|..        ....+.+++|||+.||+|+++|+..+++++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~  155 (161)
T PRK12541         82 IEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE  155 (161)
T ss_pred             hhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                        00   01111222223222221        12347799999999999999999999988754

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.51  E-value=1.5e-13  Score=130.82  Aligned_cols=138  Identities=15%  Similarity=0.111  Sum_probs=105.2

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHH
Q 011577          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (482)
Q Consensus       317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~  395 (482)
                      .+|+..+..|+ .|++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++
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            44666777777 8999999999999999975 57888899999999999999999999864  37999999999999999


Q ss_pred             HHHHhcCCccc--------------chh--HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577          396 AIFQHSRTIRL--------------PEN--IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERL  451 (482)
Q Consensus       396 ~Lrkq~r~irl--------------P~~--v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~  451 (482)
                      ++|+..+....              |..  ..+....+.+++..|..        .+..+.+++|||+.||+++++|+..
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            99986432210              000  11112233334333322        2224679999999999999999999


Q ss_pred             HHHcCC
Q 011577          452 IFITRM  457 (482)
Q Consensus       452 L~~ar~  457 (482)
                      +++++.
T Consensus       170 l~Rar~  175 (196)
T PRK12535        170 VARARA  175 (196)
T ss_pred             HHHHHH
Confidence            998865

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=99.50  E-value=1.1e-13  Score=139.98  Aligned_cols=129  Identities=14%  Similarity=0.149  Sum_probs=100.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc--
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR--  405 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir--  405 (482)
                      .|++.|+..|.+.|+.+|++++++..+++|++||.|+.+|+.+++|+..  ..|.+|++++++|.|++++|++.+...  
T Consensus         5 ~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~   82 (324)
T TIGR02960         5 AAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRPV   82 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCcc
Confidence            8999999999999999999999999999999999999999999999864  469999999999999999997653211  


Q ss_pred             ------------------------cc--------------hhH---HHHH-HHHHHHHHHHHH--------hcCCCCcHH
Q 011577          406 ------------------------LP--------------ENI---YTLL-SKVLEAKRLYIQ--------EGNHSPDKE  435 (482)
Q Consensus       406 ------------------------lP--------------~~v---~e~l-~kI~ka~~eL~~--------e~gr~pS~e  435 (482)
                                              ++              ...   .+.+ ..+..++..|..        .+..+.+++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~  162 (324)
T TIGR02960        83 GLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRAA  162 (324)
T ss_pred             ccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCCCHH
Confidence                                    00              000   0001 113333333322        233467999


Q ss_pred             HHHHHhCCCHHHHHHHHHHcCCC
Q 011577          436 DLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       436 EIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      |||+.||+|+++|+..+++++..
T Consensus       163 EIA~~lgis~~tV~~~l~Rar~~  185 (324)
T TIGR02960       163 ETAELLGTSTASVNSALQRARAT  185 (324)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHH
Confidence            99999999999999999988754

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=99.50  E-value=2e-13  Score=132.38  Aligned_cols=132  Identities=14%  Similarity=0.090  Sum_probs=102.4

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (482)
Q Consensus       324 ~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~  403 (482)
                      .....+|+.|+..|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++.   .|.+|++++++|.+++++|++.+.
T Consensus        14 ~~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~   90 (216)
T PRK12533         14 AARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANA   90 (216)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccc
Confidence            34458999999999999999999999999999999999999999999999852   599999999999999999986532


Q ss_pred             cc------cc---------------hh---HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577          404 IR------LP---------------EN---IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERL  451 (482)
Q Consensus       404 ir------lP---------------~~---v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~  451 (482)
                      ..      +.               ..   ..+....+.+++..|..        .+..+.+++|||+.||||+++|+..
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~  170 (216)
T PRK12533         91 HEVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSR  170 (216)
T ss_pred             ccccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHH
Confidence            11      00               00   00122234334333322        1334779999999999999999999


Q ss_pred             HHHcCCC
Q 011577          452 IFITRMP  458 (482)
Q Consensus       452 L~~ar~~  458 (482)
                      +++++..
T Consensus       171 L~RAr~~  177 (216)
T PRK12533        171 LARARRR  177 (216)
T ss_pred             HHHHHHH
Confidence            9988764

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.49  E-value=1.8e-13  Score=125.48  Aligned_cols=126  Identities=13%  Similarity=0.107  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc--
Q 011577          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP--  407 (482)
Q Consensus       330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP--  407 (482)
                      |+.|+..|.+.|+.+|++|.++..+++|++||+|+.+|+++++|++.   .|.+|++.+++|.+++++|+..+.....  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~~~   79 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVGTD   79 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccchh
Confidence            67899999999999999999999999999999999999999999863   5999999999999999999876532211  


Q ss_pred             ----------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          408 ----------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       408 ----------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                                ...   .+....+.++...|.        .....+.+++|||+.||+++++|+..+++++..
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~  151 (165)
T PRK09644         80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKR  151 (165)
T ss_pred             HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                      110   111122333332221        123346799999999999999999999988754

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.49  E-value=1.3e-13  Score=127.50  Aligned_cols=132  Identities=10%  Similarity=0.045  Sum_probs=99.8

Q ss_pred             hhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011577          324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (482)
Q Consensus       324 ~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r  402 (482)
                      +.|+ .|+..|+..|.+.|+.++.++.++..+++|++||+|+.+|+. ..|...  ..|.+|++++++|.+++++|++.+
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            4667 899999999999999999999999999999999999999987 446543  369999999999999999998643


Q ss_pred             Ccc--------------cchhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          403 TIR--------------LPENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       403 ~ir--------------lP~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ...              -|...   .+....+.+++..|.        ..+..+.+++|||+.||||+++|+..+++++.
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              11110   111222333333322        22334789999999999999999999998865


Q ss_pred             C
Q 011577          458 P  458 (482)
Q Consensus       458 ~  458 (482)
                      .
T Consensus       162 ~  162 (172)
T PRK12523        162 Q  162 (172)
T ss_pred             H
Confidence            4

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.49  E-value=4.9e-13  Score=131.90  Aligned_cols=91  Identities=21%  Similarity=0.337  Sum_probs=82.0

Q ss_pred             CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCC--CHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHH
Q 011577          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (482)
Q Consensus       315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~--d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRn  391 (482)
                      +.++|+..++.|+ .|++.|+..|.++|+++|.+|+++..  +.+|++|||++++|+++++|++.+|..|.+|++++|+|
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            4566788888888 89999999999999999999998875  59999999999999999999999888899999999999


Q ss_pred             HHHHHHHHhcCCcc
Q 011577          392 TIRKAIFQHSRTIR  405 (482)
Q Consensus       392 aI~~~Lrkq~r~ir  405 (482)
                      .+++++|++.+...
T Consensus        84 ~~iDylRk~~~~~~   97 (237)
T PRK08311         84 RLIDYFRKESKHNL   97 (237)
T ss_pred             HHHHHHHHhhcccc
Confidence            99999998776433

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.46  E-value=2e-13  Score=124.25  Aligned_cols=122  Identities=11%  Similarity=0.073  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-c------
Q 011577          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR-L------  406 (482)
Q Consensus       334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir-l------  406 (482)
                      ++.|.+.|+.+|.+++++..+++|++||+|+.+|+++++|++.   .|.+|++.+++|.+++++|+..+... .      
T Consensus         1 ~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~   77 (160)
T PRK09642          1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEELSLCKET   77 (160)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccccccchhh
Confidence            3579999999999999999999999999999999999999863   49999999999999999998654211 0      


Q ss_pred             ---------chhHH---HHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 ---------PENIY---TLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 ---------P~~v~---e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                               |....   +....+.++...|+.        .+..+.+++|||+.||+|+++|+..+++++..
T Consensus        78 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~  149 (160)
T PRK09642         78 EENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKW  149 (160)
T ss_pred             hhhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                     11000   111123333333222        23347899999999999999999999998754

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.46  E-value=3.9e-13  Score=128.04  Aligned_cols=124  Identities=13%  Similarity=0.159  Sum_probs=95.6

Q ss_pred             HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc-----
Q 011577          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP-----  407 (482)
Q Consensus       333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP-----  407 (482)
                      ++..|.+.|+.+|++++++..+++|++||+|+.+|+.+++|++.  ..|.+|++.+++|.+++++|++.+...++     
T Consensus        13 ~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~~   90 (201)
T PRK12545         13 YLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSALDAE   90 (201)
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhcccccccccccc
Confidence            48999999999999999999999999999999999999999875  36999999999999999999876432111     


Q ss_pred             ------------------------------hhHH---HHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011577          408 ------------------------------ENIY---TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE  446 (482)
Q Consensus       408 ------------------------------~~v~---e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~e  446 (482)
                                                    ....   +....+.+++..|.        ..+..+.+++|||+.||+|++
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~  170 (201)
T PRK12545         91 LDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTAN  170 (201)
T ss_pred             cchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence                                          0000   00112233333322        223347899999999999999


Q ss_pred             HHHHHHHHcCCC
Q 011577          447 KLERLIFITRMP  458 (482)
Q Consensus       447 tVk~~L~~ar~~  458 (482)
                      +|+..+++++..
T Consensus       171 tVk~~l~RAr~~  182 (201)
T PRK12545        171 HCSVLLYRARTR  182 (201)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988754

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.46  E-value=5.1e-13  Score=121.89  Aligned_cols=126  Identities=18%  Similarity=0.107  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-  406 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl-  406 (482)
                      .+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|++  .|+.  +..|.+|++.+++|.+.+++|+..+.... 
T Consensus         3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~~   78 (166)
T PRK09639          3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRARI   78 (166)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccccccc
Confidence            689999999999999999999999999999999999999999  6764  35799999999999999999987643211 


Q ss_pred             --------------chhH---HHHHHHHHHHHHH--------HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 --------------PENI---YTLLSKVLEAKRL--------YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 --------------P~~v---~e~l~kI~ka~~e--------L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                                    |...   .+....+.++...        +...+ .+.+++|||+.||+|+++|+..+++++..
T Consensus        79 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~  154 (166)
T PRK09639         79 LGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKK  154 (166)
T ss_pred             cchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                          1100   1111223333322        22335 67899999999999999999999988654

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.46  E-value=6.1e-13  Score=125.08  Aligned_cols=129  Identities=19%  Similarity=0.205  Sum_probs=100.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-  406 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl-  406 (482)
                      .++..++..|.+.|+.+|.+++++..+++|++||.|+.+|+.+++|++.  ..|.+|++++++|.++++++++.+.... 
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~   82 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPG--SNLPAWLFTILRNLFRSDYRKRRREVEDA   82 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCC--chHHHHHHHHHHHHHHHHHHhcccccccc
Confidence            5788999999999999999999999999999999999999999999865  3699999999999999999986543210 


Q ss_pred             -----------chh-HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 -----------PEN-IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 -----------P~~-v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                                 +.. .......+..++..|.        ..+..+.+++|||+.||+|+++|+..+++++..
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~  154 (182)
T PRK12540         83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSK  154 (182)
T ss_pred             cccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                       100 0111122333333332        223347899999999999999999999998764

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.45  E-value=5.6e-13  Score=127.76  Aligned_cols=131  Identities=20%  Similarity=0.265  Sum_probs=101.1

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577          325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (482)
Q Consensus       325 ~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~  403 (482)
                      .|+ .++++|+..|.+.|+.++.++.++..+++||+||+|+.+|+.+.+|++  + .|.+|++.+++|.+++++|+..+.
T Consensus        24 ~~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~  100 (203)
T PRK09647         24 KATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARI  100 (203)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccC
Confidence            344 899999999999999999999999999999999999999999999985  3 699999999999999999987531


Q ss_pred             c--cc-------------chhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          404 I--RL-------------PENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       404 i--rl-------------P~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      .  ..             |...   ......+..++..|.        ..+..+.+++|||+.|||++++|+..+++++.
T Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk  180 (203)
T PRK09647        101 RMEALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQ  180 (203)
T ss_pred             ccccccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            1  00             1100   011222333333221        12234789999999999999999999999875


Q ss_pred             C
Q 011577          458 P  458 (482)
Q Consensus       458 ~  458 (482)
                      .
T Consensus       181 ~  181 (203)
T PRK09647        181 Q  181 (203)
T ss_pred             H
Confidence            4

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.45  E-value=9.4e-13  Score=120.11  Aligned_cols=127  Identities=14%  Similarity=0.114  Sum_probs=97.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI---  404 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i---  404 (482)
                      .|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+..+.|++   ..|.+|++++++|.+++++|+..+..   
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   36999999999999999999754211   


Q ss_pred             ----ccc-------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          405 ----RLP-------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       405 ----rlP-------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                          ..+       ...   .+....+.++...|.        ..+..+.+++|||+.||+|+++|+..+++++.
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       000   111122333333222        22334789999999999999999999998754

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.44  E-value=5.8e-13  Score=125.50  Aligned_cols=125  Identities=14%  Similarity=0.198  Sum_probs=95.2

Q ss_pred             HHHHHHHHHHHHHHHHHccCCCCC-HhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc---
Q 011577          331 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL---  406 (482)
Q Consensus       331 e~LI~snlrLV~sIAkrY~~~g~d-~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl---  406 (482)
                      +..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++++|++.  ..|.+|++++++|.+++++|++.+....   
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            457888999999999999999888 9999999999999999999864  4799999999999999999987542211   


Q ss_pred             -------------------------------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCC
Q 011577          407 -------------------------------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGIT  444 (482)
Q Consensus       407 -------------------------------P~~v---~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS  444 (482)
                                                     |...   .+....+.++...|..        .+..+.+++|||+.||+|
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   0111123333333221        223467999999999999


Q ss_pred             HHHHHHHHHHcCC
Q 011577          445 VEKLERLIFITRM  457 (482)
Q Consensus       445 ~etVk~~L~~ar~  457 (482)
                      +++|+..+++++.
T Consensus       166 ~~tVk~~l~Rar~  178 (195)
T PRK12532        166 TSNYHTIMHRARE  178 (195)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998865

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.43  E-value=1.4e-12  Score=122.51  Aligned_cols=126  Identities=14%  Similarity=0.178  Sum_probs=97.7

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchh
Q 011577          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (482)
Q Consensus       330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~  409 (482)
                      ++.|++.|.+.|+.++.++.++..+++|++||.|+.+|+.+..|+..  ..|.+|++.+++|.+++++|++.+....+..
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~   80 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPDD   80 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence            67899999999999999999999999999999999999999999853  4799999999999999999987644332110


Q ss_pred             -------------------HHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          410 -------------------IYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       410 -------------------v~e~l~kI~ka~~eL-~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                                         +...+.++....+.+ ......+.+++|||+.||+|+++|+..+.+++.
T Consensus        81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~  148 (181)
T PRK09637         81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRV  148 (181)
T ss_pred             hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                               111112222222221 122334789999999999999999999998864

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=99.43  E-value=8.5e-13  Score=124.44  Aligned_cols=127  Identities=11%  Similarity=0.164  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc---
Q 011577          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP---  407 (482)
Q Consensus       331 e~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP---  407 (482)
                      .+.+..|.+.|+.++++++++..+++|++||+|+.+|+..++|++.  .+|.+|++.+++|.+++++|++.+....+   
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            3578899999999999999999999999999999999999999864  47999999999999999999865432111   


Q ss_pred             ------------------------------hhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHH
Q 011577          408 ------------------------------ENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVE  446 (482)
Q Consensus       408 ------------------------------~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~e  446 (482)
                                                    ...   .+....+.+++..|.        ..+..+.+++|||+.||+|++
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   001122333332221        223347899999999999999


Q ss_pred             HHHHHHHHcCCCc
Q 011577          447 KLERLIFITRMPL  459 (482)
Q Consensus       447 tVk~~L~~ar~~l  459 (482)
                      +|+..+.+++..+
T Consensus       163 tvk~rl~Rar~~L  175 (188)
T TIGR02943       163 NCHVLLYRARLSL  175 (188)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999987643

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.

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.43  E-value=9.4e-13  Score=126.46  Aligned_cols=128  Identities=13%  Similarity=0.203  Sum_probs=97.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc-
Q 011577          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP-  407 (482)
Q Consensus       329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP-  407 (482)
                      .-..++..|.+.|+.+|++++++..+++|++||+|+.+|+.+.+|+..  .+|.+|++++++|.+++++|+..+....+ 
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 011577          408 ---------------------------------ENIY---TLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGI  443 (482)
Q Consensus       408 ---------------------------------~~v~---e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGI  443 (482)
                                                       ....   +....+..++..|.        ..+..+.+++|||+.||+
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   00112222232222        223346799999999999


Q ss_pred             CHHHHHHHHHHcCCC
Q 011577          444 TVEKLERLIFITRMP  458 (482)
Q Consensus       444 S~etVk~~L~~ar~~  458 (482)
                      |+++|+..+++++..
T Consensus       177 s~~tV~~~l~RAr~~  191 (206)
T PRK12544        177 SVSNLNVLLYRARLR  191 (206)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            999999999998764

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.43  E-value=1.3e-12  Score=123.26  Aligned_cols=132  Identities=12%  Similarity=0.026  Sum_probs=100.8

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011577          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (482)
Q Consensus       325 ~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i  404 (482)
                      ....+++.++..|.+.|+.+|.++.++..+++|++||+|+.+|+.++.|++.  ..|.+|++.+++|.+.+.+++..+..
T Consensus        20 ~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~~   97 (188)
T PRK12517         20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFDL   97 (188)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccCc
Confidence            3458999999999999999999999999999999999999999999999864  46999999999999988876643221


Q ss_pred             c-c-----c-----h-hHHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          405 R-L-----P-----E-NIYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       405 r-l-----P-----~-~v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      . .     +     . ........+..++..|+.        .+..+.+++|||+.|||++++|+..+++++..
T Consensus        98 ~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~  171 (188)
T PRK12517         98 VDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQ  171 (188)
T ss_pred             cCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            1 0     0     0 001111223344433322        23346799999999999999999999988754

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.43  E-value=8.4e-13  Score=124.43  Aligned_cols=126  Identities=15%  Similarity=0.178  Sum_probs=95.3

Q ss_pred             HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc---
Q 011577          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP---  407 (482)
Q Consensus       331 e~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP---  407 (482)
                      +.-|..|.+.|+.+|.+++++..+++|++||+|+.+|+.+++|++.  .+|.+|++++++|.+++++|++.+.....   
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            3457888999999999999999999999999999999999999865  36999999999999999999876432110   


Q ss_pred             ----------------------h------h-HH--HHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHH
Q 011577          408 ----------------------E------N-IY--TLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKL  448 (482)
Q Consensus       408 ----------------------~------~-v~--e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etV  448 (482)
                                            .      . +.  +....+..++..|+.        .+..+.+++|||+.||+|+++|
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 00  001112333333322        2223689999999999999999


Q ss_pred             HHHHHHcCCC
Q 011577          449 ERLIFITRMP  458 (482)
Q Consensus       449 k~~L~~ar~~  458 (482)
                      +..+++++..
T Consensus       168 k~~l~RAr~~  177 (189)
T PRK12530        168 HVLLYRARLQ  177 (189)
T ss_pred             HHHHHHHHHH
Confidence            9999988753

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.42  E-value=8.3e-13  Score=118.84  Aligned_cols=122  Identities=12%  Similarity=0.129  Sum_probs=94.4

Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-------
Q 011577          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-------  406 (482)
Q Consensus       334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl-------  406 (482)
                      +.+|.+.|+.++.++.++..+++|++||+|+.+|+.+++|++   .+|.||++.+++|.+.++++++.+....       
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            357999999999999999999999999999999999999997   4799999999999999999976532211       


Q ss_pred             --------chhH---HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 --------PENI---YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 --------P~~v---~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                              |...   .+....+.++...|...        +..+.+++|||+.||+|+++|+..+++++..
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                    1110   11123344444444322        2246799999999999999999999988653

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.

>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=99.41  E-value=7.7e-13  Score=104.03  Aligned_cols=70  Identities=23%  Similarity=0.432  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcC
Q 011577          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (482)
Q Consensus       333 LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r  402 (482)
                      |++.|.++|+.++.+|.+++.+.+|++||++++||+++++||+++|..|.+|++.+++|.++++++++.+
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            7899999999999999999999999999999999999999999999899999999999999999998765

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 ....

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.41  E-value=2.1e-12  Score=122.23  Aligned_cols=128  Identities=17%  Similarity=0.190  Sum_probs=97.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP  407 (482)
                      ++++.|+. |.+.|+.+|+++.++..+++|++||.|+.+|+.+..|+..  ..|.+|++.+++|.+++++|+..+.....
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 7799999999999999999999999999999999999864  46999999999999999999876432110


Q ss_pred             ------------hh-HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          408 ------------EN-IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       408 ------------~~-v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                                  .. .......+..++..|..        .+..+.+++|||+.||||+++|+..+++++..
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        22347799999999999999999999988753

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.40  E-value=1.9e-12  Score=119.99  Aligned_cols=122  Identities=17%  Similarity=0.204  Sum_probs=94.0

Q ss_pred             HHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhH----
Q 011577          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI----  410 (482)
Q Consensus       335 ~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v----  410 (482)
                      ..|.+.|+.+++++.++..+++|++||+|+.+|+++++|+..  .+|.+|++.+++|.+++++|+..+...++...    
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~   79 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD   79 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence            468899999999999999999999999999999999999863  58999999999999999999976544322110    


Q ss_pred             --------HHHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          411 --------YTLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       411 --------~e~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                              .+....+.+++..|        ...+..+.+++|||+.||+|+++|+..+++++..
T Consensus        80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~  143 (170)
T TIGR02959        80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKK  143 (170)
T ss_pred             CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                    01111222222222        1223347899999999999999999999988754

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).

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.36  E-value=7.9e-12  Score=115.85  Aligned_cols=128  Identities=11%  Similarity=0.079  Sum_probs=96.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc-
Q 011577          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR-  405 (482)
Q Consensus       327 d~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir-  405 (482)
                      ..|++.++..|.+.++.++.++.++..+++||+||.|+.+|+. ..|++-  ..|.+|++.+++|.+++++|+..+... 
T Consensus         9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~--~~~~~wL~~iarn~~~d~~R~~~~~~~~   85 (172)
T PRK09651          9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTI--RDPRSFLCTIAKRVMVDLFRRNALEKAY   85 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-cccccc--cCHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3799999999999999999999999999999999999999998 356543  259999999999999999997542110 


Q ss_pred             -------------cchhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          406 -------------LPENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       406 -------------lP~~v---~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                                   -|...   .+....+..+...|..        .+..+.+++|||+.||+++++|+..+++++.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~  161 (172)
T PRK09651         86 LEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATE  161 (172)
T ss_pred             hhHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                         11111   1122223333333322        2334779999999999999999999998864

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.36  E-value=5e-12  Score=119.02  Aligned_cols=127  Identities=12%  Similarity=0.095  Sum_probs=96.6

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc---
Q 011577          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL---  406 (482)
Q Consensus       330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl---  406 (482)
                      .+..+..+.+.|+.+|.++.++..+++|++||.|+.+|+.+..|+..  ..|.+|++.+++|.+++++|++.+....   
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            34557889999999999999999999999999999999999999864  4799999999999999999986542110   


Q ss_pred             ---------ch--hHHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 ---------PE--NIYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 ---------P~--~v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                               +.  ........+.+++..|.        ..+-.+.+++|||+.||||+++|+..+++++..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~  154 (182)
T PRK12511         84 LAVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAA  154 (182)
T ss_pred             hhhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence                     00  01111222333333322        123347899999999999999999999988754

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.31  E-value=1.1e-11  Score=121.69  Aligned_cols=132  Identities=15%  Similarity=0.080  Sum_probs=96.5

Q ss_pred             HHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHh
Q 011577          322 ELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (482)
Q Consensus       322 ~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq  400 (482)
                      ....|+ .+++.+++.| +.++.++.++.++..+++||+||.|+.+|+.   |+..  ..|.+|++.+++|.+++++|++
T Consensus        11 ~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~Rk~   84 (228)
T PRK06704         11 NHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIKSK   84 (228)
T ss_pred             cccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHhcc
Confidence            334455 7888888887 7899999999999999999999999999986   5543  3599999999999999999987


Q ss_pred             cCCcccc--------hh-HHHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          401 SRTIRLP--------EN-IYTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       401 ~r~irlP--------~~-v~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      .+...+.        .. ..+....+.++...|..        .+..+.|++|||+.||+|+++|+..++++++.+
T Consensus        85 k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~L  160 (228)
T PRK06704         85 SVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL  160 (228)
T ss_pred             ccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            5432211        00 11111222333333322        123367999999999999999999999997643

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.31  E-value=1.4e-11  Score=112.29  Aligned_cols=123  Identities=17%  Similarity=0.209  Sum_probs=92.1

Q ss_pred             HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc------
Q 011577          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR------  405 (482)
Q Consensus       332 ~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir------  405 (482)
                      .++..|.+.|+.+|.++.++..+++|++||+|+++|+....|++.   .|.+|++.+++|.+++++|++.+...      
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   48999999999999999997653211      


Q ss_pred             ----cc------hhH---HHHHHHHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          406 ----LP------ENI---YTLLSKVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       406 ----lP------~~v---~e~l~kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                          .+      ...   .+....+..+...|        ...+..+.+++|||+.||+|+++|+..+.+++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~  151 (163)
T PRK07037         79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV  151 (163)
T ss_pred             cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                01      110   01112223332222        122334789999999999999999999988764

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.30  E-value=1.3e-11  Score=112.40  Aligned_cols=122  Identities=11%  Similarity=0.086  Sum_probs=91.5

Q ss_pred             HHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcc--------
Q 011577          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR--------  405 (482)
Q Consensus       334 I~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~ir--------  405 (482)
                      +..|.+.++.++.+++++..+++|++||+|+.+|+..+.|++   .+|.||++.+++|.+++++|++.+...        
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            357889999999999999999999999999999999999875   379999999999999999997532111        


Q ss_pred             -------cchhH---HHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          406 -------LPENI---YTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       406 -------lP~~v---~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                             -|...   ......+..++..|.        .....+.+++|||+.||+|+++|+..+.+++..
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~  148 (159)
T PRK12527         78 EERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKH  148 (159)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence                   01111   011222333333322        223347799999999999999999999988653

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.29  E-value=4e-11  Score=110.61  Aligned_cols=127  Identities=8%  Similarity=0.045  Sum_probs=95.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc---
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI---  404 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i---  404 (482)
                      .++.+++..|.+.++.++.++.++..+++|++||.|+.+|+..+.++.   ..|.+|++++++|.+++++|+.....   
T Consensus         9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~~   85 (168)
T PRK12525          9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAYL   85 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            789999999999999999999999999999999999999986665542   36999999999999999998753110   


Q ss_pred             -----------ccchh---HHHHHHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          405 -----------RLPEN---IYTLLSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       405 -----------rlP~~---v~e~l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                                 ..|..   ..+....+.+++..|.        ..+..+.+++|||+.||+|+++|+..+.+++.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~  160 (168)
T PRK12525         86 QSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK  160 (168)
T ss_pred             HHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                       01111   1111222333333222        22334779999999999999999999998754

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.25  E-value=4.6e-11  Score=120.15  Aligned_cols=127  Identities=12%  Similarity=0.041  Sum_probs=93.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC--c-
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT--I-  404 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~--i-  404 (482)
                      ..+..|++.|.+.++.+|++++++..++||++||.|+. |.....|+   ...|.+|++++++|.|++++|+..+.  . 
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            35678999999999999999999999999999999999 55667775   24799999999999999999975421  0 


Q ss_pred             ---cc----------chhH---HHHH-HHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          405 ---RL----------PENI---YTLL-SKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       405 ---rl----------P~~v---~e~l-~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                         .+          |...   .+.+ ..+..+...|.        .....+.+++|||+.||+|+++|+.++++++..
T Consensus        80 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~  158 (293)
T PRK09636         80 VGPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKH  158 (293)
T ss_pred             cCCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence               01          1110   0111 11222232221        122346799999999999999999999988754

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.18  E-value=9.2e-11  Score=118.73  Aligned_cols=128  Identities=12%  Similarity=-0.040  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC-c--
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT-I--  404 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~-i--  404 (482)
                      ..+..+++.|.+.++.+|++++++..++||++||.|+.+|++...+    ...|.+|++++++|.|++++|+..+. .  
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            5788999999999999999999999999999999999999987553    13699999999999999999974321 0  


Q ss_pred             -----ccc----------hhH---HHH-HHHHHHHHHHHH--------HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          405 -----RLP----------ENI---YTL-LSKVLEAKRLYI--------QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       405 -----rlP----------~~v---~e~-l~kI~ka~~eL~--------~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                           ..|          ...   .+. ...+..+...|.        .....+.+++|||+.||+|+.+|+..+++++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~  160 (290)
T PRK09635         81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR  160 (290)
T ss_pred             ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                 011          000   000 112222222221        11223679999999999999999999999876


Q ss_pred             Cc
Q 011577          458 PL  459 (482)
Q Consensus       458 ~l  459 (482)
                      .+
T Consensus       161 ~L  162 (290)
T PRK09635        161 KI  162 (290)
T ss_pred             HH
Confidence            54

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=99.17  E-value=1.9e-10  Score=115.40  Aligned_cols=124  Identities=17%  Similarity=0.086  Sum_probs=89.7

Q ss_pred             HHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc------c
Q 011577          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI------R  405 (482)
Q Consensus       332 ~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i------r  405 (482)
                      +++..|.+.++.+|+++.++..++||++||+|+.+++.  .|+..  ..|.+|++++++|.|++++|+..+..      .
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~   76 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVYVGPW   76 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence            37899999999999999999999999999999998775  55432  36999999999999999999764211      1


Q ss_pred             cc----------hhHH---HHHH-HHHHHHHHH--------HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          406 LP----------ENIY---TLLS-KVLEAKRLY--------IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       406 lP----------~~v~---e~l~-kI~ka~~eL--------~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      +|          ....   +.+. .+..+...|        ......+.+++|||+.||+|+++|+..+++++..+
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   1110 111222221        11223467999999999999999999999887543

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=99.17  E-value=1.4e-10  Score=112.13  Aligned_cols=127  Identities=15%  Similarity=0.086  Sum_probs=94.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc-
Q 011577          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP-  407 (482)
Q Consensus       329 Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP-  407 (482)
                      ++..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+...+|++.  ..|.+|+++++++.......... ....+ 
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~~-~~~~~~   78 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGANDP-EPGSPF   78 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccCC-CCCCCc
Confidence            588999999999999999999999999999999999999999999874  46999999999887644322211 11111 


Q ss_pred             -hhHHHHHHHHHHHHHH-HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          408 -ENIYTLLSKVLEAKRL-YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       408 -~~v~e~l~kI~ka~~e-L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                       ..+...+.++....++ +......+.|++|||+.||+++++|+..+++++..
T Consensus        79 ~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~  131 (261)
T PRK09191         79 EARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAE  131 (261)
T ss_pred             hHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence             1233444444333333 22223347899999999999999999999988653

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.10  E-value=4.1e-10  Score=100.85  Aligned_cols=113  Identities=11%  Similarity=0.060  Sum_probs=80.0

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHh-----hCCCCCCchhhHHHHHHHHHHHHHHHHhcCCc
Q 011577          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (482)
Q Consensus       330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiek-----FDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~i  404 (482)
                      |+.|+..|.++++.+|++|..    .+| +||.|+.+|..+.+     |++  +..|.||++.+++|.+++++|++.+..
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            468999999999999999966    224 49999999999875     544  247999999999999999999765421


Q ss_pred             cc------------c-hhH--HHHHHHHHHHHHHHHHh--------cCCCCcHHHHHHHhCCCHHHHH
Q 011577          405 RL------------P-ENI--YTLLSKVLEAKRLYIQE--------GNHSPDKEDLARRVGITVEKLE  449 (482)
Q Consensus       405 rl------------P-~~v--~e~l~kI~ka~~eL~~e--------~gr~pS~eEIAe~LGIS~etVk  449 (482)
                      ..            + ...  .+....+.+++..|+..        ...+.|++|||+.||||+++|+
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            0 000  01112233333333221        2346799999999999999996

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=99.07  E-value=4.8e-10  Score=101.60  Aligned_cols=106  Identities=11%  Similarity=0.069  Sum_probs=74.5

Q ss_pred             CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCccc-----------------------
Q 011577          350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL-----------------------  406 (482)
Q Consensus       350 ~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irl-----------------------  406 (482)
                      ++..+++|++||+|+.+|+.++.+ +  +..|.+|++.+++|.|++++|++.+....                       
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            445679999999999999998863 3  45799999999999999999986532111                       


Q ss_pred             --------chhH---HHHHHHHHHHHHHHHH--------hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          407 --------PENI---YTLLSKVLEAKRLYIQ--------EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       407 --------P~~v---~e~l~kI~ka~~eL~~--------e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                              |...   ......+.+++..|+.        .+..+.+++|||+.||+|+++|+..+++++..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~  149 (161)
T PRK09047         79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHA  149 (161)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                    0000   0011223333333221        23347799999999999999999999988654

>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=99.04  E-value=5.8e-10  Score=90.86  Aligned_cols=71  Identities=31%  Similarity=0.474  Sum_probs=62.9

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCCC
Q 011577          412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG  482 (482)
Q Consensus       412 e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~g  482 (482)
                      +.+++|.++.++|.+.+||.||.+|||+.|||++++|..++..++..+||+.+++.+++.++.++|+|+++
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~   71 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDA   71 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCC
Confidence            46789999999999999999999999999999999999999999999999999999888999999999853

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 ....

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=98.78  E-value=6.4e-08  Score=91.55  Aligned_cols=141  Identities=18%  Similarity=0.175  Sum_probs=96.1

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCC---CCCHhH--HHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011577          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (482)
Q Consensus       317 ~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~---g~d~ED--LIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR  390 (482)
                      .+|+..++.|| .|++.|+..|.+-+..+|+++...   +.+.+|  |++|+|+.+++.-...+.+.-..|-.|+...++
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            46888889999 899999999999999999877532   345554  577888877774332233333469999999999


Q ss_pred             HHHHHHHHHhcCCcc------cc---------hhHHHHHHHHHHHHHH-----------HHHhcCCCCcHHHHHHHhCCC
Q 011577          391 QTIRKAIFQHSRTIR------LP---------ENIYTLLSKVLEAKRL-----------YIQEGNHSPDKEDLARRVGIT  444 (482)
Q Consensus       391 naI~~~Lrkq~r~ir------lP---------~~v~e~l~kI~ka~~e-----------L~~e~gr~pS~eEIAe~LGIS  444 (482)
                      +.+++++|++.+..+      .+         ..-...+-.+.++...           +......+.|.+|||+.||||
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            999999996654322      11         0001111122222221           222222368999999999999


Q ss_pred             HHHHHHHHHHcCC
Q 011577          445 VEKLERLIFITRM  457 (482)
Q Consensus       445 ~etVk~~L~~ar~  457 (482)
                      +.+|+..+..++.
T Consensus       165 ~~tV~r~l~~aR~  177 (185)
T PF07638_consen  165 ERTVRRRLRRARA  177 (185)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998764

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=97.94  E-value=2.5e-06  Score=61.18  Aligned_cols=34  Identities=41%  Similarity=0.464  Sum_probs=30.2

Q ss_pred             CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH
Q 011577          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR  287 (482)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~  287 (482)
                      +|+++.||++|+++|+||++||++|+++|+.+..
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=97.27  E-value=0.0073  Score=67.65  Aligned_cols=35  Identities=31%  Similarity=0.482  Sum_probs=32.4

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR  287 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~  287 (482)
                      .+||+++||++|++.||||+|+|++++++|..+.+
T Consensus       102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~  136 (619)
T PRK05658        102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN  136 (619)
T ss_pred             CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence            47999999999999999999999999999998653

>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=96.23  E-value=0.015  Score=46.87  Aligned_cols=56  Identities=18%  Similarity=0.301  Sum_probs=46.7

Q ss_pred             HHHHHhhcH-HHHHHHHHHHHHHHHHHHHHcc----C--CCCCHhHHHHHHHHHHHHhHHhhC
Q 011577          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQ----G--RGISLHDLLQEGSMGLMKSVEKFK  374 (482)
Q Consensus       319 Li~~l~~Gd-~Are~LI~snlrLV~sIAkrY~----~--~g~d~EDLIQEG~IGLirAiekFD  374 (482)
                      ++.++.+|| .|.+++++.|.+++.+.+.|-.    +  ++.--+|+-|+--..|+++|-+|+
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 8999999999999999998732    2  244569999999999999999996

Some proteins with this domain are annotated as conjugative transposon proteins.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=96.15  E-value=0.049  Score=53.86  Aligned_cols=30  Identities=0%  Similarity=0.129  Sum_probs=26.2

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      ..+.|++|||+.||+|+++|+..+++++..
T Consensus       215 ~~~~s~~EIA~~lgis~~tV~~~~~ra~~~  244 (251)
T PRK07670        215 KEELTLTEIGQVLNLSTSRISQIHSKALFK  244 (251)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            347899999999999999999999887653

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=96.09  E-value=0.015  Score=57.97  Aligned_cols=34  Identities=29%  Similarity=0.510  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi  320 (482)
                      ++.+...+|...+|++|+..+.|+.+|++.+++.
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~  147 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQ  147 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHH
Confidence            3556778888999999999999999999987664

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

Probab=96.08  E-value=0.053  Score=53.23  Aligned_cols=34  Identities=32%  Similarity=0.589  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi  320 (482)
                      ++.++...+...+|++||.++.|+.+|++.+++.
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~  121 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVR  121 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            3445677888889999999999999999987664

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.

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

Probab=96.03  E-value=0.21  Score=50.28  Aligned_cols=149  Identities=19%  Similarity=0.184  Sum_probs=84.3

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHH
Q 011577          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (482)
Q Consensus       256 ~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~  335 (482)
                      .+..||++-.  +.--+.--.++.+      ++..+..+|+..+|++||..|.|+..|++.++.......+.        
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            5666888766  2222223333443      45567888999999999999999999999887664433322        


Q ss_pred             HHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHH
Q 011577          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  415 (482)
Q Consensus       336 snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~  415 (482)
                        -....++-......+.+.              +.   ..-+..+..+-.+...+.+..++.      .+|..      
T Consensus       152 --~~~~~sld~~~~~~~d~~--------------~~---~~~~~~~~~~~~~~~~~~l~~ai~------~L~ER------  200 (247)
T COG1191         152 --GSQLLSLDEDVLKDDDDD--------------VD---DQIENPDDGVEKEELLEILKEAIE------PLPER------  200 (247)
T ss_pred             --cccccchhhhhccccccc--------------hh---hccccchhHHHHHHHHHHHHHHHH------ccCHH------
Confidence              111222221111111111              11   111234455555556566665554      12221      


Q ss_pred             HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577          416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT  455 (482)
Q Consensus       416 kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a  455 (482)
                        .+.+  +...+..+.|..|||+.||||+.+|-.+...+
T Consensus       201 --Ek~V--l~l~y~eelt~kEI~~~LgISes~VSql~kka  236 (247)
T COG1191         201 --EKLV--LVLRYKEELTQKEIAEVLGISESRVSRLHKKA  236 (247)
T ss_pred             --HHHH--HHHHHHhccCHHHHHHHhCccHHHHHHHHHHH
Confidence              1111  12223346899999999999999998887655

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=95.98  E-value=0.046  Score=54.59  Aligned_cols=29  Identities=3%  Similarity=0.161  Sum_probs=25.6

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ..+.|++|||+.||+|.++|+.+++++..
T Consensus       219 ~e~~t~~EIA~~lgis~~~V~~~~~ral~  247 (257)
T PRK05911        219 YEELVLKEIGKILGVSESRVSQIHSKALL  247 (257)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34789999999999999999999988754

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=95.86  E-value=0.097  Score=52.35  Aligned_cols=34  Identities=26%  Similarity=0.526  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi  320 (482)
                      ++.+....|+..+|++||..+.|+..|++.+.+.
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~  152 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYN  152 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence            4556677888899999999999999999876654

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=95.73  E-value=0.068  Score=53.69  Aligned_cols=35  Identities=29%  Similarity=0.554  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~  321 (482)
                      ++.+...+|...+|++||..+.|+.+|++.+++..
T Consensus       128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~  162 (264)
T PRK07122        128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVE  162 (264)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34456778888899999999999999999877654

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=95.62  E-value=0.15  Score=51.85  Aligned_cols=29  Identities=17%  Similarity=0.243  Sum_probs=25.7

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .+.|++|||+.||||.++|+.+++++...
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~k  272 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEARALEK  272 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            47899999999999999999999887543

>PRK05949 RNA polymerase sigma factor; Validated

Probab=95.59  E-value=0.071  Score=55.42  Aligned_cols=35  Identities=26%  Similarity=0.461  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~  321 (482)
                      ++.+....+...+|++|+..+.|+.+|++.+.+..
T Consensus       179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~  213 (327)
T PRK05949        179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIRE  213 (327)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            34556667778899999999999999999876643

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=95.58  E-value=0.19  Score=52.90  Aligned_cols=133  Identities=18%  Similarity=0.267  Sum_probs=72.0

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHH-HHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG  365 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQE-G~IG  365 (482)
                      ++.++..+|...+|++||..+.|+.+|++.+++.......                   .+    ...+++.+.+ +-..
T Consensus       217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~  273 (367)
T PRK09210        217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSH  273 (367)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcch
Confidence            3456677888899999999999999999987665332111                   11    0111111110 0011


Q ss_pred             HHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCH
Q 011577          366 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV  445 (482)
Q Consensus       366 LirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~  445 (482)
                      |...+.  |..............++..+.++|.      .+|..-...+.    .  .+....+.+.|++|||+.||||.
T Consensus       274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~----l--rygl~~~~~~tl~EIa~~lgvs~  339 (367)
T PRK09210        274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLR----L--RFGLDDGRTRTLEEVGKVFGVTR  339 (367)
T ss_pred             hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHH----H--HhccCCCCCccHHHHHHHHCCCH
Confidence            111121  1111223444455555555555553      23322111111    0  01112235789999999999999


Q ss_pred             HHHHHHHHHcC
Q 011577          446 EKLERLIFITR  456 (482)
Q Consensus       446 etVk~~L~~ar  456 (482)
                      ++|+.+...|.
T Consensus       340 erVrQi~~~Al  350 (367)
T PRK09210        340 ERIRQIEAKAL  350 (367)
T ss_pred             HHHHHHHHHHH
Confidence            99999977663

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=95.26  E-value=0.33  Score=53.61  Aligned_cols=35  Identities=31%  Similarity=0.553  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~  321 (482)
                      ++.+++.+|...+|++||.++.|+.+|++.+.+..
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~  393 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVRE  393 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            45567888889999999999999999999876643

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=95.18  E-value=0.2  Score=53.99  Aligned_cols=36  Identities=19%  Similarity=0.454  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  322 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~  322 (482)
                      ++.+.+..|...+|+.|+..|.|+.+|++.+.+...
T Consensus       263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~  298 (415)
T PRK07598        263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV  298 (415)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            566778888889999999999999999998877643

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=94.95  E-value=0.11  Score=50.53  Aligned_cols=32  Identities=38%  Similarity=0.597  Sum_probs=26.2

Q ss_pred             HHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577          289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (482)
Q Consensus       289 e~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi  320 (482)
                      .+....+...+|++||..+.|+..|++.+++.
T Consensus       100 ~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~  131 (231)
T TIGR02885       100 RYMKEELSKELGREPTINELAEALGVSPEEIV  131 (231)
T ss_pred             HHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHH
Confidence            34556777888999999999999999987664

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.

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

Probab=94.83  E-value=0.28  Score=47.54  Aligned_cols=34  Identities=32%  Similarity=0.651  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi  320 (482)
                      ++.++..++...+|++|+.++.|+.+|++.+++.
T Consensus        84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~  117 (224)
T TIGR02479        84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYR  117 (224)
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHH
Confidence            3455667788889999999999999999876554

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.

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

Probab=94.73  E-value=0.42  Score=48.72  Aligned_cols=34  Identities=26%  Similarity=0.509  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi  320 (482)
                      ++.+.+..+...+|++|+..+.|+.+|++.+++.
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~  195 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVR  195 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            4455667777889999999999999999987664

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).

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=94.62  E-value=0.64  Score=48.39  Aligned_cols=34  Identities=32%  Similarity=0.460  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi  320 (482)
                      ++.++..+|...+|++||..|.|+.+|++.+++.
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~  207 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIA  207 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            4556778888899999999999999999987664

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=94.43  E-value=0.095  Score=51.84  Aligned_cols=29  Identities=17%  Similarity=0.250  Sum_probs=25.4

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ..+.|++|||+.||+++++|+.++++++.
T Consensus       219 ~~g~s~~eIA~~lgis~~~V~~~~~ra~~  247 (255)
T TIGR02941       219 EENLSQKETGERLGISQMHVSRLQRQAIS  247 (255)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34789999999999999999999987754

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

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=94.42  E-value=0.21  Score=51.65  Aligned_cols=34  Identities=26%  Similarity=0.522  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi  320 (482)
                      ++.+.+..+...+|++|+..+.|+..|++.+.+.
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~  202 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR  202 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            4556777888889999999999999999876554

>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=94.33  E-value=0.096  Score=42.41  Aligned_cols=38  Identities=32%  Similarity=0.613  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHH
Q 011577          286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL  323 (482)
Q Consensus       286 ~~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l  323 (482)
                      .++.++..+|+..+||+||.+|.|+.+|++.+++...+
T Consensus         4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l   41 (78)
T PF04539_consen    4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELL   41 (78)
T ss_dssp             HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence            35778899999999999999999999999988775443

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 ....

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=94.08  E-value=0.46  Score=46.41  Aligned_cols=30  Identities=3%  Similarity=0.147  Sum_probs=26.1

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      ..+.|++|||+.||+|+++|+..+++++..
T Consensus       198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~~  227 (236)
T PRK06986        198 QEELNLKEIGAVLGVSESRVSQIHSQAIKR  227 (236)
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            347899999999999999999999887643

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=93.97  E-value=0.34  Score=48.03  Aligned_cols=35  Identities=26%  Similarity=0.297  Sum_probs=28.3

Q ss_pred             HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHH
Q 011577          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  322 (482)
Q Consensus       288 le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~  322 (482)
                      +.+...++...+|++|+.++.|+.+|++.+++...
T Consensus       122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~  156 (254)
T TIGR02850       122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA  156 (254)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            33456677888999999999999999998777544

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.

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

Probab=93.76  E-value=1.3  Score=46.74  Aligned_cols=33  Identities=24%  Similarity=0.326  Sum_probs=29.6

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHH
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDL  285 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l  285 (482)
                      ....+..|+..+...++||++||.+|+..++.+
T Consensus        65 ~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g   97 (342)
T COG0568          65 PAGRLSFYIRAIEAAPLLTPEEEKALARRLKRG   97 (342)
T ss_pred             hhhhHHHHHHHHhhhcccChHHHHHHHHHHHcC
Confidence            345788899999999999999999999999887

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=93.72  E-value=0.71  Score=49.08  Aligned_cols=34  Identities=32%  Similarity=0.584  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi  320 (482)
                      ++.+....|...+|++||..+.|+.+|++.+++.
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            4556777888899999999999999999987663

>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=92.86  E-value=0.15  Score=38.51  Aligned_cols=30  Identities=17%  Similarity=0.172  Sum_probs=22.8

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          428 GNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      +..+.+++|||+.+|+|+++|+..+++++.
T Consensus        23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   23 YFQGMSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             HTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             HHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            445789999999999999999999998753

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.

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

Probab=92.83  E-value=0.17  Score=48.92  Aligned_cols=28  Identities=21%  Similarity=0.369  Sum_probs=25.1

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      .+.+++|||+.||++..+|+..++++..
T Consensus       193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~  220 (227)
T TIGR02980       193 EDKTQSEIAERLGISQMHVSRLLRRALK  220 (227)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4689999999999999999999988754

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.

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=92.57  E-value=0.25  Score=49.90  Aligned_cols=31  Identities=23%  Similarity=0.323  Sum_probs=27.2

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      ..+.|++|||+.||+|+++|+.++++|+..+
T Consensus       240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkL  270 (285)
T TIGR02394       240 YEPATLEEVAAEVGLTRERVRQIQVEALKKL  270 (285)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999887543

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).

>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=92.23  E-value=0.36  Score=35.98  Aligned_cols=30  Identities=20%  Similarity=0.265  Sum_probs=25.1

Q ss_pred             hcCCCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577          427 EGNHSPDKEDLARRVGITVEKLERLIFITR  456 (482)
Q Consensus       427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ar  456 (482)
                      .+..+.|++|||+.||+|.++|+.+...+.
T Consensus        16 ~y~~~~t~~eIa~~lg~s~~~V~~~~~~al   45 (50)
T PF04545_consen   16 RYFEGLTLEEIAERLGISRSTVRRILKRAL   45 (50)
T ss_dssp             HHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence            345678999999999999999999988763

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 ....

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=92.12  E-value=2.2  Score=42.41  Aligned_cols=33  Identities=24%  Similarity=0.307  Sum_probs=27.0

Q ss_pred             HHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577          289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (482)
Q Consensus       289 e~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~  321 (482)
                      .+...++...+|++|+..+.|+.+|++.+++..
T Consensus       126 ~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~  158 (258)
T PRK08215        126 LQVREKLINENSKEPTVEEIAKELEVPREEVVF  158 (258)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence            345667778899999999999999999887653

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=91.87  E-value=0.41  Score=47.41  Aligned_cols=29  Identities=17%  Similarity=0.208  Sum_probs=25.6

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ..+.+++|||+.|||++++|+.++++++.
T Consensus       219 ~~g~s~~eIA~~l~is~~tV~~~~~ra~~  247 (257)
T PRK08583        219 IENLSQKETGERLGISQMHVSRLQRQAIK  247 (257)
T ss_pred             hCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34789999999999999999999987754

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=91.63  E-value=1.5  Score=43.15  Aligned_cols=34  Identities=15%  Similarity=0.392  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHH
Q 011577          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (482)
Q Consensus       288 le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~  321 (482)
                      +.+....+...+|++|+..+.|+.+|++.+++..
T Consensus       103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~  136 (231)
T PRK12427        103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQE  136 (231)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHH
Confidence            4455677888899999999999999999877643

>PRK05572 sporulation sigma factor SigF; Validated

Probab=91.61  E-value=1.6  Score=43.24  Aligned_cols=28  Identities=21%  Similarity=0.322  Sum_probs=24.8

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      .+.|++|||+.+|++..+|..+.+++..
T Consensus       217 ~~~s~~eIA~~lgis~~~V~~~~~ral~  244 (252)
T PRK05572        217 KDKTQSEVAKRLGISQVQVSRLEKKILK  244 (252)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4689999999999999999999887753

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=91.33  E-value=0.57  Score=44.65  Aligned_cols=67  Identities=12%  Similarity=0.134  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHHHccCCCCC---HhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011577          335 NANLRLVVHVAKQYQGRGIS---LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (482)
Q Consensus       335 ~snlrLV~sIAkrY~~~g~d---~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~  401 (482)
                      ..-+..+-.+.++|.-+|-.   -+|.|.+|.-..++.+..||+++...+-+|...++-+++.+.|.+..
T Consensus        44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk  113 (179)
T PHA02547         44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK  113 (179)
T ss_pred             HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence            34455555666666555554   59999999999999999999999999999999999999998887654

>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=90.30  E-value=0.92  Score=36.48  Aligned_cols=42  Identities=26%  Similarity=0.419  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCC-HHHHHHHHHH
Q 011577          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI  454 (482)
Q Consensus       413 ~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS-~etVk~~L~~  454 (482)
                      .-.+|-..+..+..+.|..||+.|||+.+|++ ..+|...|..
T Consensus         7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~   49 (65)
T PF01726_consen    7 RQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA   49 (65)
T ss_dssp             HHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            34456666677778888899999999999997 9999988874

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.

>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=88.99  E-value=1.4  Score=32.44  Aligned_cols=35  Identities=20%  Similarity=0.235  Sum_probs=24.0

Q ss_pred             HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577          419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI  454 (482)
Q Consensus       419 ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~  454 (482)
                      ..+-.+.+..+ ..++.|||+.+|+|..+|..++++
T Consensus         6 ~~Il~~Lq~d~-r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    6 RKILRLLQEDG-RRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             HHHHHHHHH-T-TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHcC-CccHHHHHHHHCcCHHHHHHHHHH
Confidence            33333344445 579999999999999999998864

...

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=86.85  E-value=14  Score=37.43  Aligned_cols=27  Identities=15%  Similarity=0.279  Sum_probs=24.3

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITR  456 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar  456 (482)
                      .+.|++|||+.||||.++|+.+.+.+.
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al  273 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEKNAM  273 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            468999999999999999999988764

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=86.00  E-value=1.4  Score=36.62  Aligned_cols=25  Identities=12%  Similarity=0.155  Sum_probs=22.8

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFI  454 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~  454 (482)
                      .+.|++|||+.||+|+.+|+..+..
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            3789999999999999999999874

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.

>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=85.77  E-value=1.5  Score=31.29  Aligned_cols=28  Identities=14%  Similarity=0.209  Sum_probs=24.6

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      .+.+..+||+.+|++..+|...++.++.
T Consensus        25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~~   52 (55)
T cd06171          25 EGLSYEEIAEILGISRSTVRQRLHRALK   52 (55)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4679999999999999999999887643

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

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=84.44  E-value=2  Score=34.39  Aligned_cols=31  Identities=16%  Similarity=0.280  Sum_probs=24.7

Q ss_pred             HHHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577          424 YIQEGNHSPDKEDLARRVGITVEKLERLIFI  454 (482)
Q Consensus       424 L~~e~gr~pS~eEIAe~LGIS~etVk~~L~~  454 (482)
                      +..+.+...+..+||+.||++..+|+..-..
T Consensus        15 ~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   15 IYKESNGKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             HHHHhCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence            3344444899999999999999999987553

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>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=84.00  E-value=3  Score=32.05  Aligned_cols=47  Identities=21%  Similarity=0.307  Sum_probs=34.6

Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHH
Q 011577          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL  451 (482)
Q Consensus       405 rlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~  451 (482)
                      .+|......+...-+....|..++....+-.|||+.+|++..+|+.=
T Consensus         2 ~Ip~~ti~RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD   48 (50)
T PF06971_consen    2 KIPKATIRRLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD   48 (50)
T ss_dssp             S-SHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence            46666667777777777778777777789999999999999999864

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 ....

>PRK06930 positive control sigma-like factor; Validated

Probab=83.97  E-value=1  Score=42.74  Aligned_cols=30  Identities=10%  Similarity=0.095  Sum_probs=26.3

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      ..+.+++|||+.||+++++|+..+.+++..
T Consensus       128 ~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~k  157 (170)
T PRK06930        128 GYGLSYSEIADYLNIKKSTVQSMIERAEKK  157 (170)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            347899999999999999999999988653

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=83.41  E-value=4.2  Score=43.00  Aligned_cols=125  Identities=10%  Similarity=0.033  Sum_probs=82.0

Q ss_pred             HHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccchhH
Q 011577          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  410 (482)
Q Consensus       331 e~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v  410 (482)
                      +..+..-.+.+....-+|.++-...||.+||+|+..++.-.+=.+-+  .-..|++-.-||.-+|.+|+..+.-..|.+.
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            44455555555555566777777899999999987666555444433  3689999999999999999887654444322


Q ss_pred             HHHH--HHHH----------------------------HHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          411 YTLL--SKVL----------------------------EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       411 ~e~l--~kI~----------------------------ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ....  .++.                            .....|....-.+.|..|||...=+++.++.+.+-+++.
T Consensus        86 ~~~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v~GLs~~eIArAFLv~e~am~QRivRAK~  162 (415)
T COG4941          86 LLSDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLVGGLSTAEIARAFLVPEAAMAQRIVRAKA  162 (415)
T ss_pred             cccccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHHcCCcHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            1111  0000                            001112222222579999999999999999999888764

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=82.10  E-value=4.8  Score=29.53  Aligned_cols=29  Identities=21%  Similarity=0.421  Sum_probs=22.3

Q ss_pred             HHhcCCCCcHHHHHHHhCCCHHHHHHHHHH
Q 011577          425 IQEGNHSPDKEDLARRVGITVEKLERLIFI  454 (482)
Q Consensus       425 ~~e~gr~pS~eEIAe~LGIS~etVk~~L~~  454 (482)
                      ..+.+ ..|..|||+.+|++..+|...++.
T Consensus        12 l~~~~-~~t~~ela~~~~is~~tv~~~l~~   40 (48)
T PF13412_consen   12 LRENP-RITQKELAEKLGISRSTVNRYLKK   40 (48)
T ss_dssp             HHHCT-TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHcC-CCCHHHHHHHhCCCHHHHHHHHHH
Confidence            33444 589999999999999999998874

...

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=81.50  E-value=1.2  Score=34.55  Aligned_cols=28  Identities=18%  Similarity=0.224  Sum_probs=24.8

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      |..+..|||+.|||+..++...|+++..
T Consensus        22 R~~tl~elA~~lgis~st~~~~LRrae~   49 (53)
T PF04967_consen   22 RRITLEELAEELGISKSTVSEHLRRAER   49 (53)
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            5669999999999999999999988743

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=81.15  E-value=1.5  Score=45.59  Aligned_cols=30  Identities=23%  Similarity=0.368  Sum_probs=26.6

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      ..+.|++|||+.||++.++|+.++++++..
T Consensus       280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~k  309 (325)
T PRK05657        280 YEAATLEDVAREIGLTRERVRQIQVEALRR  309 (325)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            347899999999999999999999988654

>PRK00118 putative DNA-binding protein; Validated

Probab=80.58  E-value=2.6  Score=37.19  Aligned_cols=28  Identities=11%  Similarity=0.051  Sum_probs=25.3

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      .+.|+.|||+.+|+|..+|...+.+++.
T Consensus        32 eg~S~~EIAe~lGIS~~TV~r~L~RArk   59 (104)
T PRK00118         32 DDYSLGEIAEEFNVSRQAVYDNIKRTEK   59 (104)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3689999999999999999999998764

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=80.50  E-value=2.3  Score=31.06  Aligned_cols=29  Identities=17%  Similarity=0.276  Sum_probs=25.0

Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          431 SPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      +.+..|||+.+|++..+|+..+.++...+
T Consensus        18 g~s~~eia~~l~is~~tv~~~~~~~~~kl   46 (58)
T smart00421       18 GLTNKEIAERLGISEKTVKTHLSNIMRKL   46 (58)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            56999999999999999999998775443

lux regulon (activates the bioluminescence operon

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	482
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		1e-30
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		5e-30
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		5e-30
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		3e-29
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		3e-28
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		3e-28
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		3e-28
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		3e-26
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		3e-26
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		9e-21
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		1e-17
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 (328), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 82/245 (33%), Positives = 139/245 (56%), Gaps = 24/245 (9%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 311 AIGLS------------CRDLKSELH---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+  +F
Sbjct: 179 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPI-GDEKDSF 237
Query: 474 QSTFL 478
              F+
Sbjct: 238 YGDFI 242

>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613

Iteration: 1
 Score =  129 bits (323), Expect = 5e-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|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 = 5e-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 = 82/260 (31%), Positives = 139/260 (53%), Gaps = 39/260 (15%)
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 LSMQQPVWADQDTTFQSTFL 478
           +S++ P+  D+  +F   F+
Sbjct: 330 VSLETPI-GDEKDSFYGDFI 348

>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423

Iteration: 1
 Score =  123 bits (308), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 60/155 (38%), Positives = 100/155 (64%), Gaps = 3/155 (1%)
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 -VEKLERLIFITRMPLSMQQPVWADQDTTFQSTFL 478
             +++E  + I + P+S++ P+  D+  +F   F+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPI-GDEKDSFYGDFI 333

>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423

Iteration: 1
 Score =  123 bits (308), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 60/155 (38%), Positives = 100/155 (64%), Gaps = 3/155 (1%)
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 -VEKLERLIFITRMPLSMQQPVWADQDTTFQSTFL 478
             +++E  + I + P+S++ P+  D+  +F   F+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPI-GDEKDSFYGDFI 333

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score =  123 bits (308), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 60/155 (38%), Positives = 100/155 (64%), Gaps = 3/155 (1%)
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 -VEKLERLIFITRMPLSMQQPVWADQDTTFQSTFL 478
             +++E  + I + P+S++ P+  D+  +F   F+
Sbjct: 320 DAKRVEETLKIAQEPVSLETPI-GDEKDSFYGDFI 353

>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 = 78/243 (32%), Positives = 130/243 (53%), Gaps = 38/243 (15%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 6   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 62
Query: 311 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 340
            +G +                            ++LK  LH    G ++R+ LI ANLRL
Sbjct: 63  ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 122
Query: 341 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400
           VV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   
Sbjct: 123 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 182
Query: 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT--VEKLERLIFITRMP 458
           +RTIR+P ++   ++K+    R   QE    P  E++A  +G     +++E  + I + P
Sbjct: 183 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 242
Query: 459 LSM 461
           +S+
Sbjct: 243 VSL 245

>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 (290), 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: 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|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 98.2 bits (243), Expect = 9e-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 = 1e-17,   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	482
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,	4e-39
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	3e-38
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	6e-38
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	2e-25
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	3e-23
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-11
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 (372), 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 (360), 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 =  145 bits (368), Expect = 4e-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

>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 = 3e-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

>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 =  138 bits (349), Expect = 6e-38
 Identities = 39/155 (25%), Positives = 80/155 (51%), Gaps = 2/155 (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 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQD 470
           ++A  +GI+ E +       R+P S+ + V+ +  
Sbjct: 135 EIADHLGISPEDVVLAQEAVRLPTSIHETVYENDG 169

>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 = 2e-25
 Identities = 31/164 (18%), Positives = 68/164 (41%), Gaps = 9/164 (5%)

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 RVGITVEKLERLIFITRMPLSMQ-QPVWADQDTTFQSTFLDAAG 482
            +GI+ E+L + +        +  + V+ D    +      +  
Sbjct: 124 ELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTN 167

>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 = 99.6 bits (248), Expect = 3e-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 = 64.9 bits (157), Expect = 3e-11
 Identities = 68/534 (12%), Positives = 148/534 (27%), Gaps = 152/534 (28%)

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------------------DTTFQSTFLD 479
               ++              P + DQ                   T F+  FLD
Sbjct: 450 ----VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD 499

>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	482
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	99.81
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.76
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.72
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.7
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.68
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.5
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.39
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.36
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	99.26
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	99.17
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	97.93
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	94.74
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	94.13
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	93.64
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	92.77
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	92.45
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	91.92
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	91.45
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	90.93
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	90.66
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	90.55
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	90.53
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	89.9
3c57_A	95	Two component transcriptional regulatory protein;	89.16
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	87.73
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	87.24
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	86.72
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	86.05
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	85.47
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	84.91
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	84.38
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	83.99
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	82.49
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	82.17

>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=8e-38  Score=329.12  Aligned_cols=229  Identities=32%  Similarity=0.563  Sum_probs=203.3

Q ss_pred             CCCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHhhhCCCCcHHHHHH---
Q 011577          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAK---  310 (482)
Q Consensus       252 ~~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~------------------~l~~~~g~~pt~~ewA~---  310 (482)
                      ...|+++.||++|+++|+||++||++|+++|+.++.++....                  ......|+.|+..+|+.   
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            356899999999999999999999999999999764433211                  12224567788888743   


Q ss_pred             ---------HhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCch
Q 011577          311 ---------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF  381 (482)
Q Consensus       311 ---------a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rF  381 (482)
                               +.+++..+|+..+++|..|+++||.+|+++|++||++|.++|.+++|||||||||||+|+++|||.+|++|
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--CCHHHHHHHHHHcCCCc
Q 011577          382 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPL  459 (482)
Q Consensus       382 STYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LG--IS~etVk~~L~~ar~~l  459 (482)
                      +||++|||||.|.++|+++.+.+++|.++...++++.++.+.+.+.+++.|+.+|||+.+|  +++++|..++..+...+
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             cCcccCCCCCCCcccccccCC
Q 011577          460 SMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       460 SLD~~i~~d~~~~l~d~i~D~  480 (482)
                      |||.+++++++..+.|+++|.
T Consensus       331 SLd~~~~~d~d~~l~d~l~d~  351 (438)
T 1l9z_H          331 SLETPIGDEKDSFYGDFIPDE  351 (438)
T ss_pred             ccccccccccchhhhhhhccc
Confidence            999999877766777777664

>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=1e-38  Score=312.63  Aligned_cols=209  Identities=33%  Similarity=0.575  Sum_probs=131.8

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHHH--------h-----------------hhCCCCcHH
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR-LEKEKSKLQ--------S-----------------QFGREPTLI  306 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~-le~~~~~l~--------~-----------------~~g~~pt~~  306 (482)
                      .+|++++||++|+++||||++||++|+++|+.++. .+.+.....        .                 ..+.+|+..
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            47999999999999999999999999999999875 333322110        0                 024689999


Q ss_pred             HHHHHhcCCH----HHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchh
Q 011577          307 EWAKAIGLSC----RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA  382 (482)
Q Consensus       307 ewA~a~gmdd----~eLi~~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFS  382 (482)
                      +||.+.+++.    .+|+..+++|+.|+++||..|.++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+
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    456777778889999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhC--CCHHHHHHHHHHcCCCcc
Q 011577          383 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLS  460 (482)
Q Consensus       383 TYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LG--IS~etVk~~L~~ar~~lS  460 (482)
                      ||++||||++|.++++++.+.+++|.++.+.+.++.++.+.|...+++.||++|||+.||  ||+++|++++.+++.++|
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 011577          461 M  461 (482)
Q Consensus       461 L  461 (482)
                      |
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=4.4e-38  Score=329.80  Aligned_cols=225  Identities=34%  Similarity=0.583  Sum_probs=200.2

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhh---------------------hCCCCcHHH----
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQ---------------------FGREPTLIE----  307 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~~~---------------------~g~~pt~~e----  307 (482)
                      ..|++++||++|+++|+||++||++|+++|+.+..++.   .|...                     .|+.|+..+    
T Consensus        77 ~~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~---~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (423)
T 2a6h_F           77 TSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIK---KLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDP  153 (423)
T ss_dssp             THHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHH---HHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTT
T ss_pred             CCcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHH---HHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhh
Confidence            46899999999999999999999999999999754332   22222                     234554333    


Q ss_pred             -----HHH---HhcCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCC
Q 011577          308 -----WAK---AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGC  379 (482)
Q Consensus       308 -----wA~---a~gmdd~eLi~~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~  379 (482)
                           |+.   +.++++.+|+..+++|..|+++||.+|+++|++||++|.++|.+++|||||||||||+|+++|||.+|+
T Consensus       154 ~~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~  233 (423)
T 2a6h_F          154 KTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRF  233 (423)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCC
T ss_pred             hhhhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCC
Confidence                 332   346778899999998889999999999999999999999999999999999999999999999999999


Q ss_pred             chhhHHHHHHHHHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhC--CCHHHHHHHHHHcCC
Q 011577          380 RFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRM  457 (482)
Q Consensus       380 rFSTYA~~wIRnaI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LG--IS~etVk~~L~~ar~  457 (482)
                      +|+|||+||||+.|.++|+++.+.+++|.++...++++.++.+.+.+.+++.|+.+|||+.||  +++++|..++..+..
T Consensus       234 ~FstYa~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~  313 (423)
T 2a6h_F          234 KFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQE  313 (423)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSC
T ss_pred             CHHHHHHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccC
Confidence            999999999999999999999999999999999999999999999999999999999999999  999999999999999


Q ss_pred             CccCcccCCCCCCCcccccccCC
Q 011577          458 PLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       458 ~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      .+|||.|++++++..+.|+++|+
T Consensus       314 ~~Sld~~~~~~~~~~l~d~l~d~  336 (423)
T 2a6h_F          314 PVSLETPIGDEKDSFYGDFIPDE  336 (423)
T ss_dssp             CEESSCBCSSSSSCBGGGSSCCS
T ss_pred             CcccccccCCCCccchhhhhccc
Confidence            99999999887777888888775

>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=3.2e-27  Score=257.65  Aligned_cols=167  Identities=35%  Similarity=0.708  Sum_probs=158.0

Q ss_pred             CHHHHHHHHhhcH-HH---HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011577          315 SCRDLKSELHSGN-SS---REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (482)
Q Consensus       315 dd~eLi~~l~~Gd-~A---re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR  390 (482)
                      +..+|+.+++.|+ .|   |+.||..|.++|+++|++|++++.+++||+||||||||+++++||+.+|++|+||++||||
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            4567888999998 56   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCC
Q 011577          391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD  470 (482)
Q Consensus       391 naI~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~  470 (482)
                      |.|.++++++.+.+++|.++.+.+++++++.+.+.+.+|+.|+.+|||+.||+++++|+.++..++.++||+.+++++++
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 011577          471 TTFQSTFLDAA  481 (482)
Q Consensus       471 ~~l~d~i~D~~  481 (482)
                      ..+.++++|+.
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            78888887753

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=99.81  E-value=1.5e-20  Score=176.32  Aligned_cols=153  Identities=25%  Similarity=0.458  Sum_probs=52.5

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       314 mdd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      +++.+|+..++.|+ .|++.|+..|.++|+.+|++|.++..+++||+||||++||+++++||+.+|..|.||+++|++|.
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            34567888888898 89999999999999999999999999999999999999999999999998889999999999999


Q ss_pred             HHHHHHHhcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCC
Q 011577          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA  467 (482)
Q Consensus       393 I~~~Lrkq~r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~  467 (482)
                      |++++|++. .+++|..+.....+++.+...+....++.++.++|++.+|++.+.+...+.......|++.|+.+
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 78999999999999999999999888889999999999999999999988877778888887543

>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=9.5e-18  Score=157.44  Aligned_cols=136  Identities=21%  Similarity=0.298  Sum_probs=121.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHcc---CCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577          327 NSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (482)
Q Consensus       327 d~Are~LI~snlrLV~sIAkrY~---~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~  403 (482)
                      +.|++.||..|.++|+.+|++|.   +++.+++||+||||++||+++++||+.+|.+|.||+++||+|.|++++|++.  
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             cccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcC--CCccCcccC
Q 011577          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPV  465 (482)
Q Consensus       404 irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar--~~lSLD~~i  465 (482)
                       +.|........++.++...+....++.|+.+|||+.+|++++.+..++....  ..+|+|.++
T Consensus        89 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~  151 (239)
T 1rp3_A           89 -FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVF  151 (239)
T ss_dssp             -TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccc
Confidence             5677888888899999999999999999999999999999999988876432  335666543

>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=99.72  E-value=2.7e-17  Score=150.52  Aligned_cols=141  Identities=17%  Similarity=0.230  Sum_probs=111.4

Q ss_pred             CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (482)
Q Consensus       315 dd~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI  393 (482)
                      ++.+|+..++.|+ .|++.|+..|.+.|+.+|++|.+ ..+++|++||+|+++|+++++|++..  .|.+|++.+++|.+
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            4667888888888 89999999999999999999999 99999999999999999999999864  59999999999999


Q ss_pred             HHHHHHhcCCccc----------------------chh---HHHHHHHHHHHHH-------HH-HHhcCCCCcHHHHHHH
Q 011577          394 RKAIFQHSRTIRL----------------------PEN---IYTLLSKVLEAKR-------LY-IQEGNHSPDKEDLARR  440 (482)
Q Consensus       394 ~~~Lrkq~r~irl----------------------P~~---v~e~l~kI~ka~~-------eL-~~e~gr~pS~eEIAe~  440 (482)
                      ++++|+..+....                      |..   ..+....+..+..       .+ ...+..+.|++|||+.
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   0011122223332       22 2234457899999999


Q ss_pred             hCCCHHHHHHHHHHcCCC
Q 011577          441 VGITVEKLERLIFITRMP  458 (482)
Q Consensus       441 LGIS~etVk~~L~~ar~~  458 (482)
                      ||||+++|+..+++++..
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            999999999999988653

>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=3.6e-17  Score=165.77  Aligned_cols=86  Identities=42%  Similarity=0.914  Sum_probs=79.7

Q ss_pred             HHHHHHHhhcH----HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHH
Q 011577          317 RDLKSELHSGN----SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (482)
Q Consensus       317 ~eLi~~l~~Gd----~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRna  392 (482)
                      ..|+.+++.|+    .|++.||..|.++|+++|++|++++.+++||+||||||||+++++|++.+|.+|+||++|||+|.
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            55788888887    59999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcC
Q 011577          393 IRKAIFQHSR  402 (482)
Q Consensus       393 I~~~Lrkq~r  402 (482)
                      |++++|++.+
T Consensus       330 ~~~~lr~~~r  339 (339)
T 1sig_A          330 ITRSIADQAR  339 (339)
T ss_dssp             HHHHHHHC--
T ss_pred             HHHHHHHhcC
Confidence            9999998753

>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=2.5e-14  Score=126.31  Aligned_cols=105  Identities=18%  Similarity=0.296  Sum_probs=75.3

Q ss_pred             CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc------------------------
Q 011577          352 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP------------------------  407 (482)
Q Consensus       352 g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP------------------------  407 (482)
                      |.+++|++||||++||+++++||+.+ .+|.||++++++|.+++++|++.+....+                        
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 78999999999999999999865322111                        


Q ss_pred             ----------hh----------HHHHHH-HHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          408 ----------EN----------IYTLLS-KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       408 ----------~~----------v~e~l~-kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                                ..          +...+. .+....+.+...+..+.|++|||+.||||.++|+..+++++.
T Consensus        80 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~~L~~~~r~v~~~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~  150 (164)
T 3mzy_A           80 NNYKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRIRK  150 (164)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hhhcccCCCHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                      00          111222 222222232224556889999999999999999999998864

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.39  E-value=9.6e-15  Score=131.77  Aligned_cols=127  Identities=9%  Similarity=0.054  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCCcccc--
Q 011577          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP--  407 (482)
Q Consensus       330 re~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~irlP--  407 (482)
                      |+.|+..|.+.|+.+|++++++..+++|++||+|+++|+++++|++.  ..|.+|++.+++|.+++++|+.......+  
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            57799999999999999999999999999999999999999999875  36999999999999999998753211101  


Q ss_pred             ----hhHHHHHHHHHHHHHHHH-HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          408 ----ENIYTLLSKVLEAKRLYI-QEGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       408 ----~~v~e~l~kI~ka~~eL~-~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                          ..+...+..+....+++. ..+..+.|++|||+.||||+++|+..+.+++..
T Consensus        81 ~~~~~~l~~~l~~Lp~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~rar~~  136 (157)
T 2lfw_A           81 EGTEAVARARLARMTPLSRQALLLTAMEGFSPEDAAYLIEVDTSEVETLVTEALAE  136 (157)
T ss_dssp             SSSSSTTTTTTTTSCTTHHHHHTTTSSSCCCHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence                112223333333333322 234457899999999999999999999988653

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.36  E-value=4.7e-13  Score=132.44  Aligned_cols=131  Identities=11%  Similarity=0.013  Sum_probs=103.0

Q ss_pred             hcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhcCC
Q 011577          325 SGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (482)
Q Consensus       325 ~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~r~  403 (482)
                      +|+ .+|+.|+..|.+.++.+|++|+++..+++|++||.|+.+|+..++|++.  ..|.+|++++++|.+++++|+....
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            445 6999999999999999999999999999999999999999999999874  4699999999999999998864321


Q ss_pred             cc----cchhHHHHHHHHHHHHHHH-HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          404 IR----LPENIYTLLSKVLEAKRLY-IQEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       404 ir----lP~~v~e~l~kI~ka~~eL-~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ..    ....+...+.++....++. ......+.+++|||+.||+++++|+..+.+++.
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    1134556666665555543 333445789999999999999999999887753

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=99.26  E-value=7.5e-12  Score=106.16  Aligned_cols=84  Identities=18%  Similarity=0.156  Sum_probs=72.3

Q ss_pred             HHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHH
Q 011577          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  396 (482)
Q Consensus       318 eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~  396 (482)
                      +|+..++.|+ .|++.|+..|.+.|+.+|.++ ++..+++|++||+|+.+|+.+.+|++.  ..|.+|++.+++|.++++
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 888999999999999999999999874  479999999999999999


Q ss_pred             HHHhcCCc
Q 011577          397 IFQHSRTI  404 (482)
Q Consensus       397 Lrkq~r~i  404 (482)
                      +|++.+..
T Consensus        90 ~R~~~~~~   97 (112)
T 2o7g_A           90 IRHVRSRP   97 (112)
T ss_dssp             TC------
T ss_pred             HHHhhccc
Confidence            98876543

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=99.17  E-value=1.9e-11  Score=99.15  Aligned_cols=76  Identities=14%  Similarity=0.135  Sum_probs=68.3

Q ss_pred             hhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011577          324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (482)
Q Consensus       324 ~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~  401 (482)
                      ..|+ .+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++.  ..|.+|++.+++|.+++++|++.
T Consensus         7 ~~g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~   83 (87)
T 1h3l_A            7 TAERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ   83 (87)
T ss_dssp             HHHHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred             CcccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence            4556 8999999999999999999999999999999999999999999999875  47999999999999999998765

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=97.93  E-value=1.5e-09  Score=105.52  Aligned_cols=142  Identities=6%  Similarity=-0.080  Sum_probs=103.4

Q ss_pred             HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHH----HHHHHHHHHhHHhhCCCCCCchhhHHHHHHH
Q 011577          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLL----QEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (482)
Q Consensus       316 d~eLi~~l~~Gd-~Are~LI~snlrLV~sIAkrY~~~g~d~EDLI----QEG~IGLirAiekFDp~kG~rFSTYA~~wIR  390 (482)
                      ++.|+.+++.+| .+++.+...|.++++.+............|+.    ||.|+.+|+.+..|++.  ..|.+|++.+++
T Consensus        84 ~~~ll~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~--~~~~~WL~~ia~  161 (258)
T 3clo_A           84 EDCIYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNT--PAGNVWLIFCLY  161 (258)
T ss_dssp             CHHHHTTBCHHHHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEEC--TTSCEEEEEEEE
T ss_pred             HHHHHHhCChHHHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCC--CchHHHHHHHHH
Confidence            346777887777 78999999999999999988877777888886    99999999999999864  369999999999


Q ss_pred             HHHHHHHHHhcCCcc----------cchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          391 QTIRKAIFQHSRTIR----------LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       391 naI~~~Lrkq~r~ir----------lP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      |.+.++++.......          .+..+...+..+....++.......+.+++|||+.||+|+++|+..+++++..+
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          011122233333333333211112478999999999999999999999886543

>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=94.74  E-value=0.0093  Score=65.04  Aligned_cols=34  Identities=32%  Similarity=0.570  Sum_probs=13.7

Q ss_pred             CCcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHH
Q 011577          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI  286 (482)
Q Consensus       253 ~~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~  286 (482)
                      .+||+++||++|++.||||+++|++|+++|..+.
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            5799999999999999999999999999999854

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=94.13  E-value=0.026  Score=45.93  Aligned_cols=31  Identities=10%  Similarity=0.078  Sum_probs=26.9

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          428 GNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      +..+.+++|||+.|||+..+|+..+++++..
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            3457899999999999999999999988643

>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=93.64  E-value=0.82  Score=41.77  Aligned_cols=29  Identities=10%  Similarity=0.115  Sum_probs=25.9

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ..+.|++|||+.||||.++|+.++++++.
T Consensus       201 ~~g~s~~EIA~~lgis~~~V~~~~~ra~~  229 (239)
T 1rp3_A          201 YEELPAKEVAKILETSVSRVSQLKAKALE  229 (239)
T ss_dssp             TSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            45789999999999999999999988754

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=92.77  E-value=0.11  Score=40.31  Aligned_cols=50  Identities=14%  Similarity=0.072  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       410 v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      +...+..+....+++...+..+.+++|||+.||++..+|+..+.+++..+
T Consensus        10 l~~~l~~L~~~e~~vl~l~~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl   59 (79)
T 1x3u_A           10 IRARLQTLSERERQVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMAKM   59 (79)
T ss_dssp             HHHHHHHHCHHHHHHHHHHTTTCCHHHHHHHTTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            33444444444444333345578999999999999999999998876544

>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=92.45  E-value=0.13  Score=39.26  Aligned_cols=30  Identities=13%  Similarity=0.206  Sum_probs=26.7

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      .+.|++|||+.||+|.++|+..+.++...+
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            578999999999999999999999886543

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=91.92  E-value=1.3  Score=46.42  Aligned_cols=29  Identities=14%  Similarity=0.187  Sum_probs=26.1

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .+.|++|||+.||||.++|+.+++++...
T Consensus       394 e~~TleEIAe~LgIS~erVRqi~~RAlkK  422 (438)
T 1l9z_H          394 REHTLEEVGAYFGVTRERIRQIENKALRK  422 (438)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            57899999999999999999999888654

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=91.45  E-value=0.11  Score=47.63  Aligned_cols=32  Identities=19%  Similarity=0.232  Sum_probs=0.0

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          428 GNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      +..+.|++|||+.||||+++|+..+++++..+
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            34577999999999999999999999887643

>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=90.93  E-value=0.15  Score=42.94  Aligned_cols=29  Identities=10%  Similarity=0.167  Sum_probs=25.8

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .+.|++|||+.||+|.++|+.++.+|...
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~rAlkk   66 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAKALRK   66 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            57899999999999999999999887543

>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=90.66  E-value=0.4  Score=37.04  Aligned_cols=29  Identities=14%  Similarity=0.187  Sum_probs=25.6

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .+.|++|||+.||+|.++|+..+.++...
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~ra~~k   57 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIENKALRK   57 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            57899999999999999999998877543

>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=90.55  E-value=0.058  Score=43.20  Aligned_cols=31  Identities=16%  Similarity=0.146  Sum_probs=26.7

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      ..+.+++|||+.||++..+|+..+.+++..+
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            3478999999999999999999998876543

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=90.53  E-value=0.38  Score=38.62  Aligned_cols=29  Identities=10%  Similarity=0.185  Sum_probs=26.2

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .+.|++|||+.||+|.++|+..+.+++..
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~ra~~k   65 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEVKALRK   65 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            57899999999999999999999988654

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=89.90  E-value=0.51  Score=35.41  Aligned_cols=30  Identities=17%  Similarity=0.058  Sum_probs=26.3

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      ..+.+++|||+.||++..+|+..+++++..
T Consensus        29 ~~g~s~~eIA~~lgis~~tv~~~~~ra~~~   58 (70)
T 2o8x_A           29 LLGLSYADAAAVCGCPVGTIRSRVARARDA   58 (70)
T ss_dssp             TSCCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            447899999999999999999999988643

>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=89.16  E-value=0.2  Score=41.09  Aligned_cols=30  Identities=10%  Similarity=0.120  Sum_probs=26.2

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      .+.+++|||+.|||+..+|+..+.+++..+
T Consensus        41 ~g~s~~eIA~~l~is~~tV~~~l~r~~~kL   70 (95)
T 3c57_A           41 EGLTNKQIADRMFLAEKTVKNYVSRLLAKL   70 (95)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            368999999999999999999998876544

>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=87.73  E-value=0.44  Score=40.59  Aligned_cols=29  Identities=10%  Similarity=-0.022  Sum_probs=25.9

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ..+.|++|||+.||+|+.+|+..+++++.
T Consensus        39 ~~g~s~~EIA~~lgiS~~tV~~~l~ra~~   67 (113)
T 1xsv_A           39 LEDYSLSEIADTFNVSRQAVYDNIRRTGD   67 (113)
T ss_dssp             TSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            44789999999999999999999998764

>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=87.24  E-value=0.85  Score=31.13  Aligned_cols=26  Identities=4%  Similarity=0.068  Sum_probs=22.9

Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577          431 SPDKEDLARRVGITVEKLERLIFITR  456 (482)
Q Consensus       431 ~pS~eEIAe~LGIS~etVk~~L~~ar  456 (482)
                      +.+..|||+.|||+..+|...+....
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            46999999999999999999987543

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=86.72  E-value=0.5  Score=34.76  Aligned_cols=31  Identities=10%  Similarity=0.170  Sum_probs=26.2

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCCcc
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMPLS  460 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lS  460 (482)
                      .+.+.+|||+.||+++.+|+..+.++...+-
T Consensus        12 ~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~   42 (61)
T 2jpc_A           12 EGYTNHGISEKLHISIKTVETHRMNMMRKLQ   42 (61)
T ss_dssp             TSCCSHHHHHHTCSCHHHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHC
Confidence            3679999999999999999999988765443

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=86.05  E-value=0.075  Score=43.13  Aligned_cols=30  Identities=13%  Similarity=0.159  Sum_probs=26.3

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      .+.+++|||+.|||+..+|+..+.+++..+
T Consensus        43 ~g~s~~eIA~~l~is~~tV~~~l~r~~~kL   72 (91)
T 2rnj_A           43 KGYSNQEIASASHITIKTVKTHVSNILSKL   72 (91)
T ss_dssp             TTCCTTHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            368999999999999999999999886544

>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=85.47  E-value=0.56  Score=38.36  Aligned_cols=32  Identities=9%  Similarity=0.121  Sum_probs=26.9

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMPLSM  461 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL  461 (482)
                      .+.+++|||+.|||++.+|+..+.++...+-+
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            46799999999999999999999887655433

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=84.91  E-value=1.4  Score=33.30  Aligned_cols=31  Identities=13%  Similarity=0.111  Sum_probs=26.1

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      ..+.+++|||+.||++..+|+..+.++...+
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            3467999999999999999999998775443

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=84.38  E-value=1.7  Score=34.86  Aligned_cols=27  Identities=11%  Similarity=0.209  Sum_probs=23.6

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFIT  455 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~a  455 (482)
                      |..||..|||+.+|+|..+|+.-|..-
T Consensus        22 g~~psv~EIa~~lgvS~~TVrr~L~~L   48 (77)
T 2jt1_A           22 GAPVKTRDIADAAGLSIYQVRLYLEQL   48 (77)
T ss_dssp             TSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            448999999999999999999888743

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=83.99  E-value=1.1  Score=32.41  Aligned_cols=24  Identities=17%  Similarity=0.304  Sum_probs=21.4

Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHH
Q 011577          431 SPDKEDLARRVGITVEKLERLIFI  454 (482)
Q Consensus       431 ~pS~eEIAe~LGIS~etVk~~L~~  454 (482)
                      +.+..|||+.||++..+|...+..
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            569999999999999999988753

>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=82.49  E-value=1.2  Score=38.08  Aligned_cols=28  Identities=14%  Similarity=0.126  Sum_probs=25.2

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      .+.|++|||+.||+|..+|+..+++++.
T Consensus        37 ~g~s~~EIA~~lgiS~~tV~~~l~ra~~   64 (113)
T 1s7o_A           37 DDYSLAEIADEFGVSRQAVYDNIKRTEK   64 (113)
T ss_dssp             TCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3679999999999999999999998764

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=82.17  E-value=0.6  Score=39.00  Aligned_cols=31  Identities=10%  Similarity=0.135  Sum_probs=26.6

Q ss_pred             CCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577          431 SPDKEDLARRVGITVEKLERLIFITRMPLSM  461 (482)
Q Consensus       431 ~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL  461 (482)
                      +.+++|||+.|||++.+|+..+.++...+-.
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            5799999999999999999999887655444

---

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	482
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	6e-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) {	5e-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 (277), 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 = 6e-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 = 43.5 bits (103), 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 = 39.4 bits (92), Expect = 5e-05
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 9/78 (11%)

Query: 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MP 458
           SR +R          ++ E      ++    P  E++A+ +GI+ E+L + +        
Sbjct: 2   SRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI 55

Query: 459 LSMQQPVWADQDTTFQST 476
           LS+++  + D    +   
Sbjct: 56  LSLEEV-FRDFARDYSEL 72

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	482
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	100.0
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.83
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.77
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.48
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.94
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	98.82
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.64
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.52
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	96.4
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.32
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	94.42
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	93.05
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	92.43
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	90.91
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	90.4
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	90.31
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	87.51
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	85.52
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	84.61
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	81.81
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	81.8
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	80.78

>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=7.9e-34  Score=262.18  Aligned_cols=150  Identities=37%  Similarity=0.635  Sum_probs=122.0

Q ss_pred             CcHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------------hhhCCCCcHHHHH------
Q 011577          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ------------------SQFGREPTLIEWA------  309 (482)
Q Consensus       254 ~d~l~~YL~~i~~~~lLT~eEE~eL~~~Iq~l~~le~~~~~l~------------------~~~g~~pt~~ewA------  309 (482)
                      +||+++||++|+++||||+|||++|+++|+.+..+.....+..                  ...+..|...+|.      
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            5899999999999999999999999999998775543322221                  1122233322222      


Q ss_pred             ---HHhcCC---HHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhh
Q 011577          310 ---KAIGLS---CRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAS  383 (482)
Q Consensus       310 ---~a~gmd---d~eLi~~l~~Gd~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFST  383 (482)
                         ......   .+.+......|..|+++||.+|++||++||++|.+.|.+++||||||+|||++|+++|||++|++|+|
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               211111   24466777788899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhcCC
Q 011577          384 YAYWWVRQTIRKAIFQHSRT  403 (482)
Q Consensus       384 YA~~wIRnaI~~~Lrkq~r~  403 (482)
                      ||+|||+++|.++|++++|+
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=99.83  E-value=2.8e-21  Score=191.51  Aligned_cols=83  Identities=42%  Similarity=0.913  Sum_probs=76.8

Q ss_pred             HHHHHHhhcH----HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHH
Q 011577          318 DLKSELHSGN----SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (482)
Q Consensus       318 eLi~~l~~Gd----~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI  393 (482)
                      .+...++.|.    .|+++||+.|++||.+||++|.++|++++||||+|++||++|+++|||.+|++|+|||+||||++|
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            3445555565    699999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHh
Q 011577          394 RKAIFQH  400 (482)
Q Consensus       394 ~~~Lrkq  400 (482)
                      .++|+++
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=99.77  E-value=2.8e-19  Score=147.49  Aligned_cols=74  Identities=24%  Similarity=0.379  Sum_probs=69.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCC---CCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHHHhc
Q 011577          328 SSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~---g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lrkq~  401 (482)
                      ..+++||..|++||.++|++|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|+++||+..
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   78999999999999999999999999999999999999999999999853

>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=98.94  E-value=3.8e-10  Score=88.41  Aligned_cols=69  Identities=16%  Similarity=0.135  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHccCCCCCHhHHHHHHHHHHHHhHHhhCCCCCCchhhHHHHHHHHHHHHHHH
Q 011577          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  398 (482)
Q Consensus       328 ~Are~LI~snlrLV~sIAkrY~~~g~d~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRnaI~~~Lr  398 (482)
                      .+|++++..|.+.++.+|.+++++..+++|++||.|+.+|+.+++|++.  ..|.+|++++++|.+++++|
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

>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=98.82  E-value=3.5e-09  Score=80.74  Aligned_cols=58  Identities=26%  Similarity=0.461  Sum_probs=55.1

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhC--CCHHHHHHHHHHcCCCccC
Q 011577          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLSM  461 (482)
Q Consensus       404 irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LG--IS~etVk~~L~~ar~~lSL  461 (482)
                      ||+|.|+.+.++++.++.++|.+++||+||.+|||+.||  +++++|+.++..++.++||
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

>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=98.64  E-value=2.4e-08  Score=75.16  Aligned_cols=55  Identities=18%  Similarity=0.268  Sum_probs=51.8

Q ss_pred             CCcccchhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcC
Q 011577          402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR  456 (482)
Q Consensus       402 r~irlP~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar  456 (482)
                      +.|++|+++.+.++++.++.++|.+++||.||.+|||+.||+++++|..+|..++
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=98.52  E-value=6.4e-09  Score=82.28  Aligned_cols=72  Identities=15%  Similarity=0.226  Sum_probs=62.0

Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHc--CCCccCcccCCCCCCCcccccccCC
Q 011577          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQSTFLDA  480 (482)
Q Consensus       408 ~~v~e~l~kI~ka~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~a--r~~lSLD~~i~~d~~~~l~d~i~D~  480 (482)
                      +.+.+..+++.++...|.+++||.||.+|||+.|||++++|..++...  ...+|||.+++ +++.++.|+++|.
T Consensus         3 Rs~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~-d~~~~~~e~lpss   76 (77)
T d1rp3a1           3 RQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFR-DFARDYSELIPSS   76 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHTTTGGGS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCcc-CCCCchhccCCCC
Confidence            456688899999999999999999999999999999999999998754  46799999765 4456788998875

>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=96.40  E-value=0.0038  Score=45.87  Aligned_cols=39  Identities=31%  Similarity=0.479  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHHhh
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS  325 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l~~  325 (482)
                      ++.++..+|...+|++||.+|.|+.+|++.+++...+..
T Consensus        16 ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_          16 KIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             HHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            677789999999999999999999999999998876654

>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=95.32  E-value=0.018  Score=44.11  Aligned_cols=37  Identities=41%  Similarity=0.591  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHhcCCHHHHHHHH
Q 011577          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL  323 (482)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~gmdd~eLi~~l  323 (482)
                      +++++..+|+..+||+||.+|.|+.+||+.+++...+
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            6788999999999999999999999999998887654

>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=94.42  E-value=0.021  Score=42.49  Aligned_cols=32  Identities=19%  Similarity=0.163  Sum_probs=27.5

Q ss_pred             HhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          426 QEGNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       426 ~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      ..+..+.+++|||+.||+|+++|+..+++++.
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            33455789999999999999999999998864

>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=93.05  E-value=0.052  Score=40.11  Aligned_cols=30  Identities=10%  Similarity=0.053  Sum_probs=26.5

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHcCC
Q 011577          428 GNHSPDKEDLARRVGITVEKLERLIFITRM  457 (482)
Q Consensus       428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar~  457 (482)
                      +..+.|++|||+.||+|+++|+..+++++.
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            445789999999999999999999998754

>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=92.43  E-value=0.19  Score=36.89  Aligned_cols=37  Identities=30%  Similarity=0.561  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHhhhCCCCcHHHHHHHhc--CCHHHHHHH
Q 011577          286 IRLEKEKSKLQSQFGREPTLIEWAKAIG--LSCRDLKSE  322 (482)
Q Consensus       286 ~~le~~~~~l~~~~g~~pt~~ewA~a~g--mdd~eLi~~  322 (482)
                      -++.++..+|...+||+||.+|.|+++|  ++.+.+...
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            3567788999999999999999999987  445555443

>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=90.91  E-value=0.25  Score=37.20  Aligned_cols=42  Identities=19%  Similarity=0.317  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHhcCCCCcHHHHHHHhCC-CHHHHHHHHHHc
Q 011577          414 LSKVLEAKRLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFIT  455 (482)
Q Consensus       414 l~kI~ka~~eL~~e~gr~pS~eEIAe~LGI-S~etVk~~L~~a  455 (482)
                      -.+|-+.+..+..+.|..||++|||+.+|+ |..+|...+..-
T Consensus         7 Q~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~L   49 (71)
T d1jhfa1           7 QQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKAL   49 (71)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            345666777777888889999999999999 799999988743

>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=90.40  E-value=0.11  Score=42.46  Aligned_cols=31  Identities=13%  Similarity=0.040  Sum_probs=26.9

Q ss_pred             cCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          428 GNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       428 ~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      +..+.|++|||+.||||.++|+..+++|+..
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            3347899999999999999999999988653

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=90.31  E-value=0.14  Score=41.80  Aligned_cols=32  Identities=9%  Similarity=-0.125  Sum_probs=27.7

Q ss_pred             hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          427 EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .+..+.|+.|||+.||||.++|+..+++|+..
T Consensus        30 ~~~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~   61 (106)
T d1xsva_          30 FYLEDYSLSEIADTFNVSRQAVYDNIRRTGDL   61 (106)
T ss_dssp             HHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            34457899999999999999999999988653

>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=87.51  E-value=0.22  Score=37.20  Aligned_cols=42  Identities=12%  Similarity=0.059  Sum_probs=31.2

Q ss_pred             HHHHHHHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccC
Q 011577          420 AKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSM  461 (482)
Q Consensus       420 a~~eL~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSL  461 (482)
                      ...++...+..+.+..|||+.|||++.+|+..+......+-+
T Consensus        16 rE~~vl~~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   57 (70)
T d1yioa1          16 REQQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQKLNV   57 (70)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            334444445557899999999999999999998876554433

>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=85.52  E-value=0.6  Score=34.03  Aligned_cols=35  Identities=9%  Similarity=0.023  Sum_probs=27.8

Q ss_pred             HHhcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCCc
Q 011577          425 IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPL  459 (482)
Q Consensus       425 ~~e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~l  459 (482)
                      ......+.|.+|||+.||+++.+|+..+......+
T Consensus        13 l~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl   47 (65)
T d1l3la1          13 LRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRF   47 (65)
T ss_dssp             HHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence            33445578999999999999999999988665443

>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=84.61  E-value=0.68  Score=33.83  Aligned_cols=32  Identities=9%  Similarity=-0.009  Sum_probs=26.5

Q ss_pred             hcCCCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          427 EGNHSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       427 e~gr~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      ....+.+.+|||+.||+++.+|+..+......
T Consensus        15 l~~~G~s~~eIA~~L~is~~TV~~~~~~i~~K   46 (67)
T d1fsea_          15 LLVQDKTTKEIASELFISEKTVRNHISNAMQK   46 (67)
T ss_dssp             HHTTTCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HHHccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            34457899999999999999999998866544

>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=81.81  E-value=1.2  Score=32.54  Aligned_cols=27  Identities=15%  Similarity=0.261  Sum_probs=24.0

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHc
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFIT  455 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~a  455 (482)
                      +...|.+|||+.||||.++|+.+...|
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            556799999999999999999987765

>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=81.80  E-value=0.8  Score=33.55  Aligned_cols=29  Identities=17%  Similarity=0.127  Sum_probs=24.6

Q ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHcCCC
Q 011577          430 HSPDKEDLARRVGITVEKLERLIFITRMP  458 (482)
Q Consensus       430 r~pS~eEIAe~LGIS~etVk~~L~~ar~~  458 (482)
                      .+.+..|||+.||+++.+|+..+......
T Consensus        20 ~G~s~~eIA~~l~iS~~TV~~~~~~i~~K   48 (67)
T d1a04a1          20 QGLPNKMIARRLDITESTVKVHVKHMLKK   48 (67)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            36799999999999999999998765443

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=80.78  E-value=0.16  Score=40.05  Aligned_cols=52  Identities=13%  Similarity=0.205  Sum_probs=35.2

Q ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHHHcCCCccCcccCCCCCCCcccccccCCCC
Q 011577          429 NHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQSTFLDAAG  482 (482)
Q Consensus       429 gr~pS~eEIAe~LGIS~etVk~~L~~ar~~lSLD~~i~~d~~~~l~d~i~D~~g  482 (482)
                      +...|.+|||+.+|||.++|+.+...|...+-  .+...+.-..|.|++.|.+|
T Consensus        36 ~~~~tl~eI~~~lgiSrERVRQie~~al~kLr--~~~~~~~L~~~l~~~~~~~~   87 (87)
T d1ttya_          36 GKPKTLEEVGQYFNVTRERIRQIEVKALRKLR--HPSRSKYLKSLLSLMDENEG   87 (87)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHB--TTBSSHHHHHHHHHTTTCC-
T ss_pred             CCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHh--CcHHHHHHHHHHHhhcccCC
Confidence            45669999999999999999999887744332  12111112357777777776