Citrus Sinensis ID: 008556

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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-------490-------500-------510-------520-------530-------540-------550-------560-
Protein Sequence
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccHHHHHHHcHHHHHHHHHHcccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHcccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccEEEEEHHccccccccHHHHHHHccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHcccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHcccccccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHcccccccccccccccccccccccHHHHccccEEccccccHHHccccccEcccccccHccHHHHHHHcccccccEEcccEEccEEEcccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccHHHHHHHHHHHHcccccccccccccccccHHHccccccccHHHHHHHcccccccccccccccccHHcHHHHHcHcccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHcccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHc
Coil and Loop (DISEMBL)
meagrnllssppsfpsrtrvkhslsssasssssssapavasvptssvarhfptsvllqeqrdeyrpllhmfkedktsqatsdsrnIETEAFFveeknsgdlDQLVQDLEHqflhwpdlwnlsppmkrgedpsvsltmqslsndteesvdaepfDAVALARKALSASKEAAslaenpklngaeftdisltsslgypleevkqfsqprflerrskkrkvskpqvtnhetynSRKASVKKKLsegfdrndplrlflwgpetrklltaDEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRdlkselhsgnssREKLINANLRLVVHVAKQYqgrgislhdLLQEGSMGLMKSVEkfkpqagcrfasYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIqegnhspdkedlaRRVGITVEKLERLIFITrmplsmqqpvwadqdtTFQEITadtgveipdisVQKQLMRQHVRNLLtllnpkerCIVRLRFgiedgkpkslsevgnIFGLSKERVRQLESRALYRLKQSLggkasygyadlli
Flexible Loop (DISEMBL)
meagrnllssppsfpsrTRVKHSLSssasssssssapAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMfkedktsqatsdsrNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAslaenpklngaeFTDISLTSslgypleevkqfsqprflerrskkrkvskpqvtnhetynsrkasvkkklsegfdrndplrlfLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLqsqfgreptLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFqhsrtirlpeNIYTLLSKVLEAKRLYIqegnhspdkedlarRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNlltllnpkerCIVRLRfgiedgkpkslsevgnifglskeRVRQLESRALYrlkqslggkasygyadlli
Low Complexity Region (SEG)
MEAGRNLLSSPPSFPSRTRVKHslsssasssssssapavasvptssvaRHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDavalarkalsaskeaaslaeNPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered region (IsUnstruct)
******************************************************************************************FFV******DLDQLVQDLEHQFLHWPDLWNL******************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE*********FGREPTLIEWAKAIGLSCRDL************KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG********LARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY*****
Disordered Region (DISOPRED)
************************************************************************************************************EHQFLH**************************************************************KLNGAEFT***************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL*******SPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered Region (DISEMBL)
**********************************************VARHFPTSVLLQEQRDEYRPLLHMFKED*********RNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQS**********AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLE*************TNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK********SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered Region (DISPRO)
************************************PAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM**********************VDAEPFDAVALARKALSASKEAASLAENPKLN*****************************************************************RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV*ADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFExxxxxxxxxxxxxxxxxxxxxFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
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	561	2.2.26 [Sep-21-2011]
Q9LD95	547	RNA polymerase sigma fact	yes	no	0.955	0.979	0.550	1e-166
P26683	390	RNA polymerase sigma fact	yes	no	0.597	0.858	0.372	2e-66
O22056	572	RNA polymerase sigma fact	no	no	0.602	0.590	0.381	3e-65
P38023	399	RNA polymerase sigma fact	yes	no	0.531	0.746	0.394	1e-63
P74565	425	RNA polymerase sigma fact	N/A	no	0.552	0.729	0.342	6e-58
P52322	416	RNA polymerase sigma fact	no	no	0.532	0.718	0.345	1e-56
Q31ME3	320	RNA polymerase sigma fact	no	no	0.531	0.931	0.387	6e-56
Q03066	416	RNA polymerase sigma-C fa	no	no	0.534	0.721	0.360	7e-53
Q31QG5	320	RNA polymerase sigma fact	no	no	0.536	0.940	0.382	3e-52
Q59996	404	Probable RNA polymerase s	N/A	no	0.531	0.737	0.348	6e-52

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

 Score =  584 bits (1506), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 315/572 (55%), Positives = 401/572 (70%), Gaps = 36/572 (6%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASS---SSSSSAPAVASVPTSSVARHFPTSVLL 57
           MEA RNL+SS PSF ++T +K S SS +S       ++ P V S   +S++RHFP SVL 
Sbjct: 1   MEATRNLVSSSPSFQTKTHLKSSYSSPSSVVMLHDQTTTPVVNSRHLNSLSRHFPASVLS 60

Query: 58  QEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QDLEHQF 112
           QE R+E RPL H  ++D+TSQ T + R                 D+LV     +  E Q 
Sbjct: 61  QEPREESRPLSHALRDDRTSQLTLERRQ---------------FDELVSSREDEKFEQQL 105

Query: 113 LHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAA 170
           LH   LWNL  SP     + P+V   +           DAE  D VALA+KALSASK+AA
Sbjct: 106 LHSTGLWNLLISPLTSETKLPAVVSPL----------ADAELCDVVALAQKALSASKQAA 155

Query: 171 SLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYN 229
            L ++ + N ++   D   TSS     E+       R LERR+K R+  K    + E Y 
Sbjct: 156 LLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKRQLERRAKNRRAPKSNDVDDEGYV 215

Query: 230 SRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 289
            +K S KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K+KL+S
Sbjct: 216 PQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLES 275

Query: 290 QFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHD 349
           Q G EPT+ EWA+A+G+S   LKS++H G SSREKLI ANLRLVVH+AKQYQ RG++  D
Sbjct: 276 QNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQD 335

Query: 350 LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKV 409
           LLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y LL KV
Sbjct: 336 LLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKV 395

Query: 410 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 469
            EA++  +QEGN+ P KE+LA  VG++ EKL++L++ TR PLSMQQP+W+DQDTTFQEIT
Sbjct: 396 SEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEIT 455

Query: 470 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS 529
            D+G+E P +SV KQLMR HVRNLL +L+PKER I++LRFGI+ GK +SLSE+G I+GLS
Sbjct: 456 PDSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLS 515

Query: 530 KERVRQLESRALYRLKQSLGGKASYGYADLLI 561
           KERVRQLESRALYRLKQ++     + YADLL+
Sbjct: 516 KERVRQLESRALYRLKQNMNSHGLHAYADLLV 547

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

 Score =  254 bits (648), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 130/349 (37%), Positives = 220/349 (63%), Gaps = 14/349 (4%)

Query: 198 EVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPE 257
           ++ +F +P+  E  +K  K +K +         R  S KK  +E     D +RL+L    
Sbjct: 44  DIDEFLEPQTDEDDAKSGKAAKSR--------RRTQSKKKHYTE-----DSIRLYLQEIG 90

Query: 258 TRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 317
             +LL ADEE EL  +I DL+ LE+ + +L  +  R+P   EWA+A+ L     +  LH 
Sbjct: 91  RIRLLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQLPLPAFRYRLHI 150

Query: 318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 377
           G  +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF  + G +F++YA
Sbjct: 151 GRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 210

Query: 378 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 437
            WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P +E++A R+ +T+
Sbjct: 211 TWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTI 270

Query: 438 EKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 497
           EKL  +    ++P+S++ P+  ++D+   +     G E P+  V K L+R+ +  +L  L
Sbjct: 271 EKLRFIAKSAQLPISLETPIGKEEDSRLGDFIESDG-ETPEDQVSKNLLREDLEKVLDSL 329

Query: 498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
           +P+ER ++RLR+G++DG+ K+L E+G IF +++ER+RQ+E++AL +L+ 
Sbjct: 330 SPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 378

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

 Score =  249 bits (637), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 131/343 (38%), Positives = 215/343 (62%), Gaps = 5/343 (1%)

Query: 206 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 264
           R  ER++++ K  +   +   +  +  +  KK+L ++  D NDPLR       + KLLT 
Sbjct: 216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275

Query: 265 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 324
            EE EL A IQDL++LE+ +++L  + GR+PT  +WA A G+  + L+  +H G   ++K
Sbjct: 276 REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDK 335

Query: 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384
           +I +N+RLV+ +AK YQG G++L DL+QEG  GL++  EKF    G +F++YA+WW++Q 
Sbjct: 336 MIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQA 395

Query: 385 IRKAIFQHSRTIRLPENIYTLLSKVLEA-KRLYIQEGNHSPDKEDLARRVGITVEKLERL 443
           +RK++   SR IRLP ++     +V EA K+LY + G H P  E++A   G+++++L  +
Sbjct: 396 VRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKH-PKNEEIAEATGLSMKRLMAV 454

Query: 444 IFITRMPLSMQQPVWADQDTTFQEITAD-TGVEIPDISVQKQLMRQHVRNLLTLLNPKER 502
           +   + P S+ Q +  +Q+    E+ AD   V   DI + K+ MRQ +  +L  L  +E+
Sbjct: 455 LLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILI-KEFMRQDLDKVLDSLGTREK 513

Query: 503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
            ++R RFG+EDG+ K+L E+G + G+S+ERVRQ+ES A  +LK
Sbjct: 514 QVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLK 556

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

 Score =  244 bits (624), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 118/299 (39%), Positives = 199/299 (66%), Gaps = 1/299 (0%)

Query: 247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 306
           D +RL+L      +LL ADEE EL  QI DL+ LE+ + +L  Q  R P+  EWA A+  
Sbjct: 89  DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148

Query: 307 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 366
              + +  L  G  +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF 
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 208

Query: 367 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 426
            + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P +
Sbjct: 209 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTE 268

Query: 427 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 486
           E++A R+ +T+EKL  +    ++P+S++ P+  ++D+   +     G E P+  V K L+
Sbjct: 269 EEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDEVAKNLL 327

Query: 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           R+ +  +L+ L+P+ER ++RLR+G++DG+ K+L E+G +F +++ER+RQ+E++AL +L+
Sbjct: 328 REDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLR 386

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

 Score =  225 bits (574), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 123/359 (34%), Positives = 209/359 (58%), Gaps = 49/359 (13%)

Query: 231 RKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQ 290
           RK +VKKK        D +R++L      +LL A+EE EL  QI DL+ LE  +  L  Q
Sbjct: 59  RKDAVKKKPYT----EDSIRIYLQEIGRIRLLRAEEEIELARQIADLLELELIRDNLTLQ 114

Query: 291 FGREPTLIEWAKAI----------------GLSCRDLKSELHSGNS-------------- 320
             R+P+ +EW K +                    +D+ S L + ++              
Sbjct: 115 LERQPSELEWGKQVWKLETAKQRLVGDKKKEPKKKDIDSYLANPDNELSLENEWSQQPNK 174

Query: 321 --------------SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 366
                         +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF 
Sbjct: 175 NFAAFRRRLFLDRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 234

Query: 367 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 426
            + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P +
Sbjct: 235 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTE 294

Query: 427 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 486
           E++A ++ +T+EKL  +    ++P+S++ P+  ++D+   +     G E P+  V K L+
Sbjct: 295 EEIAEKMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDEVSKNLL 353

Query: 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           R+ + N+L  L+P+ER ++RLR+G++DG+ K+L E+G IF +++ER+RQ+E++AL +L+
Sbjct: 354 REDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 412

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

 Score =  221 bits (563), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 117/339 (34%), Positives = 201/339 (59%), Gaps = 40/339 (11%)

Query: 247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEK------------------------ 282
           D +R++L      +LL A+EE EL  +I DL++LE+                        
Sbjct: 67  DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126

Query: 283 ----EKSK-------LQSQFGRE----PTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 327
               EKS+       +++  G+     P L EW           K  L+ G  ++EK++ 
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186

Query: 328 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 387
           +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF  + G +F++YA WW+RQ I +
Sbjct: 187 SNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITR 246

Query: 388 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 447
           AI   SRTIRLP ++Y  +S++ +  ++  QE    P +E++A ++ +T+EKL  +    
Sbjct: 247 AIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSA 306

Query: 448 RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRL 507
           ++P+S++ P+  ++D+   +     G E P+  V K L+R+ + N+L  L+P+ER ++RL
Sbjct: 307 QLPISLETPIGKEEDSRLGDFIEADG-ETPEDEVSKNLLREDLENVLDTLSPRERDVLRL 365

Query: 508 RFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
           R+G++DG+ K+L E+G IF +++ER+RQ+E++AL +L+ 
Sbjct: 366 RYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 404

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

 Score =  219 bits (557), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 116/299 (38%), Positives = 187/299 (62%), Gaps = 1/299 (0%)

Query: 247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 306
           D +R +L      +LLTA+EE     Q+Q L+ L   +++L+ + G EP+  EWA A+ L
Sbjct: 11  DLVRAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDL 70

Query: 307 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 366
           +  DL  ++  G  ++ K+I ANLRLVV +AK+YQ R +   DL+QEG++GL + VEKF 
Sbjct: 71  NLEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFD 130

Query: 367 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 426
           P  G +F++YAYWW+RQ I +AI Q SRTIRLP +I   L+K+ + +R   Q+   S   
Sbjct: 131 PSKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATA 190

Query: 427 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 486
            +LA  + + +E++   I + R P+S+   V   QDT  QE+  D     P   V+++ +
Sbjct: 191 SELAEVLELPLEQVREYIQMNRQPVSLDVKVGDSQDTELQELLEDEQSS-PSDYVEQESL 249

Query: 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           R+ +RNL+  L P+++ ++ LR+G+++G   SL++VG    +S+ERVR+LE +A+  L+
Sbjct: 250 RRDLRNLMAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAMDHLR 308

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

 Score =  208 bits (530), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 124/344 (36%), Positives = 190/344 (55%), Gaps = 44/344 (12%)

Query: 246 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE---------------------KEK 284
            D +RL+L      +LL  DEE     ++Q  ++L                      + +
Sbjct: 59  TDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYLKLRIVLANAVKQGDEVATPYLHLIEVQ 118

Query: 285 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN----------------------SSR 322
            +L S+ G  P+L  WA   G++  DLK  L  G                        S+
Sbjct: 119 ERLASELGHRPSLERWAATAGINLCDLKPILSEGKRRWAEIAKMTVEELEKMQSQGLQSK 178

Query: 323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 382
           E +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF++YAYWW+R
Sbjct: 179 EHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIR 238

Query: 383 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 442
           Q I +AI   SRTIRLP +I   L+K+ +A+R   QE   +P  EDLA  + +T  ++  
Sbjct: 239 QGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLEDLAIELDMTPTQVRE 298

Query: 443 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKER 502
           ++      +S++  V  D+DT   E+    GV  P+  + ++ +++ +++LL  L  +ER
Sbjct: 299 VLLRVPRSVSLETKVGKDKDTELGELLETDGV-TPEEMLMRESLQRDLQHLLADLTSRER 357

Query: 503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
            ++ +RFG+ DG P SL+E+G    LS+ERVRQ+ES+AL +L+Q
Sbjct: 358 DVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKLRQ 401

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

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

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

 Score =  206 bits (524), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 116/303 (38%), Positives = 188/303 (62%), Gaps = 2/303 (0%)

Query: 246 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG-REPTLIEWAKAI 304
           +D +R +L       LLT +EE  L  ++Q  ++L++ +  LQS+ G R+P+ +EWA A 
Sbjct: 9   SDLVRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAA 68

Query: 305 GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK 364
           GLS  +L+ + H G  ++ K+I ANLRLVV VAK+Y  R + L DL+QEG++G+ + VEK
Sbjct: 69  GLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEK 128

Query: 365 FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSP 424
           F P  G RF++YAYWW+RQ I +AI + +RTIRLP +I   L+K+ + +R   Q+   + 
Sbjct: 129 FDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKMQRQLSQQLGRTA 188

Query: 425 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 484
              +LA  + +T  ++   +   R PLS+   V  +QDT   ++  +T    P+    + 
Sbjct: 189 TLPELAAALDLTPAQVRDYLEKARHPLSLDLRVGDNQDTELGDLL-ETDCTTPEEFTLQA 247

Query: 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544
            MR+ +  LL  L  ++R ++ LR+G+EDG+  +L+ +G+   +S+ERVRQLE  AL+ L
Sbjct: 248 SMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRERVRQLEREALHTL 307

Query: 545 KQS 547
           +Q+
Sbjct: 308 RQA 310

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

 Score =  205 bits (522), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 119/341 (34%), Positives = 189/341 (55%), Gaps = 43/341 (12%)

Query: 246 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK------------------- 286
            D +RL+L       LL  DEE  +  Q+Q  +RL + +++                   
Sbjct: 48  TDLVRLYLQDIGRIPLLKRDEEVHIAQQVQSYLRLVEIQNRAAESDAAIDQYQTAIAVHD 107

Query: 287 -LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN----------------------SSRE 323
            L  Q G  P+   WAK +G +   LK  L SG                       +++ 
Sbjct: 108 QLLVQLGHRPSYERWAKILGQTVATLKQTLKSGKKRWAELAGLTVEELENIEKQGITAKA 167

Query: 324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 383
            +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF++Y+YWW+RQ
Sbjct: 168 HMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYSYWWIRQ 227

Query: 384 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 443
            I +AI   SR IRLP +I   L+K+  A+R   QE  H+P  +++A  +G+T E++  +
Sbjct: 228 GITRAIATQSRMIRLPVHITEKLNKIKRAQRKISQEKGHTPKIDEVAEELGMTPEQVREV 287

Query: 444 IFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERC 503
           +      +S++  V  D+DT   ++  +T  + P+  + ++ ++  ++ +L  L P+E+ 
Sbjct: 288 LTQVPRSVSLELKVGQDKDTELMDLL-ETDTQSPEDELMREALQNDMQEILLDLTPREQE 346

Query: 504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544
           ++ LRFG +DG   SLSE+G I  LS+ERVRQ+E++AL +L
Sbjct: 347 VIALRFGFQDGVAHSLSEIGRILNLSRERVRQIEAKALQKL 387

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)

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	561
224068757	535	predicted protein [Populus trichocarpa]	0.951	0.998	0.628	0.0
297741628	561	unnamed protein product [Vitis vinifera]	0.989	0.989	0.633	0.0
359481391	572	PREDICTED: RNA polymerase sigma factor r	0.991	0.972	0.620	0.0
255556952	548	RNA polymerase sigma factor rpoD, putati	0.962	0.985	0.615	0.0
356536959	571	PREDICTED: RNA polymerase sigma factor r	0.992	0.975	0.573	1e-174
356548319	574	PREDICTED: RNA polymerase sigma factor r	0.992	0.970	0.562	1e-174
449451030	562	PREDICTED: RNA polymerase sigma factor s	0.991	0.989	0.566	1e-171
312282671	547	unnamed protein product [Thellungiella h	0.955	0.979	0.554	1e-166
297827203	546	RNA polymerase sigma-70 factor [Arabidop	0.955	0.981	0.555	1e-166
18404292	547	RNApolymerase sigma-subunit F [Arabidops	0.955	0.979	0.550	1e-164

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

 Score =  711 bits (1836), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/560 (62%), Positives = 432/560 (77%), Gaps = 26/560 (4%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSAPAVASVPTSSVARHFPTSVLLQEQ 60
           MEAGR LLSS PSFP+RT +K+SL+SS       + PAV+S+PT+S A+HFPTSVLLQEQ
Sbjct: 1   MEAGRTLLSSSPSFPTRTHLKNSLTSSVLILREQATPAVSSIPTTSTAQHFPTSVLLQEQ 60

Query: 61  RDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWN 120
           RDE+RPL ++FKED+ SQAT D R  E      E K+S +LDQLV++ E+Q  HWP  WN
Sbjct: 61  RDEFRPLQNIFKEDRASQATLDRRKTEIGTSGHEGKDSDELDQLVENFEYQLHHWPAYWN 120

Query: 121 LSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNG 180
           L                      T++ +D EP + + LA++ALSASK AA LA+N     
Sbjct: 121 L----------------------TDKLIDVEPTNVINLAKRALSASKHAAFLADN----N 154

Query: 181 AEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLS 240
            +  +++ TSS  + LEEVK     R L R+S  R+  K +    ETY+S+ A ++K+LS
Sbjct: 155 TDLDNLASTSSSSFSLEEVKIVRSRRHLARQSLNRRAPKTKDLIFETYDSKSADIQKRLS 214

Query: 241 EGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEW 300
           +GFD NDPLRLFLWGPET++LLTA EEFELIAQIQDL+ LE  K++L+SQFGREPTL+EW
Sbjct: 215 QGFDPNDPLRLFLWGPETKQLLTAKEEFELIAQIQDLMNLEGVKNRLESQFGREPTLVEW 274

Query: 301 AKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK 360
           A+A+GLSC  LK +LHSGN SREKLINANLR+VVH+AK+YQ RG+ L DLLQEG++GLMK
Sbjct: 275 AQAVGLSCHVLKLQLHSGNRSREKLINANLRMVVHIAKRYQNRGLGLQDLLQEGTVGLMK 334

Query: 361 SVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG 420
           S+EKFKPQAGCRFA+YAYWW+RQTI KAIFQHSRTIRLPEN+Y LL KV+EAKR YIQEG
Sbjct: 335 SIEKFKPQAGCRFATYAYWWIRQTITKAIFQHSRTIRLPENVYGLLGKVMEAKRSYIQEG 394

Query: 421 NHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480
           NH P  E++ARRVGI ++KLE+L+  TR PLSMQQ VW+DQ+TTFQEITADT +EIPD+S
Sbjct: 395 NHQPTAEEIARRVGIAIDKLEKLLCFTRTPLSMQQTVWSDQNTTFQEITADTEIEIPDMS 454

Query: 481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540
           V KQLMR+H+R LL +L+ KER I+RLRFGIEDGK KSLSE+GN+FGLSKERVRQLESRA
Sbjct: 455 VAKQLMRKHIRGLLNILSLKERRIIRLRFGIEDGKQKSLSEIGNVFGLSKERVRQLESRA 514

Query: 541 LYRLKQSLGGKASYGYADLL 560
           LY+LKQ +G      YADLL
Sbjct: 515 LYKLKQCVGSHGLDAYADLL 534

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  710 bits (1832), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/567 (63%), Positives = 434/567 (76%), Gaps = 12/567 (2%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSAPAVASVPTSSVARHFPTSVLLQEQ 60
           MEAG N+LSS PSFP RT  ++S SSS        APAVAS+PT+ +AR FPTSVLLQEQ
Sbjct: 1   MEAGTNILSSTPSFPPRTHFRNS-SSSVLMLHDQVAPAVASIPTT-IARKFPTSVLLQEQ 58

Query: 61  RDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWN 120
           RDEYRP     K+++T QAT + R +E      +E+NS D +Q + + E Q L  P LW 
Sbjct: 59  RDEYRPFPQALKDERTFQATLEKRQMEI-VVSADEENSDDHNQYMVNFERQLLLQPGLWY 117

Query: 121 LSPPMKRGE-DPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLN 179
             P  + GE  P  S  M+S++ D E S+D +P D +ALA+KALSASK+A SL EN KL 
Sbjct: 118 SLPSSQTGEKSPFSSSIMKSITTDIENSMDVKPCDVLALAKKALSASKQAVSLYENAKLL 177

Query: 180 GAEFTD-----ISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKAS 234
           GA+  D     +   SS   PLEE K     R LERRSKKR+   P+V  HE + SR+A 
Sbjct: 178 GADLEDSPSPSLGAISSPNLPLEE-KTVRSTRLLERRSKKRR--NPKVAVHENHGSRRAE 234

Query: 235 VKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE 294
           V++K++EG+D  DPLRLFLWGPETRKLLTA EE ELI QIQ+L+RLE+ K +LQS   RE
Sbjct: 235 VQRKINEGYDPKDPLRLFLWGPETRKLLTAKEESELIVQIQELMRLEEVKKRLQSHLKRE 294

Query: 295 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG 354
           PT++EWA+A+GLSC+ L+S+LHSGN SR+KLI ANLR+VVH+AKQYQGRG++L DLLQEG
Sbjct: 295 PTVVEWAEAVGLSCQVLQSQLHSGNRSRQKLIYANLRMVVHIAKQYQGRGLNLQDLLQEG 354

Query: 355 SMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKR 414
           SMGLM SVEKFKP AGCRFASYAYWW+RQ +RKAIFQHSRTIRLPEN+Y+LL KV EAKR
Sbjct: 355 SMGLMNSVEKFKPNAGCRFASYAYWWIRQAVRKAIFQHSRTIRLPENMYSLLGKVKEAKR 414

Query: 415 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV 474
           L+IQEG+H P KE++A RVGIT+EKL+RL+  TRMPLSMQQPVWADQDTTFQE+TADTG+
Sbjct: 415 LFIQEGHHDPTKEEIAERVGITIEKLQRLLLHTRMPLSMQQPVWADQDTTFQEVTADTGI 474

Query: 475 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 534
           EIPD+SV KQLMRQHVRNLL +L PKER I+RLRFGI DG P++LSE+G +FG SKERVR
Sbjct: 475 EIPDVSVAKQLMRQHVRNLLHVLTPKERRIIRLRFGIGDGIPRTLSEIGLVFGFSKERVR 534

Query: 535 QLESRALYRLKQSLGGKASYGYADLLI 561
           QLE RAL++LKQ L       Y DLL+
Sbjct: 535 QLEQRALHKLKQCLSSHGLESYTDLLV 561

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 =  705 bits (1819), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/577 (62%), Positives = 434/577 (75%), Gaps = 21/577 (3%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSAS----------SSSSSSAPAVASVPTSSVARH 50
           MEAG N+LSS PSFP RT  ++S SS  +                APAVAS+PT+ +AR 
Sbjct: 1   MEAGTNILSSTPSFPPRTHFRNSSSSGNAFFFYVVLFVLMLHDQVAPAVASIPTT-IARK 59

Query: 51  FPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEH 110
           FPTSVLLQEQRDEYRP     K+++T QAT + R +E      +E+NS D +Q + + E 
Sbjct: 60  FPTSVLLQEQRDEYRPFPQALKDERTFQATLEKRQMEI-VVSADEENSDDHNQYMVNFER 118

Query: 111 QFLHWPDLWNLSPPMKRGE-DPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEA 169
           Q L  P LW   P  + GE  P  S  M+S++ D E S+D +P D +ALA+KALSASK+A
Sbjct: 119 QLLLQPGLWYSLPSSQTGEKSPFSSSIMKSITTDIENSMDVKPCDVLALAKKALSASKQA 178

Query: 170 ASLAENPKLNGAEFTD-----ISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 224
            SL EN KL GA+  D     +   SS   PLEE K     R LERRSKKR+   P+V  
Sbjct: 179 VSLYENAKLLGADLEDSPSPSLGAISSPNLPLEE-KTVRSTRLLERRSKKRR--NPKVAV 235

Query: 225 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 284
           HE + SR+A V++K++EG+D  DPLRLFLWGPETRKLLTA EE ELI QIQ+L+RLE+ K
Sbjct: 236 HENHGSRRAEVQRKINEGYDPKDPLRLFLWGPETRKLLTAKEESELIVQIQELMRLEEVK 295

Query: 285 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 344
            +LQS   REPT++EWA+A+GLSC+ L+S+LHSGN SR+KLI ANLR+VVH+AKQYQGRG
Sbjct: 296 KRLQSHLKREPTVVEWAEAVGLSCQVLQSQLHSGNRSRQKLIYANLRMVVHIAKQYQGRG 355

Query: 345 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 404
           ++L DLLQEGSMGLM SVEKFKP AGCRFASYAYWW+RQ +RKAIFQHSRTIRLPEN+Y+
Sbjct: 356 LNLQDLLQEGSMGLMNSVEKFKPNAGCRFASYAYWWIRQAVRKAIFQHSRTIRLPENMYS 415

Query: 405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464
           LL KV EAKRL+IQEG+H P KE++A RVGIT+EKL+RL+  TRMPLSMQQPVWADQDTT
Sbjct: 416 LLGKVKEAKRLFIQEGHHDPTKEEIAERVGITIEKLQRLLLHTRMPLSMQQPVWADQDTT 475

Query: 465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 524
           FQE+TADTG+EIPD+SV KQLMRQHVRNLL +L PKER I+RLRFGI DG P++LSE+G 
Sbjct: 476 FQEVTADTGIEIPDVSVAKQLMRQHVRNLLHVLTPKERRIIRLRFGIGDGIPRTLSEIGL 535

Query: 525 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 561
           +FG SKERVRQLE RAL++LKQ L       Y DLL+
Sbjct: 536 VFGFSKERVRQLEQRALHKLKQCLSSHGLESYTDLLV 572

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  692 bits (1785), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/569 (61%), Positives = 426/569 (74%), Gaps = 29/569 (5%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSS-------SSAPAVASVPTSSVARHFPT 53
           ME  R  LSSPP FPSRT  K+SLSSS +   +        + PAV S PT+S+AR+FPT
Sbjct: 1   METARTFLSSPPPFPSRTHFKNSLSSSDAYVDNFVFMLHEQAVPAVTSAPTTSIARNFPT 60

Query: 54  SVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFL 113
           SVLLQEQRDE+RPLL++FKEDKT QAT D++ ++      E   S  LDQL+    H  L
Sbjct: 61  SVLLQEQRDEFRPLLNIFKEDKTFQATVDTKQMDPGTSDQEGICSDVLDQLIL---HSNL 117

Query: 114 HWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLA 173
            W                  SLTMQS++ +T+E +  EP + + LARKALSASKEAA LA
Sbjct: 118 SW------------------SLTMQSITTNTDELMVVEPTNVIDLARKALSASKEAALLA 159

Query: 174 EN-PKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRK 232
           +    L+    T +  T    + LEEVK     R LER+SK R+V+K +   HE Y+SR+
Sbjct: 160 QKCANLDDTVSTGLEPTDLSNFSLEEVKTVRSTRRLERQSKNRRVTKTKEIFHEPYSSRR 219

Query: 233 ASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 292
           A V+KK++EGFD  DPLRLFLWGPET++LLTA EE ELI Q+QDL+ LE  K K + QFG
Sbjct: 220 AGVQKKINEGFDPKDPLRLFLWGPETKQLLTAKEESELIGQVQDLMSLENVKEKFKLQFG 279

Query: 293 REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 352
           R+PTL+EWA A+GLS   ++S+LHSGN SREKLINANLR+VVH+AKQYQGRG+SL DLLQ
Sbjct: 280 RDPTLVEWADAVGLSYSVMQSQLHSGNRSREKLINANLRMVVHIAKQYQGRGLSLQDLLQ 339

Query: 353 EGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA 412
           EGSMGLMKS+EKFKPQ GCRFA+YAYWW+RQT+RKAIFQHSRTIRLPEN+Y  L KV EA
Sbjct: 340 EGSMGLMKSIEKFKPQVGCRFATYAYWWIRQTVRKAIFQHSRTIRLPENVYHTLGKVSEA 399

Query: 413 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADT 472
           KR YI EGNH+P KE+LA+R+GIT  +LERL+++ RMPLSMQQ VWADQ+TTFQEITAD 
Sbjct: 400 KRSYIMEGNHNPTKEELAKRIGITTVRLERLLYMARMPLSMQQTVWADQETTFQEITADI 459

Query: 473 GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKER 532
            VEIP++ V KQLMR+HV +LL +LNP+ER I+RLR+GIEDGK KSLSE+G++FGLSKER
Sbjct: 460 EVEIPELCVAKQLMRKHVLSLLNILNPRERKIIRLRYGIEDGKKKSLSEIGSVFGLSKER 519

Query: 533 VRQLESRALYRLKQSLGGKASYGYADLLI 561
           VRQLESRALY+LKQ L       YADLL+
Sbjct: 520 VRQLESRALYKLKQCLASHGLEAYADLLV 548

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 =  617 bits (1592), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 330/575 (57%), Positives = 421/575 (73%), Gaps = 18/575 (3%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSS------SSAPAVASVPTSSVARHFPTS 54
           ME  R +  S P FP RT    S   S+SS+SS       ++P VAS  ++  A++FP S
Sbjct: 1   MEFARTMFCSSPPFPPRTHHPWSTLPSSSSTSSVLMLHEQASPTVASWSSNFSAQNFPAS 60

Query: 55  VLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLH 114
           VLL EQRDEYRPLLHM KEDKTSQA   +R ++T     EE N+ + DQ+V D      H
Sbjct: 61  VLLPEQRDEYRPLLHMSKEDKTSQAMLSTRQMDTVTVH-EENNTENADQVVLDFRKHLHH 119

Query: 115 WPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAE 174
           WP+L   S  +  GE  + S T++ +S D E   +   F+ V+LA+KALS SK+ +S+ E
Sbjct: 120 WPNLQLTSSQI--GE-VAASSTLEHVSVDLERRPNGVQFNGVSLAKKALSTSKQESSVVE 176

Query: 175 NPKLNGAEFTDISLTS-SLGYP-LEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRK 232
           + K   A+    SL S SL  P +   K     R LERRSK+RKV K +V + ETY +RK
Sbjct: 177 DLKSIKADDVPFSLASTSLADPSIGRNKTVRSTRLLERRSKQRKVPKSKVIDDETYLARK 236

Query: 233 ASVKKKL------SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK 286
              ++KL      +E  D++DPLRLFLWGPET++LLT ++E +LI+QIQDL+RLE+ K+ 
Sbjct: 237 DDAQEKLRAEKKKNEELDQDDPLRLFLWGPETKQLLTLEQESQLISQIQDLLRLEEVKTN 296

Query: 287 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGIS 346
           LQSQFGREPT+ EWA+  GL+CR L+S+LHSGN SREKLI ANLR+VVHVAK YQGRG+S
Sbjct: 297 LQSQFGREPTMAEWAEGAGLNCRLLQSQLHSGNRSREKLIQANLRMVVHVAKSYQGRGLS 356

Query: 347 LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL 406
           L DLLQEGSMGLMKSVEKF P AG RF +YA+WW+RQ IRKA+F+HSRTIRLPE ++ LL
Sbjct: 357 LQDLLQEGSMGLMKSVEKFNPLAGSRFGNYAFWWIRQAIRKAVFRHSRTIRLPEKVFILL 416

Query: 407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ 466
            KV+EAK+LYIQEGN  P KE+LARRVG+TVEK+++L+F  R+P+SMQQ VWADQ+TTFQ
Sbjct: 417 GKVMEAKKLYIQEGNLHPTKEELARRVGVTVEKIDKLLFSARIPISMQQTVWADQNTTFQ 476

Query: 467 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF 526
           EITAD  VE  D++V+KQLMR+HV N+L++L+PKER I+RLR+G EDG+ KSLSE+G+IF
Sbjct: 477 EITADPTVEATDVTVEKQLMRRHVLNVLSVLHPKERRIIRLRYGFEDGEQKSLSEIGDIF 536

Query: 527 GLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 561
           GLSKERVRQLE RALY+LK+ L  +    Y DLL+
Sbjct: 537 GLSKERVRQLEIRALYKLKKCLVKQGLDAYVDLLL 571

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 =  617 bits (1590), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 325/578 (56%), Positives = 417/578 (72%), Gaps = 21/578 (3%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSS-------SAPAVASVPTSSVARHFPT 53
           ME  R +  S P FP RT   H  ++   SSS+S       ++P VAS  ++  A++FP 
Sbjct: 1   MEFSRTMFCSSPPFPPRTH--HPWNTLPLSSSTSVLMLREQASPTVASWSSNFSAQNFPA 58

Query: 54  SVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFL 113
           SVLLQEQRDEYRPLLHM KEDKTSQA   +R ++T     EE N+ + DQ+V D      
Sbjct: 59  SVLLQEQRDEYRPLLHMSKEDKTSQAMLSTRQMDT-VMVHEENNTENADQVVLDFRKHLH 117

Query: 114 HWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLA 173
           +WP L NL    + GE  S S T+Q +S+D +   +    + V+LA+KALS SK+ +S+ 
Sbjct: 118 YWPHLQNLLASSQTGE-ISASSTLQQVSSDLDRHTNGVQCNRVSLAKKALSTSKQGSSVV 176

Query: 174 ENPKLNGAEFTDISL---TSSLGYP-LEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYN 229
           E+ K   A+   I     ++ L  P +   K     R LERRSK+RKV K +V + ETY 
Sbjct: 177 EDLKSIKADDDSIPFGLASTGLADPSIGRNKTVRSTRLLERRSKQRKVPKSKVIDDETYL 236

Query: 230 SRKAS------VKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKE 283
           +RK        V+KK +E  D+NDPL  FL GPET++LLT ++E +LI+QIQDL+RLE+ 
Sbjct: 237 ARKDDAHEKLRVEKKKNEELDQNDPLCFFLRGPETKQLLTLEQESQLISQIQDLLRLEEV 296

Query: 284 KSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGR 343
           K+KLQSQFGREPT+ EWA+ +GL+CR L ++L SG+ SREKLI ANLR+VVHVAK YQGR
Sbjct: 297 KTKLQSQFGREPTMAEWAEGVGLNCRMLHAQLRSGSRSREKLIQANLRMVVHVAKSYQGR 356

Query: 344 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 403
           G+SL DLLQEGSMGLMKSVEKF P  G RF +YA+WW+RQ IRKA+F+HSRTIRLPE ++
Sbjct: 357 GLSLQDLLQEGSMGLMKSVEKFNPLVGSRFGNYAFWWIRQAIRKAVFRHSRTIRLPEKVF 416

Query: 404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 463
            LL KV+EAK+LYIQEGN  P KE+LARRVG+TVEK+++L+F  R+P+SMQQ VWADQ+T
Sbjct: 417 ILLGKVMEAKKLYIQEGNLHPTKEELARRVGVTVEKIDKLLFSARIPISMQQTVWADQNT 476

Query: 464 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVG 523
           TFQEITAD  VE  D+SV+KQLMRQHV N+L++L+PKER I+RLR+G EDG+ KSLSE+G
Sbjct: 477 TFQEITADPTVEATDVSVEKQLMRQHVLNVLSILHPKERRIIRLRYGFEDGEQKSLSEIG 536

Query: 524 NIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 561
           +IFGLSKERVRQLE RALY+LK+ L  +    Y DLL+
Sbjct: 537 DIFGLSKERVRQLEIRALYKLKKCLVKQGLDAYVDLLL 574

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 =  607 bits (1564), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 320/565 (56%), Positives = 413/565 (73%), Gaps = 9/565 (1%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSAPA----VASVP-TSSVARHFPTSV 55
           MEAG NLLSS   F SR   +  L+ S SS++S S+ +    V   P  +S AR+F TS 
Sbjct: 1   MEAGLNLLSSSSPFISRCHPRSFLAPSCSSAASPSSSSSSSSVYMFPEQASPARYFSTSF 60

Query: 56  LLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHW 115
           L QEQ  E RP   + K+D++SQ T + R IE  +  ++E +  D D L+ +L+HQ + W
Sbjct: 61  LSQEQHHECRPQSQILKDDRSSQMTLERRLIE-RSVPIDEGSRDDHDHLIWELKHQAVEW 119

Query: 116 PDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAEN 175
           P L +  PP++  E    S+  +S +   E  V  EP + +ALA+KALSASK+AA L + 
Sbjct: 120 PGLLSSWPPVQMEEYKISSIEKESYNAAGEMLVKDEPENVIALAKKALSASKQAALLVDE 179

Query: 176 PKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASV 235
            +L G      SL  SL    +E +     R  +RRSKKRKV K   T  E  N R    
Sbjct: 180 TELVGTSLDYSSLDDSLS---KEGRTVRSTRLQDRRSKKRKVPKHVTTIDEISNFRGKDS 236

Query: 236 KKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 295
           ++K SE FD NDPLRLFLWGPET+KLLTA EE ELI QIQDL+ L+  K++LQSQF REP
Sbjct: 237 RRKTSEKFDPNDPLRLFLWGPETKKLLTAQEESELIVQIQDLMILDNVKARLQSQFDREP 296

Query: 296 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGS 355
           TL+EWA+A+G++C+ L+S+LH   +SREKLINANLR+VVH+AKQYQGRG+SLHDLLQ GS
Sbjct: 297 TLVEWAEALGITCQHLQSQLHVFQTSREKLINANLRMVVHIAKQYQGRGLSLHDLLQVGS 356

Query: 356 MGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 415
           +GLMKSVEKFKPQAGCRF SYAYWW+R +I KAIFQHSRTIRLPEN+Y LL KV EAK  
Sbjct: 357 LGLMKSVEKFKPQAGCRFGSYAYWWIRHSITKAIFQHSRTIRLPENVYALLGKVTEAKNY 416

Query: 416 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE 475
           +++ GN+ P KE+LA RVGITVE+ ++L+F++R+P S+QQPVWADQ+TTFQEITAD+ V+
Sbjct: 417 FVRAGNYKPSKEELAARVGITVERFDKLMFMSRIPRSLQQPVWADQETTFQEITADSEVD 476

Query: 476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQ 535
            PD+SV+++LMR+H+RNLL++L+PKER I+RLRFGIEDG+ K+L E+GN+FGLSKERVRQ
Sbjct: 477 TPDVSVERELMRRHIRNLLSILSPKERRIIRLRFGIEDGREKTLLEIGNMFGLSKERVRQ 536

Query: 536 LESRALYRLKQSLGGKASYGYADLL 560
           LE+RALY+LK+    +    YADLL
Sbjct: 537 LENRALYKLKRCCNSQGLGAYADLL 561

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 =  592 bits (1526), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 317/572 (55%), Positives = 399/572 (69%), Gaps = 36/572 (6%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASS---SSSSSAPAVASVPTSSVARHFPTSVLL 57
           MEA RNL+SS PSF ++T +K   SS +S       ++ P V S   +S++RHFP SVL 
Sbjct: 1   MEATRNLVSSSPSFQTKTHLKSGFSSPSSVVMLHEQTATPVVNSRHLTSLSRHFPASVLS 60

Query: 58  QEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QDLEHQF 112
           QE R+E +PL H  +ED+TSQ T + R                 D+LV     +  E Q 
Sbjct: 61  QELREESKPLSHALREDRTSQLTLERRQ---------------FDELVSSREDEKFEQQL 105

Query: 113 LHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAA 170
           LH   LWNL  SP     + P+V             S DA+  D VALA+KALSASK+AA
Sbjct: 106 LHSAGLWNLLISPLTTEKQLPAV----------VSPSADADLCDLVALAQKALSASKQAA 155

Query: 171 SLAENPKLNGAEFT-DISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYN 229
            L EN + +  +   D   TSS     E+       R LERR+K R+  K    + E Y 
Sbjct: 156 LLVENSEADPPDNPRDSLSTSSSMSLPEKGTIVRSKRQLERRAKNRRAPKSNNMDSEGYV 215

Query: 230 SRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 289
            +K + KKK+ +GFD +D L+LFLWGPET++LLTA EE ELIA IQ LI+LEK K+KL+S
Sbjct: 216 PQKINAKKKMKQGFDTDDALQLFLWGPETKQLLTAKEEAELIAHIQHLIKLEKVKTKLES 275

Query: 290 QFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHD 349
           Q G EPT+ EWA+A+GLS   LKSE+H G SSREKLI ANLRLVVH+AKQYQ RG++  D
Sbjct: 276 QNGCEPTIGEWAEAMGLSSPVLKSEIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQD 335

Query: 350 LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKV 409
           LLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y LL KV
Sbjct: 336 LLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKV 395

Query: 410 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 469
            EA++  IQ+GN+ P KE LA  VG++ EKL++L++ TR PLSMQQP+W+DQDTTFQE+T
Sbjct: 396 SEARKTCIQDGNYRPSKEQLASHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEVT 455

Query: 470 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS 529
            D+G+E P +SV KQLMR HVRNLL +L+PKE+ I++LRFGI+ GK +SLSE+G I+GLS
Sbjct: 456 PDSGIETPSMSVGKQLMRNHVRNLLNVLSPKEKRIIKLRFGIDGGKQRSLSEIGEIYGLS 515

Query: 530 KERVRQLESRALYRLKQSLGGKASYGYADLLI 561
           KERVRQLESRALYRLKQ++       YADLL+
Sbjct: 516 KERVRQLESRALYRLKQNMSSHGLNAYADLLV 547

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 =  590 bits (1520), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 317/571 (55%), Positives = 402/571 (70%), Gaps = 35/571 (6%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKH--SLSSSASSSSSSSAPAVASVPTSSVARHFPTSVLLQ 58
           MEA RNL+SS PSF ++T +K   S SS       ++ P V S   +S++RHFP SVL Q
Sbjct: 1   MEATRNLVSSSPSFQTKTHLKSYSSPSSVVMLHEQTTTPVVNSRHLNSLSRHFPASVLSQ 60

Query: 59  EQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QDLEHQFL 113
           E R+E RPL H  +ED+TSQ T + R                 D+LV     +  E Q L
Sbjct: 61  EPREESRPLSHALREDRTSQLTLERRQ---------------FDELVSSREDEKFEQQLL 105

Query: 114 HWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAS 171
           H   LWNL  SP     + P V   +           DAE  D VALA+KALSASK+AA 
Sbjct: 106 HSAGLWNLLISPLTAETKLPPVVPPL----------ADAELCDIVALAQKALSASKQAAL 155

Query: 172 LAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQP-RFLERRSKKRKVSKPQVTNHETYNS 230
           LA++ + N ++ T  SL++S    L E     +  R LERR+K R+  K    ++E Y  
Sbjct: 156 LADDTEANPSDNTRGSLSTSSSMSLPEKGAIVRSKRQLERRAKNRRAPKSNDVDNEGYVP 215

Query: 231 RKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQ 290
           +K + KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K+KL+SQ
Sbjct: 216 QKINAKKKFKQGVDTDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQ 275

Query: 291 FGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDL 350
            G EPT+ EWA+A+G+S  DLKSE+H G SSREKLI ANLRLVVH+AKQYQ RG++  DL
Sbjct: 276 NGCEPTIGEWAEAMGISSPDLKSEIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDL 335

Query: 351 LQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVL 410
           LQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y LL KV 
Sbjct: 336 LQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVS 395

Query: 411 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA 470
           EA++  +QEGN+ P KE LA  VG++ EKL++L++ TR PLSMQQP+W+DQDTTFQEIT 
Sbjct: 396 EARKTCVQEGNYRPSKEQLAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITP 455

Query: 471 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 530
           D+G+E P +SV KQ+MR HVRNLL +L+PKER I++LRFGI+ GK +SLSE+G I+GLSK
Sbjct: 456 DSGIETPTMSVGKQMMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSK 515

Query: 531 ERVRQLESRALYRLKQSLGGKASYGYADLLI 561
           ERVRQLESRALYRLKQ +     + YADLL+
Sbjct: 516 ERVRQLESRALYRLKQHMNSHGLHAYADLLV 546

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 =  584 bits (1506), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 315/572 (55%), Positives = 401/572 (70%), Gaps = 36/572 (6%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASS---SSSSSAPAVASVPTSSVARHFPTSVLL 57
           MEA RNL+SS PSF ++T +K S SS +S       ++ P V S   +S++RHFP SVL 
Sbjct: 1   MEATRNLVSSSPSFQTKTHLKSSYSSPSSVVMLHDQTTTPVVNSRHLNSLSRHFPASVLS 60

Query: 58  QEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QDLEHQF 112
           QE R+E RPL H  ++D+TSQ T + R                 D+LV     +  E Q 
Sbjct: 61  QEPREESRPLSHALRDDRTSQLTLERRQ---------------FDELVSSREDEKFEQQL 105

Query: 113 LHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAA 170
           LH   LWNL  SP     + P+V   +           DAE  D VALA+KALSASK+AA
Sbjct: 106 LHSTGLWNLLISPLTSETKLPAVVSPL----------ADAELCDVVALAQKALSASKQAA 155

Query: 171 SLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYN 229
            L ++ + N ++   D   TSS     E+       R LERR+K R+  K    + E Y 
Sbjct: 156 LLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKRQLERRAKNRRAPKSNDVDDEGYV 215

Query: 230 SRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 289
            +K S KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K+KL+S
Sbjct: 216 PQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLES 275

Query: 290 QFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHD 349
           Q G EPT+ EWA+A+G+S   LKS++H G SSREKLI ANLRLVVH+AKQYQ RG++  D
Sbjct: 276 QNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQD 335

Query: 350 LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKV 409
           LLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y LL KV
Sbjct: 336 LLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKV 395

Query: 410 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT 469
            EA++  +QEGN+ P KE+LA  VG++ EKL++L++ TR PLSMQQP+W+DQDTTFQEIT
Sbjct: 396 SEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEIT 455

Query: 470 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS 529
            D+G+E P +SV KQLMR HVRNLL +L+PKER I++LRFGI+ GK +SLSE+G I+GLS
Sbjct: 456 PDSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLS 515

Query: 530 KERVRQLESRALYRLKQSLGGKASYGYADLLI 561
           KERVRQLESRALYRLKQ++     + YADLL+
Sbjct: 516 KERVRQLESRALYRLKQNMNSHGLHAYADLLV 547

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	561
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.964	0.989	0.495	3.9e-131
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.631	0.618	0.492	8.3e-90
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.602	0.590	0.381	1.6e-63
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.427	0.382	0.377	1.5e-50
TIGR_CMR|DET_0551	520	DET_0551 "RNA polymerase sigma	0.411	0.444	0.370	6e-48
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.490	0.743	0.357	2.6e-47
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.639	0.622	0.312	1.8e-46
TIGR_CMR|CJE_1081	622	CJE_1081 "RNA polymerase sigma	0.509	0.459	0.310	4.7e-46
TIGR_CMR|GSU_1525	328	GSU_1525 "RNA polymerase sigma	0.424	0.725	0.347	4.7e-46
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.442	0.767	0.382	7.9e-46

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

 Score = 1286 (457.8 bits), Expect = 3.9e-131, P = 3.9e-131
 Identities = 281/567 (49%), Positives = 366/567 (64%)

Query:     1 MEAGRNLLSSPPSFPSRTRVKHXXXXXXXXXXXXXXXXXXXXXXXXXXRHFPTSVLLQEQ 60
             MEA RNL+SS PSF ++T +K                           RH   S+     
Sbjct:     1 MEATRNLVSSSPSFQTKTHLK----SSYSSPSSVVMLHDQTTTPVVNSRHL-NSL----S 51

Query:    61 RDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQD--LEHQFLHWPDL 118
             R     +L     +++   +   R+  T    +E +   +L    +D   E Q LH   L
Sbjct:    52 RHFPASVLSQEPREESRPLSHALRDDRTSQLTLERRQFDELVSSREDEKFEQQLLHSTGL 111

Query:   119 WNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDXXXXXXXXXXXXXXXXXXXXNP 176
             WNL  SP     + P+V   +  L+       DAE  D                    + 
Sbjct:   112 WNLLISPLTSETKLPAV---VSPLA-------DAELCDVVALAQKALSASKQAALLVDDT 161

Query:   177 KLNGAE-FTD-ISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKAS 234
             + N ++   D +S +SS+  P E+       R LERR+K R+  K    + E Y  +K S
Sbjct:   162 EANPSDNIKDSLSTSSSMSLP-EKGNIVRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTS 220

Query:   235 VKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE 294
              KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K+KL+SQ G E
Sbjct:   221 AKKKYKQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCE 280

Query:   295 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG 354
             PT+ EWA+A+G+S   LKS++H G SSREKLI ANLRLVVH+AKQYQ RG++  DLLQEG
Sbjct:   281 PTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEG 340

Query:   355 SMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKR 414
             SMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y LL KV EA++
Sbjct:   341 SMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARK 400

Query:   415 LYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV 474
               +QEGN+ P KE+LA  VG++ EKL++L++ TR PLSMQQP+W+DQDTTFQEIT D+G+
Sbjct:   401 TCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGI 460

Query:   475 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 534
             E P +SV KQLMR HVRNLL +L+PKER I++LRFGI+ GK +SLSE+G I+GLSKERVR
Sbjct:   461 ETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVR 520

Query:   535 QLESRALYRLKQSLGGKASYGYADLLI 561
             QLESRALYRLKQ++     + YADLL+
Sbjct:   521 QLESRALYRLKQNMNSHGLHAYADLLV 547

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 = 896 (320.5 bits), Expect = 8.3e-90, P = 8.3e-90
 Identities = 176/357 (49%), Positives = 249/357 (69%)

Query:   206 RFLERRSKKRKVSKPQVTNHETY--NSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLT 263
             R LERRSK+R   +  + +      NS+K    KK     + ++P +LFL   ET + LT
Sbjct:   216 RLLERRSKRRYAPRASIADVSCSADNSKKKEKSKKYGRVLEPDEPFKLFLRDRETTEFLT 275

Query:   264 ADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 323
             A EE  L ++IQ L+++E+   KL+ Q GREPTL EWA+A+G+S ++L+S + +G   RE
Sbjct:   276 AKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCRE 335

Query:   324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 383
             K+  +N RLV+HVA++Y+G G+ + DL+Q+G  GLMK+ EKF P  GCRF +YAYWW+RQ
Sbjct:   336 KMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQ 395

Query:   384 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 443
             +I+K+IF++SR IRLPE++Y LL KV +A+   I EG   P   ++ARR GIT+EKL +L
Sbjct:   396 SIKKSIFKNSRLIRLPESVYALLRKVGKARMECIMEGEQ-PTNANVARRAGITIEKLAKL 454

Query:   444 IFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERC 503
                TR P SMQ  VW+D+  TFQEIT D  VE PD+SV + +MRQ VR+ L +L+P+E+ 
Sbjct:   455 RAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSVDRMMMRQQVRDFLGILSPREKE 514

Query:   504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 560
             I+  RFGI DG+PK+L  +G++FGLSKER+RQL++RAL +LK+S   +    Y DLL
Sbjct:   515 IIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSASLQGFDVYFDLL 571

GO:0009536 "plastid" evidence=RCA

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

 Score = 648 (233.2 bits), Expect = 1.6e-63, P = 1.6e-63
 Identities = 131/343 (38%), Positives = 215/343 (62%)

Query:   206 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 264
             R  ER++++ K  +   +   +  +  +  KK+L ++  D NDPLR       + KLLT 
Sbjct:   216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275

Query:   265 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 324
              EE EL A IQDL++LE+ +++L  + GR+PT  +WA A G+  + L+  +H G   ++K
Sbjct:   276 REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDK 335

Query:   325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384
             +I +N+RLV+ +AK YQG G++L DL+QEG  GL++  EKF    G +F++YA+WW++Q 
Sbjct:   336 MIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQA 395

Query:   385 IRKAIFQHSRTIRLPENIYTLLSKVLEA-KRLYIQEGNHSPDKEDLARRVGITVEKLERL 443
             +RK++   SR IRLP ++     +V EA K+LY + G H P  E++A   G+++++L  +
Sbjct:   396 VRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKH-PKNEEIAEATGLSMKRLMAV 454

Query:   444 IFITRMPLSMQQPVWADQDTTFQEITADT-GVEIPDISVQKQLMRQHVRNLLTLLNPKER 502
             +   + P S+ Q +  +Q+    E+ AD   V   DI + K+ MRQ +  +L  L  +E+
Sbjct:   455 LLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILI-KEFMRQDLDKVLDSLGTREK 513

Query:   503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
              ++R RFG+EDG+ K+L E+G + G+S+ERVRQ+ES A  +LK
Sbjct:   514 QVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLK 556

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 = 467 (169.5 bits), Expect = 1.5e-50, Sum P(3) = 1.5e-50
 Identities = 91/241 (37%), Positives = 154/241 (63%)

Query:   317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASY 376
             + N +++++I ANLRLVV +AK+Y  RG+   DL+QEG++GLMK+V+KF  + G +F++Y
Sbjct:   386 TANRAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTY 445

Query:   377 AYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT 436
             A WWVRQ I +AI   +RTIR+P ++   ++K+    R  + E    P  E+L+ R+ I 
Sbjct:   446 ATWWVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLNIN 505

Query:   437 VEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTL 496
             VEK+ +++ I + P+S++ P+  D  +TF +   D     P+ +     +R+    +L+ 
Sbjct:   506 VEKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLST 565

Query:   497 LNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 555
             L PKE  I+R+RFGI + GK  +L EVG +F +++ER+RQ+E++AL +L+     +   G
Sbjct:   566 LTPKEERILRMRFGIGKSGKDHTLEEVGRLFNVTRERIRQIEAKALRKLRHPSRARKLRG 625

Query:   556 Y 556
             +
Sbjct:   626 F 626

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|DET_0551 DET_0551 "RNA polymerase sigma factor RpoD" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 461 (167.3 bits), Expect = 6.0e-48, Sum P(2) = 6.0e-48
 Identities = 86/232 (37%), Positives = 154/232 (66%)

Query:   314 ELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 373
             E+ +  + R  LI ANLRLVV VAK++ GRG+ L DL+QEG++GL+++VEKF    G +F
Sbjct:   277 EIDAKRAERH-LIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKF 335

Query:   374 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRV 433
             ++YA WW+RQ I +AI   +RTIR+P ++   ++K+L   R   Q+    P  +++A  +
Sbjct:   336 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIAVEM 395

Query:   434 GITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNL 493
              +  EK+  +  ++++P+S++ P+  ++D+   +   D     P  +  +QL+++ +  +
Sbjct:   396 DLPPEKVREIAKVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTV 455

Query:   494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
             L  L P+ER +++LRFG+EDG+ ++L EVG  F +++ER+RQ+E++AL +L+
Sbjct:   456 LGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLR 507

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 = 495 (179.3 bits), Expect = 2.6e-47, P = 2.6e-47
 Identities = 100/280 (35%), Positives = 174/280 (62%)

Query:   266 EEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 325
             +E +L   I + I ++        + GR P L    + I L+ R  K E      ++ KL
Sbjct:    83 DEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTP-EEEIELAKR--KEE--GDEEAKRKL 137

Query:   326 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 385
               ANLRLVV +AK+Y GRG+   DL+QEG++GL+K+VEKF  + G +F++YA WW+RQ I
Sbjct:   138 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAI 197

Query:   386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 445
              +AI   +RTIR+P ++   ++K++   R  +QE    P  E++A+ +GI+ +K+  ++ 
Sbjct:   198 TRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEEIAKEMGISEDKVREIMK 257

Query:   446 ITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIV 505
             I + P+S++ P+  ++D+   +   D   + P       L+R+ +  +L  L  +E+ ++
Sbjct:   258 IAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDEVLKTLTEREQKVL 317

Query:   506 RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
             RLRFG++DG+ ++L EVG IFG+++ER+RQ+E++AL +L+
Sbjct:   318 RLRFGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLR 357

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 = 487 (176.5 bits), Expect = 1.8e-46, P = 1.8e-46
 Identities = 117/375 (31%), Positives = 211/375 (56%)

Query:   185 DISLTSSLGYPLEEVKQFSQPR---FLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSE 241
             D+ L ++L   LEE    +  R     ER+  K K+++  VT+    +   A + ++L E
Sbjct:   192 DVRL-AALNAELEEESLSASRRQELLAERQELKEKLAE-MVTSLRLKDRHIAKIAQRLKE 249

Query:   242 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQ--IQDLIRLEKEKSKLQSQFGR--EPTL 297
                + D +   +   E    ++AD   E+ A   +   I+L  E ++   +  R  E  L
Sbjct:   250 LSAKVDTIMAEIAAIEKEAGVSADTLKEIAASEAVGKGIKLSLEDAQKHEKKVRSAEKKL 309

Query:   298 IEWAKAIGLSCRDLKSELHS---GNS----SREKLINANLRLVVHVAKQYQGRGISLHDL 350
              +  +  G   R+L   L +   G +    ++ +L+ ANLRLVV +AK+Y  RG+   DL
Sbjct:   310 KKVEEESGFKARELSDALRAIDRGEAKSKLAKSELVEANLRLVVSIAKKYTNRGLQFLDL 369

Query:   351 LQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVL 410
             +QEG++GLMK+V+KF+ Q G +F++YA WW+RQ I +AI   +RTIR+P ++   ++K++
Sbjct:   370 IQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLI 429

Query:   411 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA 470
                R  +QE    P  E++A R+ + ++K+ +++ I + P+S++ P+  ++D+   +   
Sbjct:   430 RTSRQLVQEIGREPSPEEIAERMNLPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIE 489

Query:   471 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 530
             D GV  P  +V K  + +    +L  L P+E  ++R+RFGI +    +L EVG  F +++
Sbjct:   490 DKGVVSPLEAVIKANLSEQTARVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTR 549

Query:   531 ERVRQLESRALYRLK 545
             ER+RQ+E++AL +L+
Sbjct:   550 ERIRQIEAKALRKLR 564

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 = 450 (163.5 bits), Expect = 4.7e-46, Sum P(2) = 4.7e-46
 Identities = 91/293 (31%), Positives = 175/293 (59%)

Query:   267 EFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 326
             E  +++   ++ +L + K   +  F  E + +   K I      +K      + ++ ++ 
Sbjct:   333 ETTMVSTYMEIKKLFQTKEASEKSFDLEKSRL---KEI---LEQIKRGKKISDEAKGRMA 386

Query:   327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 386
              +NLRLVV +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I 
Sbjct:   387 KSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAIS 446

Query:   387 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 446
             +AI   +RTIR+P ++   ++++ +  R ++Q+    PD   +A+ VG++V+K++++I I
Sbjct:   447 RAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVGLSVDKVKQVIKI 506

Query:   447 TRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVR 506
             T+ P+S++ P+  + D  F +   D     P   + K  +++ +  +L  LN +E+ ++R
Sbjct:   507 TKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVLDQLNDREKAVIR 566

Query:   507 LRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 558
             +RFG+ +D   ++L E+G    +++ERVRQ+ES A+ +LK    G+    Y +
Sbjct:   567 MRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHPKVGRKLKNYIE 619

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 = 434 (157.8 bits), Expect = 4.7e-46, Sum P(2) = 4.7e-46
 Identities = 83/239 (34%), Positives = 152/239 (63%)

Query:   309 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 367
             ++L   +  G+ ++R+K+I +NLRLVV +AK+Y  RG+   DL++EG+MGL+K+VE+FK 
Sbjct:    79 KELAGRIAKGDKAARDKMIESNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKL 138

Query:   368 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 427
                CRF++YA WW+RQ+I +A+   SRTIRLP ++   ++K+L+  R  +Q  N  P  +
Sbjct:   139 SKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDDINKMLKITRELVQRLNREPSVK 198

Query:   428 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 487
             ++A  + +    + RL+ + +   S+++P+  + D    +   DT    P + ++     
Sbjct:   199 EVATEMKVNSAYVRRLMVLLKKTYSIERPMGENSDYFLIDTIEDTSTVSPAVLLEDLNKY 258

Query:   488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
             + V      L+  E+ I+ LRFG+ED +P++L  +G  FG+++ER+RQ+E+++L +L++
Sbjct:   259 EIVSKWFASLSENEQTILTLRFGLEDKEPQTLDTIGRSFGVTRERIRQIEAKSLEKLRK 317

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 481 (174.4 bits), Expect = 7.9e-46, P = 7.9e-46
 Identities = 96/251 (38%), Positives = 163/251 (64%)

Query:   297 LIEWAKAIGLSC-RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGS 355
             L+E  K +G +  RDL + +  G ++R  L+ ANLRLVV +AK+Y GRG+ L DL+QEG+
Sbjct:    61 LLETRKRLGENRKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGN 120

Query:   356 MGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 415
             +GL++++EKF    G +F++YA WW+RQ I + +   SRTIRLP ++   ++K+   KR 
Sbjct:   121 LGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRE 180

Query:   416 YIQE-GNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV 474
               Q  G  + D E+LA   GI ++K+  L+  +R P+S+  PV ++++    +   D   
Sbjct:   181 MHQHLGREATD-EELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEA 239

Query:   475 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 534
                + +V  +L+   +R++L  L+ +E  ++RLRFG++DG+P++L ++G +FGLS+ERVR
Sbjct:   240 MSAENAVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVR 299

Query:   535 QLESRALYRLK 545
             Q+E   + +L+
Sbjct:   300 QIERDVMSKLR 310

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

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

GO:0016987 "sigma factor activity" evidence=IGI

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

GO:0040007 "growth" evidence=IMP

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

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

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

---

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	0.5506	0.9554	0.9798	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	561
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	2e-97
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	2e-81
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	3e-78
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	5e-75
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	6e-73
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	6e-73
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	4e-69
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	4e-61
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	2e-58
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-56
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	3e-56
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	7e-54
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	1e-44
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	2e-31
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	7e-30
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	3e-27
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	3e-27
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	2e-24
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	5e-22
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	4e-21
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	1e-20
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	6e-19
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	8e-19
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	1e-17
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	6e-17
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	8e-17
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	2e-15
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	2e-13
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	8e-13
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	1e-12
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	2e-12
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	3e-12
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	8e-12
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	6e-11
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	2e-10
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	4e-10
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	6e-10
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	1e-09
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	4e-09
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	2e-08
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	9e-07
PRK08295	208	PRK08295, PRK08295, RNA polymerase factor sigma-70	1e-04
TIGR02859	198	TIGR02859, spore_sigH, RNA polymerase sigma-H fact	1e-04
PRK12427	231	PRK12427, PRK12427, flagellar biosynthesis sigma f	0.002
COG1595	182	COG1595, RpoE, DNA-directed RNA polymerase special	0.002

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

 Score =  297 bits (763), Expect = 2e-97
 Identities = 126/285 (44%), Positives = 194/285 (68%), Gaps = 1/285 (0%)

Query: 261 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 320
           LLT +EE EL  Q+Q ++ LE+ + +L+ Q GREP+  EWA A GLS  +L+  L  G  
Sbjct: 15  LLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQR 74

Query: 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380
           ++EK+I ANLRLVV VAK+YQ RG+ L DL+QEGS+GL ++VEKF P  G +F++YAYWW
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWW 134

Query: 381 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 440
           +RQ I +AI   SRTIRLP +I   L+K+ + +R   Q+   +P + ++A  + +  E++
Sbjct: 135 IRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQV 194

Query: 441 ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 500
             L+   R P+S+  PV  ++DT   ++  D G   P+  V+++ +RQ + +LL  L P+
Sbjct: 195 RELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELTPR 253

Query: 501 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           ER ++RLRFG++ G+P +L+E+G    LS+ERVRQ+E++AL +L+
Sbjct: 254 ERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298

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 =  259 bits (663), Expect = 2e-81
 Identities = 121/317 (38%), Positives = 206/317 (64%), Gaps = 8/317 (2%)

Query: 230 SRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 289
             K   KK  +E     D +R++L      +LL  DEE EL  +I DL+ LE+ + + +S
Sbjct: 51  RIKIGPKKVYTE-----DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFES 105

Query: 290 QFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHD 349
           + GREP+  EWA+ + +     +  L  G  ++EK++ +NLRLVV +AK+Y  RG+S  D
Sbjct: 106 ELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQD 165

Query: 350 LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKV 409
           L+QEGS+GL+++ EKF  + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++
Sbjct: 166 LIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRI 225

Query: 410 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE-I 468
            +  ++  QE    P +E++A  + +T+EKL  +    ++P+S++ P+  ++D+   + I
Sbjct: 226 KKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI 285

Query: 469 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL 528
            AD   E P+  V K L+R+ +  +L  L+P+ER ++RLR+G++DG+ K+L E+G IF +
Sbjct: 286 EADG--ETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNV 343

Query: 529 SKERVRQLESRALYRLK 545
           ++ER+RQ+E++AL +L+
Sbjct: 344 TRERIRQIEAKALRKLR 360

Length = 373

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

 Score =  249 bits (639), Expect = 3e-78
 Identities = 110/306 (35%), Positives = 181/306 (59%), Gaps = 21/306 (6%)

Query: 261 LLTADEEFELIAQIQDLIRLEKEKSKL-QSQFGREPTL---------------IEWAKAI 304
           LL  + E EL  Q++D   L +    L   + GREP+                IE A  +
Sbjct: 23  LLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLL 82

Query: 305 GLS-CRDLKSELHSGNSSRE---KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK 360
                + L   L  G    +   KL+ +NLRLVV +AK+Y GRG+   DL+QEG++GLMK
Sbjct: 83  TPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMK 142

Query: 361 SVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG 420
           +VEKF P+ G +F++YA WW+RQ I +AI   +RTIR+P +   L++K+   KR  +QE 
Sbjct: 143 AVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQEL 202

Query: 421 NHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 480
              P  E++A  +G++ +K+  ++     P+S+  P+  D+D+   +   D     P+ +
Sbjct: 203 GREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELGDFLEDDKSVSPEDA 262

Query: 481 VQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539
           V+++ +++ +  +L   L  +ER ++RLRFG++DG+PK+L E+G  FG+S+ERVRQ+E++
Sbjct: 263 VERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAK 322

Query: 540 ALYRLK 545
           AL +L+
Sbjct: 323 ALRKLR 328

Length = 342

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

 Score =  240 bits (615), Expect = 5e-75
 Identities = 122/294 (41%), Positives = 185/294 (62%), Gaps = 1/294 (0%)

Query: 261 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 320
           LLT ++E     Q+Q ++ L + K  L  + GREP+L EWA+A+ LS  +LK  L  G  
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380
           +++K+I ANLRLVV +AK+YQ R +   DL+QEG++GL + VEKF P  G +F++YAYWW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 381 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 440
           +RQ I +AI Q +RTIRLP +I   L+K+ + +R   Q+   S    ++A+ + +   ++
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQI 211

Query: 441 ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 500
              + + R P+S+   V  +QDT   E+  D G   PD  + ++L+RQ + NLL  L P+
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELSELLEDEGPS-PDQYITQELLRQDLNNLLAELTPQ 270

Query: 501 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY 554
           +R ++ LRFG+EDGK  SL++VG    LS+ERVRQLE +AL  L++       Y
Sbjct: 271 QREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRRANVKEY 324

Length = 327

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

 Score =  232 bits (593), Expect = 6e-73
 Identities = 91/224 (40%), Positives = 155/224 (69%)

Query: 322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 381
           +++L+ +NLRLVV +AK+Y  RG+S  DL+QEG++GLMK+VEKF  + G +F++YA WW+
Sbjct: 2   KKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWI 61

Query: 382 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 441
           RQ I +AI   +RTIR+P ++   ++K+++A+R   QE    P  E+LA R+G+  EK+ 
Sbjct: 62  RQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVR 121

Query: 442 RLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKE 501
            +  I + P+S++ P+  ++D+   +   DT +E PD    K+L+R+ +  +L  L  +E
Sbjct: 122 EIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTERE 181

Query: 502 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
             ++R+R+G+ DG+P +L EVG  F +++ER+RQ+ES+AL +L+
Sbjct: 182 EKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLR 225

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|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated

 Score =  235 bits (600), Expect = 6e-73
 Identities = 121/308 (39%), Positives = 189/308 (61%), Gaps = 1/308 (0%)

Query: 247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 306
           D +R +L       LLT +EE     Q+Q L+ L++ + +L  + GREPT  EWAKA  L
Sbjct: 8   DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKL 67

Query: 307 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 366
           S  +L+S +  G +++ K++ ANLRLVV VAK+Y  R + L DL+QEG++G+ + VEKF 
Sbjct: 68  SEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFD 127

Query: 367 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 426
           P  G RF++YAYWW+RQ I +AI + SRTIRLP +I   L+K+ +A+R   Q+   +   
Sbjct: 128 PTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATI 187

Query: 427 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 486
            +LA  + +T +++   +   R PLS+   V  +QDT   E+  DTG    D + Q  L 
Sbjct: 188 GELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFATQSSL- 246

Query: 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
           +  +  L+  L P+++ ++ LRFG+EDG+P +L+++G    +S+ERVRQ+E  AL +L++
Sbjct: 247 QLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306

Query: 547 SLGGKASY 554
                  Y
Sbjct: 307 RKANIQEY 314

Length = 317

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

 Score =  228 bits (583), Expect = 4e-69
 Identities = 128/348 (36%), Positives = 193/348 (55%), Gaps = 55/348 (15%)

Query: 247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKE--------------------KSK 286
           D +RL+L      +LL  DEE     ++Q  ++L                       + +
Sbjct: 60  DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRER 119

Query: 287 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS----------------------SREK 324
           L S+ G  P+L  WAK   +S  DLK  L  G                        ++E 
Sbjct: 120 LTSELGHRPSLERWAKTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEH 179

Query: 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384
           +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF++YAYWW+RQ 
Sbjct: 180 MIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQG 239

Query: 385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI 444
           I +AI   SRTIRLP +I   L+K+ +A+R   QE   +P  ED+A+ + +T  ++  + 
Sbjct: 240 ITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV- 298

Query: 445 FITRMP--LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRN----LLTLLN 498
            + R+P  +S++  V  D+DT   ++     +E  DIS ++ LMR+ ++     LL  L 
Sbjct: 299 -LLRVPRSVSLETKVGKDKDTELGDL-----LETDDISPEEMLMRESLQRDLQHLLADLT 352

Query: 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
            +ER ++R+RFG+ DG   SL+E+G    LS+ERVRQ+ES+AL +L+Q
Sbjct: 353 SRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ 400

Length = 415

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

 Score =  204 bits (520), Expect = 4e-61
 Identities = 111/302 (36%), Positives = 186/302 (61%), Gaps = 17/302 (5%)

Query: 247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 306
           D +R++L G     LLTA +E EL  +I+         + L ++      L+E  K +  
Sbjct: 26  DLVRVYLNGIGKTALLTAADEVELAKRIE---------AGLYAE-----HLLETRKRLSE 71

Query: 307 SC-RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 365
           +  RDL + +  G ++R  L+ ANLRLVV +AK+Y GRG+ L DL+QEG++GL++++EKF
Sbjct: 72  ARKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKF 131

Query: 366 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKR-LYIQEGNHSP 424
               G +F++YA WW+RQ I + +   SRTIRLP ++   ++K+   KR L+ Q G  + 
Sbjct: 132 DYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREAT 191

Query: 425 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 484
           D E+LA   GI  EK+  L+  +R P+S+  PV +D++    +   D+     + +V   
Sbjct: 192 D-EELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAG 250

Query: 485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544
           L+   +R++L  L+ +E+ ++RLRFG++DG+P++L ++G +FGLS+ERVRQ+E   + +L
Sbjct: 251 LLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKL 310

Query: 545 KQ 546
           + 
Sbjct: 311 RN 312

Length = 324

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

 Score =  196 bits (499), Expect = 2e-58
 Identities = 86/228 (37%), Positives = 137/228 (60%)

Query: 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380
           +R+ +I +NLRLVV +AK Y  RG+ L DL++EG++GLM +VEKF P+ G RF++YA WW
Sbjct: 47  ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWW 106

Query: 381 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 440
           +RQTI +AI   +RTIRLP ++   L+  L A R   ++    P  E++A  +   VE +
Sbjct: 107 IRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDV 166

Query: 441 ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 500
            R++ +     S+  P+  D   +  +  AD     P+  VQ   ++Q +   L  LN +
Sbjct: 167 SRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNER 226

Query: 501 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
           +R ++  RFG+   +P +L EV    GL++ERVRQ++  AL +L++ L
Sbjct: 227 QREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274

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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score =  197 bits (503), Expect = 2e-56
 Identities = 105/290 (36%), Positives = 170/290 (58%), Gaps = 21/290 (7%)

Query: 260 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 319
           KLL A+EE EL        R+E         +  E  L E  K      RDL+     G 
Sbjct: 224 KLLNAEEEVELA------KRIEAG------LYAEE-LLAEGEKLDPELRRDLQWIGRDGK 270

Query: 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 379
            ++  L+ ANLRLVV +AK+Y  RG+S  DL+QEG++GL+K+VEKF    G +F++YA W
Sbjct: 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATW 330

Query: 380 WVRQTIRKAIFQHSRTIRLP----ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI 435
           W+RQ I +A+   +RTIR+P    E I    +K+   +R  +QE    P  E+LA+ +G 
Sbjct: 331 WIRQAITRAMADQARTIRIPVHMVETI----NKLGRIERELLQELGREPTPEELAKEMGF 386

Query: 436 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 495
           T EK+  +    R P+S+ + +  + D+ F +   D+    P  +V   L++  ++ +L 
Sbjct: 387 TPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLE 446

Query: 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
            L+ +E  ++R+RFG+ DG+PK+L E+G ++G+++ER+RQ+ES+ L +L+
Sbjct: 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496

Length = 509

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

 Score =  191 bits (488), Expect = 3e-56
 Identities = 86/229 (37%), Positives = 144/229 (62%)

Query: 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 379
           ++R+++I +NLRLVV +AK+Y  RG++L DL++EG++GL+++VEKF P+ G RF++YA W
Sbjct: 86  AARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 145

Query: 380 WVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK 439
           W+RQTI +AI   +RTIRLP ++   L+  L A R    + +H P  E++A  +   V+ 
Sbjct: 146 WIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDD 205

Query: 440 LERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 499
           + R++ +     S+  P+  D + +  +I AD     P+ + Q   M+Q +   L  LN 
Sbjct: 206 VSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELND 265

Query: 500 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
           K+R ++  RFG+   +  +L +V    GL++ERVRQ++  AL RL++ L
Sbjct: 266 KQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314

Length = 325

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

 Score =  186 bits (475), Expect = 7e-54
 Identities = 103/308 (33%), Positives = 174/308 (56%), Gaps = 42/308 (13%)

Query: 240 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIE 299
             G   NDP+R++L       LLTA+EE EL                             
Sbjct: 89  PPGVKINDPVRMYLKEIGRVPLLTAEEEIEL----------------------------- 119

Query: 300 WAKAIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGL 358
            AK I             G+  ++++L  ANLRLVV +AK+Y GRG+   DL+QEG+MGL
Sbjct: 120 -AKRIE-----------EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGL 167

Query: 359 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQ 418
           MK+VEKF  + G +F++YA WW+RQ I +AI   +RTIR+P ++   ++K++  +R  +Q
Sbjct: 168 MKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQ 227

Query: 419 EGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 478
           E    P  E++A  + +  EK+  ++ I + P+S++ P+  + D+   +   D     P 
Sbjct: 228 ELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPA 287

Query: 479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 538
                +L+++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E+
Sbjct: 288 DHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEA 347

Query: 539 RALYRLKQ 546
           +AL +L+ 
Sbjct: 348 KALRKLRH 355

Length = 367

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

 Score =  166 bits (424), Expect = 1e-44
 Identities = 92/278 (33%), Positives = 167/278 (60%), Gaps = 16/278 (5%)

Query: 273 QIQDLIRLEKEKSKLQSQFGREPT-LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLR 331
              ++ +L++E   ++ + G     L E  + I       K E  +  + +E ++ ANLR
Sbjct: 339 VYDEIKKLQQELEAIEEETGLTIEELKEINRQI------SKGEAKARRAKKE-MVEANLR 391

Query: 332 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 391
           LV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I  
Sbjct: 392 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 451

Query: 392 HSRTIRLP----ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 447
            +RTIR+P    E I    +K+    R  +QE    P  E+LA R+G+  +K+ +++ I 
Sbjct: 452 QARTIRIPVHMIETI----NKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIA 507

Query: 448 RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRL 507
           + P+S++ P+  D+D+   +   D   E+P  +  ++ +R+   ++L  L P+E  ++R+
Sbjct: 508 KEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRM 567

Query: 508 RFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           RFGI+     +L EVG  F +++ER+RQ+E++AL +L+
Sbjct: 568 RFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605

Length = 619

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

 Score =  121 bits (306), Expect = 2e-31
 Identities = 64/247 (25%), Positives = 124/247 (50%), Gaps = 19/247 (7%)

Query: 309 RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLH-DLLQEGSMGLMKSVEKFKP 367
             L      G+    +LI   L LV  +A++++ RG S + DL+Q G +GL+K++E++ P
Sbjct: 12  EKLLEYYAEGDEEARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDP 71

Query: 368 QAGCRFASYAYWWVRQTIRKAIFQHSR---TIRLPENIYTLLSKVLEAKRLYIQEGNHSP 424
             G +F++YA     + IR  I  + R   ++++P ++  L  ++ EA     QE    P
Sbjct: 72  SKGTKFSTYA----VRRIRGEILDYLRKNDSVKVPRSLRELGRRIEEAIDELEQELGREP 127

Query: 425 DKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 482
             E++A  +GI  E+    +        LS+ + V  D D    +      +E PD  V+
Sbjct: 128 TDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDDQ-----IENPDDGVE 182

Query: 483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542
           K+ + + ++  +  L  +E+ ++ LR+  E     +  E+  + G+S+ RV +L  +A+ 
Sbjct: 183 KEELLEILKEAIEPLPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVSRLHKKAIK 238

Query: 543 RLKQSLG 549
           +L++ L 
Sbjct: 239 KLRKELN 245

Length = 247

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

 Score =  118 bits (297), Expect = 7e-30
 Identities = 72/240 (30%), Positives = 128/240 (53%), Gaps = 25/240 (10%)

Query: 324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 383
           KL+ ++LR VV +A+ Y+G G+   DL+QEG++GLMK+V++F P+ G R  S+A  W++ 
Sbjct: 39  KLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKA 98

Query: 384 TIRKAIFQHSRTIRLPENIYTLLSKVL------EAKRLYIQEGNHSPDK-EDLARRVGIT 436
            I + I ++ R +++     T   + L        KRL   +G  +P++ E +A  +G++
Sbjct: 99  EIHEYILRNWRLVKVAT---TKAQRKLFFNLRKMKKRL---QGWLNPEEVEAIAEELGVS 152

Query: 437 VEKLERLIFITRMP---LSMQQPVWADQDTTFQEIT--ADTGVEIPDISVQKQ---LMRQ 488
               E     +R+    +S+   +  D+D     I    D   +  D   ++Q   L RQ
Sbjct: 153 ER--EVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDTLEEEQWEELQRQ 210

Query: 489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
            + N L  L+ + R I+  R+  +D    +L E+   +G+S ER+RQ+E  A+ +LK +L
Sbjct: 211 ALANALGSLDARSRRIIEARWLDDD--KLTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268

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

 Score =  109 bits (275), Expect = 3e-27
 Identities = 69/231 (29%), Positives = 121/231 (52%), Gaps = 13/231 (5%)

Query: 322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 381
           REKL+  NL LV  +A++++ RG    DL+Q G++GL+K++++F P  G +F+++A   +
Sbjct: 5   REKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTI 64

Query: 382 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 441
              I++     +  +R+P  +  L  K+ +A     Q    SP   ++A R+G++ E++ 
Sbjct: 65  MGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVV 124

Query: 442 RLIFITRM--PLSMQQPVWADQDTTFQEIT-ADT-GVEIPDISVQKQLMRQHVRNLLTLL 497
             +        LS+   +  D       I   DT G E  D +++    R  ++ LL  L
Sbjct: 125 EALEAGNAYQALSLDASIEDDDGD---PIALLDTLGDE--DDALETVEDRLALKPLLAAL 179

Query: 498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
             +ER I+ LRF  ED   K+ SE+    G+S+  V +L  RAL +L++ L
Sbjct: 180 PERERRILLLRF-FED---KTQSEIAERLGISQMHVSRLLRRALKKLREQL 226

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

 Score =  111 bits (279), Expect = 3e-27
 Identities = 67/257 (26%), Positives = 130/257 (50%), Gaps = 49/257 (19%)

Query: 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380
           +  ++I+A++RLV+ +A +++  G+ ++DL+QEG +GL+++  +F+P    RF++YA WW
Sbjct: 41  ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWW 100

Query: 381 VRQTI------------------RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNH 422
           +R +I                  +KA+F + R +R              A+   + + + 
Sbjct: 101 IRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLR--------------AR---LAQADE 143

Query: 423 SPDKEDLARRV----GITVEKLERLIFITRMP-LSMQQPVWADQDTTFQEITA--DTGVE 475
              K+++ R +    G+++  +E +      P  S+  P   + +   + +    D    
Sbjct: 144 ELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDS-P 202

Query: 476 IPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 531
           +PD  V+     +  R+ +   L  LN +E  I+R R   ED    +L  +G   G+SKE
Sbjct: 203 LPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRED--GATLEALGEELGISKE 260

Query: 532 RVRQLESRALYRLKQSL 548
           RVRQ+E+RAL +L+++L
Sbjct: 261 RVRQIEARALEKLRRAL 277

Length = 289

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

 Score =  103 bits (259), Expect = 2e-24
 Identities = 71/250 (28%), Positives = 126/250 (50%), Gaps = 38/250 (15%)

Query: 324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 383
           +L+ ++LR VVH+A+ Y+G G+   DL+QEG++GLMK+V++F P+ G R  S+A  W++ 
Sbjct: 52  QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKA 111

Query: 384 TIRKAIFQHSRTIRLPENIYTL---------LSKVLEAKRLYIQEGNHSPDK-EDLARRV 433
            I + I ++ R ++    + T          L K    KRL    G  +P++ E +A  +
Sbjct: 112 EIHEYILRNWRIVK----VATTKAQRKLFFNLRKA--KKRL----GWLNPEEVEMVAEEL 161

Query: 434 GITVE---KLERLIFITRMP---LSMQQPVWADQDTTFQEIT--ADTGVEIPDISVQKQL 485
           G++ E   ++E      R+     S+  P+  D + +        D   +  D+  +   
Sbjct: 162 GVSEEEVREMES-----RLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNW 216

Query: 486 MRQHVRNL---LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542
             Q    L   L  L+ + R I+  R+  +D    +L E+   +G+S ERVRQ+E  A+ 
Sbjct: 217 EDQRRALLADALEGLDERSRDIIEARWLDDD--KSTLQELAAEYGVSAERVRQIEKNAMK 274

Query: 543 RLKQSLGGKA 552
           +LK ++   A
Sbjct: 275 KLKAAIEAAA 284

Length = 284

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

 Score = 95.4 bits (238), Expect = 5e-22
 Identities = 67/244 (27%), Positives = 133/244 (54%), Gaps = 21/244 (8%)

Query: 309 RDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 367
           R+L   + +G   +REKLIN NLRLV+ V +++  RG ++ DL Q G +GLMK+++ F  
Sbjct: 25  RELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDL 84

Query: 368 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 427
               +F++YA   +   IR+ +  ++  IR+  ++  +  K L+ +   I E +  P  E
Sbjct: 85  SQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVE 143

Query: 428 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQ-DTTF--QEITADTGVE---IPDISV 481
           ++A+ + +  E++   +   + P+S+ +P++ D  D  +   +I+ +   +   + +I++
Sbjct: 144 EIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKNKDENWLEEIAL 203

Query: 482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 541
            K+ M++        LN +E+ I+ LRF     + K+  EV    G+S+ +V +LE  AL
Sbjct: 204 -KEAMKK--------LNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAAL 250

Query: 542 YRLK 545
             ++
Sbjct: 251 KHMR 254

Length = 258

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

 Score = 92.6 bits (230), Expect = 4e-21
 Identities = 68/244 (27%), Positives = 128/244 (52%), Gaps = 19/244 (7%)

Query: 309 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 367
           R+L   + SG+ ++REKLIN NLRLV+ V +++  RG  + DL Q G +GLMKS++ F  
Sbjct: 22  RELFIRMQSGDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDL 81

Query: 368 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 427
               +F++YA   +   IR+ + + +  IR+  ++  +  K L+ +   I E +  P   
Sbjct: 82  SQNVKFSTYAVPMIIGEIRRYL-RDNNPIRVSRSLRDIAYKALQVRDKLISENSKEPTVS 140

Query: 428 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 487
           ++A+ + +  E++   +   + P+S+ +P++ D          D    +  IS +K    
Sbjct: 141 EIAKELKVPQEEVVFALDAIQDPVSLFEPIYND--------GGDPIYVMDQISDEKNKDS 192

Query: 488 QHVRNL-----LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542
           Q +  +     +  LN +E+ I+ +RF   +GK +   EV    G+S+ +V +LE  AL 
Sbjct: 193 QWLEGIALKEAMKRLNEREKMILNMRF--FEGKTQ--MEVAEEIGISQAQVSRLEKAALK 248

Query: 543 RLKQ 546
            +++
Sbjct: 249 HMRK 252

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|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor

 Score = 90.9 bits (226), Expect = 1e-20
 Identities = 66/236 (27%), Positives = 122/236 (51%), Gaps = 13/236 (5%)

Query: 316 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 374
            +G+  +R+KLI  NLRLV  + K++  RG    DL Q G +GL+K+++KF      +F+
Sbjct: 6   QNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFS 65

Query: 375 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG 434
           +YA   +   I++ + +    I++  ++  L  K+   K    +E    P   +LA  +G
Sbjct: 66  TYAVPMIMGEIKRFL-RDDGIIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALG 124

Query: 435 ITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI--TADTGVEIPDISVQKQLMRQHVRN 492
           ++ E++   +   R P S+   V  D       +   AD G E  D  ++K  +++ +  
Sbjct: 125 VSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKGSEDSDW-LEKIALKEAISK 183

Query: 493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
               L+ +ER I+ LR+     K K+ +EV N+ G+S+ +V +LE + L ++K+ L
Sbjct: 184 ----LDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231

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|218138 pfam04542, Sigma70_r2, Sigma-70 region 2

 Score = 80.7 bits (200), Expect = 6e-19
 Identities = 27/71 (38%), Positives = 44/71 (61%)

Query: 325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 384
           L+   L LV  +A++Y G G    DL+QEG +GL+++VE+F P+ G  F+++ Y  +R  
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 385 IRKAIFQHSRT 395
           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|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor

 Score = 85.2 bits (211), Expect = 8e-19
 Identities = 57/227 (25%), Positives = 103/227 (45%), Gaps = 56/227 (24%)

Query: 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380
           +R  LI  NLRLV H+ K++   G  + DL+  G++GL+K+++ F P  G R A+YA   
Sbjct: 49  ARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYA--- 105

Query: 381 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 440
             + I   I  H R +                K+                          
Sbjct: 106 -ARCIENEILMHLRAL----------------KK-------------------------- 122

Query: 441 ERLIFITRMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 497
                 T+  +S+Q P+  D+   + +  +I    G  + +  V+  L  + +   L++L
Sbjct: 123 ------TKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQ-VELNLEIKKLYKKLSVL 175

Query: 498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 544
           + +ER ++ +R+G+ DG+ K+  E+  I G+S+  V ++E RAL +L
Sbjct: 176 DGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKL 222

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

 Score = 82.3 bits (204), Expect = 1e-17
 Identities = 65/239 (27%), Positives = 120/239 (50%), Gaps = 17/239 (7%)

Query: 316 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 374
             G+  +R+ L+  NLRLV  V +++  RG    DL Q G +GL+K+V+KF      +F+
Sbjct: 27  QDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFS 86

Query: 375 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG 434
           +YA   +   I++ + +   T+++  ++    +K+ + K    +E    P  E+LA  +G
Sbjct: 87  TYAVPMIIGEIQRFL-RDDGTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLG 145

Query: 435 ITVEKLERLIFITRMPLSMQQPVWADQD---TTFQEITADTGVEIPDISVQKQLMRQHVR 491
           +T E++      +R P S+ + V  +     T   +I   +  +  D    K+ +R+   
Sbjct: 146 VTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSEEDWFDKIALKEAIRE--- 202

Query: 492 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 550
                L+ +ER IV LR+     K K+ SEV    G+S+ +V +LE + L ++K+ L  
Sbjct: 203 -----LDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLDE 252

Length = 252

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

 Score = 79.9 bits (197), Expect = 6e-17
 Identities = 63/233 (27%), Positives = 111/233 (47%), Gaps = 56/233 (24%)

Query: 319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAY 378
            S++  LI  NLRLVV++A++++  GI + DL+  G++GL+K+V  F P    + A+YA 
Sbjct: 51  ESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYA- 109

Query: 379 WWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 438
                         SR I   EN      ++L    +Y++  N                 
Sbjct: 110 --------------SRCI---EN------EIL----MYLRRNNK---------------- 126

Query: 439 KLERLIFITRMPLSMQQPV---WADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 495
                   TR  +S  +P+   W   +    ++   T  +I    +++++ R+ +R  L 
Sbjct: 127 --------TRSEVSFDEPLNVDWDGNELLLSDVLG-TDSDIVYKYLEEEVDRELLRKALA 177

Query: 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
            LN +E+ I+ LRFG+  G  K+  EV ++ G+S+  + +LE R L RLK+ +
Sbjct: 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEI 230

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

 Score = 79.2 bits (196), Expect = 8e-17
 Identities = 56/234 (23%), Positives = 113/234 (48%), Gaps = 19/234 (8%)

Query: 325 LINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 381
           LI   L LV  +A +        + L DL+Q G  GL+ ++E++ P  G +F +YA    
Sbjct: 1   LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYA---- 56

Query: 382 RQTIRKAIFQHSRTIR-LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 440
            Q IR A+    R +  +P ++     K+  A R         P +E++A  +G+ +++ 
Sbjct: 57  VQRIRGAMLDELRRLDWVPRSLRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEY 116

Query: 441 ERL---IFITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 495
            +    I    + +S+ + +    D   +  +   D   E P+  ++++ +R+ +   + 
Sbjct: 117 RQALNEINALSL-VSLDE-LLESGDDGGSLIDRIEDDKSEDPEEELEREELREALAEAIE 174

Query: 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549
            L+ +E+ ++ L +  E     +L E+G + GL++ RV Q+ S+AL +L+  L 
Sbjct: 175 SLSEREQLVLSLYYYEE----LNLKEIGEVLGLTESRVSQIHSQALKKLRAKLS 224

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

 Score = 75.4 bits (186), Expect = 2e-15
 Identities = 54/231 (23%), Positives = 106/231 (45%), Gaps = 56/231 (24%)

Query: 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380
           +R  LI  NLRLV H+ K+++  G  + DL+  G++GL+K++E F    G + A+YA   
Sbjct: 50  ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA--- 106

Query: 381 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSP---DKEDLARRVGITV 437
             + I   I  H R           L K    K + +Q+    P   DKE          
Sbjct: 107 -ARCIENEILMHLRN----------LKKTK--KEVSLQD----PIGVDKEG--------- 140

Query: 438 EKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 497
                        +S+   + +++D   +++         ++ ++ + + + +  L    
Sbjct: 141 -----------NEISLIDILGSEEDDVIEQV---------ELKMEVEKLYKKIDIL---- 176

Query: 498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
           + +E+ ++ +R+G+ +GK K+  E+    G+S+  V ++E RAL +L + L
Sbjct: 177 DEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227

Length = 233

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

 Score = 70.3 bits (173), Expect = 2e-13
 Identities = 52/194 (26%), Positives = 95/194 (48%), Gaps = 10/194 (5%)

Query: 322 REKLINANLRLVVHVAKQY-QGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380
           R +L+  NL LV   A ++         DL+Q GS+GL++++E+F P  G  F+S+A  +
Sbjct: 27  RNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPY 86

Query: 381 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 440
           +R  I+  +   S T+R+P     L  +  + ++   QE    P  +++A+ + I++E+ 
Sbjct: 87  IRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEW 146

Query: 441 E--RLIFITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDISVQKQLM-RQHVRNLLT 495
           +  +L    R PLS+  PV  D+D  T+  ++  D        S Q     R  ++  L 
Sbjct: 147 QEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPDPRYR----SFQLAQEDRIRLQQALA 202

Query: 496 LLNPKERCIVRLRF 509
            L  + R ++   F
Sbjct: 203 QLEERTREVLEFVF 216

Length = 256

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

 Score = 68.1 bits (167), Expect = 8e-13
 Identities = 61/235 (25%), Positives = 110/235 (46%), Gaps = 17/235 (7%)

Query: 323 EKLINANLRLV-VHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 379
           ++LI   + LV  HV +   G  + +S  DL   G +GL  ++EKF P    +F +YA +
Sbjct: 25  DELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASF 84

Query: 380 WVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 438
                IR AI    R    LP ++     KV  A     Q    +   +++A  +G+T E
Sbjct: 85  ----RIRGAIIDGLRKEDWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEE 140

Query: 439 KLERLI---FITRMPLSM-QQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLL 494
           ++E  +   F   + LS+ ++    D          D     P+  + K+ + + +   +
Sbjct: 141 EVEATMNEGFFANL-LSIDEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKI 199

Query: 495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549
             L+ KE+ ++ L +  E     +L+E+G +  LS  R+ Q+ S+AL++LK+ L 
Sbjct: 200 KQLSEKEQLVISLFYKEE----LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250

Length = 251

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

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 23/74 (31%), Positives = 40/74 (54%)

Query: 405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 464
           LL+K+  A+R   QE    P  E++A  +GI+ EK+  ++   R P+S+  PV  ++D  
Sbjct: 2   LLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDGE 61

Query: 465 FQEITADTGVEIPD 478
             ++  D   E P+
Sbjct: 62  LGDLLEDDDAESPE 75

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

 Score = 67.1 bits (164), Expect = 2e-12
 Identities = 57/230 (24%), Positives = 113/230 (49%), Gaps = 9/230 (3%)

Query: 322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 381
           R++++   L L  H+A+++ GRG    DL+Q   +GL+ +V +F  + G  F S+A   +
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTI 101

Query: 382 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL- 440
              +R+    +S ++++P  +  L  ++  A     Q    +P   +LA  +G+  E++ 
Sbjct: 102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVV 161

Query: 441 ERLIFITRM-PLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 499
           E L+  +    LS+     +  D       ADT  ++ D  + +   R+ +R LL  L  
Sbjct: 162 EGLVAGSAYNTLSIDSGGGSGDDDARA--IADTLGDV-DAGLDQIENREALRPLLAALPE 218

Query: 500 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 549
           +ER ++ LRF     +  + +++    G+S+  V +L ++ L RL+  L 
Sbjct: 219 RERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264

Length = 264

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

 Score = 64.7 bits (158), Expect = 3e-12
 Identities = 37/178 (20%), Positives = 74/178 (41%), Gaps = 23/178 (12%)

Query: 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 379
            + E+L    L LV   A++Y G      DL+QE  + L++++++F P+    F ++ + 
Sbjct: 1   EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFR 58

Query: 380 WVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK 439
             R  I   + +  R  R  + +  LL      +    Q        E+    +   +EK
Sbjct: 59  IARNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQ--------EEEREALREALEK 110

Query: 440 L---ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLL 494
           L   ER + +    L         +  +++EI    G+ +  +  + +  R+ +R LL
Sbjct: 111 LPEREREVLV----LRYL------EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158

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|218139 pfam04545, Sigma70_r4, Sigma-70, region 4

 Score = 59.7 bits (146), Expect = 8e-12
 Identities = 24/54 (44%), Positives = 36/54 (66%), Gaps = 4/54 (7%)

Query: 493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
            L  L P+ER ++ LRFG    +  +L E+G   G+S+ERVRQ+E RAL +L++
Sbjct: 1   ALASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50

Region 4 of sigma-70 like sigma-factors are 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. Length = 50

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

 Score = 62.2 bits (152), Expect = 6e-11
 Identities = 55/245 (22%), Positives = 114/245 (46%), Gaps = 24/245 (9%)

Query: 316 HSGNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCR 372
             G   +++L+     LV  +A + + R    + L DL+Q G +GL+++  ++  + G  
Sbjct: 4   AEGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGAS 63

Query: 373 FASYAYWWVRQTIRKAIFQHSRTIRL---PENIYTLLSKVLEAKRLYIQEGNHSPDKEDL 429
           F +YA     Q IR A+    R   L   P ++     +V +A R   QE    P   ++
Sbjct: 64  FETYA----GQRIRGAMLDELR--SLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTEV 117

Query: 430 ARRVGITVEKL-ERLI---FITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQL 485
           A ++G+++E+  E L+         +   +    D     ++   +  ++     ++ + 
Sbjct: 118 AEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQDEDPLQ----QLEDEE 173

Query: 486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           +R+ +   +  L  +E+ ++ L +  E     +L E+G + G+S+ RV Q+ S+A+ RL+
Sbjct: 174 LREALVEAIESLPEREQLVLSLYYQEE----LNLKEIGAVLGVSESRVSQIHSQAIKRLR 229

Query: 546 QSLGG 550
             LG 
Sbjct: 230 ARLGE 234

Length = 236

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

 Score = 61.6 bits (150), Expect = 2e-10
 Identities = 57/241 (23%), Positives = 113/241 (46%), Gaps = 25/241 (10%)

Query: 322 REKLINANLRLVVHVAKQYQGR-GISLH------DLLQEGSMGLMKSVEKFKPQAGCRFA 374
           RE LI     LV +VA    GR  + +       DL+  G  GL+ ++EKF P+   +F 
Sbjct: 33  REYLILKYSPLVKYVA----GRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFK 88

Query: 375 SYAYWWVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRV 433
           +YA       IR AIF   R+I  +P ++     ++  A  +       +P  E++A  +
Sbjct: 89  TYAV----TRIRGAIFDELRSIDWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADEL 144

Query: 434 GITVEKLE----RLIFITRMPLSMQQPVWADQDT-TFQEITADTGVEIPDISVQKQLMRQ 488
           GI++E+      +L   + + L+       + D  +  +         PD   +++ +++
Sbjct: 145 GISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKR 204

Query: 489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
            +   +  L  +E+ ++ L +  ED    +L E+G + G+++ R+ QL ++A+ +L+  L
Sbjct: 205 VIVEAIKTLPEREKKVLILYY-YED---LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260

Query: 549 G 549
            
Sbjct: 261 A 261

Length = 268

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

 Score = 60.0 bits (145), Expect = 4e-10
 Identities = 61/236 (25%), Positives = 106/236 (44%), Gaps = 16/236 (6%)

Query: 322 REKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAY 378
           R+ LI   L LV +VA +        +   DL   G  GL+++VE+F P+   RF  YA 
Sbjct: 25  RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84

Query: 379 WWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 438
           + ++  I   I    +   +P +++   +K+ +A     Q     P   +L   + I+ +
Sbjct: 85  FLIKAAI---IDDLRKQDWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQ 141

Query: 439 KLERLIFITR----MPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRN 492
           +L       R    + L+ + P  +D +     +E  AD   E     V K+     +  
Sbjct: 142 ELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERIADERAETGYDVVDKKEFSSILAE 201

Query: 493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
            +  L  KER ++ L +  E      L E+G I G+S+ RV Q+ S+AL +L+ +L
Sbjct: 202 AILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKLRATL 253

Length = 257

>gnl|CDD|100119 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)

 Score = 54.4 bits (132), Expect = 6e-10
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           R+ +   L  L  +ER ++ LRFG    +  S  E+  I G+S+  VRQ   RAL +L+
Sbjct: 1   RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55

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 periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP). Length = 55

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

 Score = 58.9 bits (143), Expect = 1e-09
 Identities = 61/238 (25%), Positives = 119/238 (50%), Gaps = 28/238 (11%)

Query: 323 EKLINANLRLVVHVAKQYQGRGISLH-DLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 381
           EKL+     LV  +A +Y  +G S H DL+Q G +GL+ ++ ++ P  G  F ++A   +
Sbjct: 32  EKLVKHYKNLVESLAYKYS-KGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTI 90

Query: 382 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK-L 440
              I++ +   + ++ +P  I  L  K+ +A      E   SP   ++A R+G++ E+ L
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVL 150

Query: 441 ERLIFITRM-----PLSMQQPVWADQD---TTFQEITA--DTGVEIPDISVQKQLMRQHV 490
           E +     M      LS+   + AD D    T  +I    + G E      +++++ + +
Sbjct: 151 EAM----EMGKSYQALSVDHSIEADSDGSTVTLLDIVGQQEDGYE----LTEQRMILEKI 202

Query: 491 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
              L +L+ +E+ I++  F IE+    S  E G   G+S+  V +L+ +A+ +L+++ 
Sbjct: 203 ---LPVLSDREKSIIQCTF-IEN---LSQKETGERLGISQMHVSRLQRQAIKKLREAA 253

Length = 257

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

 Score = 56.8 bits (138), Expect = 4e-09
 Identities = 27/69 (39%), Positives = 46/69 (66%), Gaps = 1/69 (1%)

Query: 310 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQ 368
            L ++L  G  + R  LI  NLRLVV++A++++  GI++ DL+  G++GL+K+V  F P+
Sbjct: 41  YLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPE 100

Query: 369 AGCRFASYA 377
              + A+YA
Sbjct: 101 KKIKLATYA 109

Length = 234

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

 Score = 54.9 bits (132), Expect = 2e-08
 Identities = 52/229 (22%), Positives = 111/229 (48%), Gaps = 10/229 (4%)

Query: 322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 381
           +EKL++    LV  +A +Y   G    DL+Q G +GL+ ++ ++    G  F  +A   +
Sbjct: 31  QEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTI 90

Query: 382 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 441
              I++ +   + ++ +P  I  L  K+ +A          SP   ++A  +G++ E++ 
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150

Query: 442 RLIFITR--MPLSMQQPVWADQDTTFQEITADTG-VEIPDISVQKQLMRQHVRNLLTLLN 498
            ++ + +    LS+   + AD D +        G VE      +++++   +  +L +L+
Sbjct: 151 EIMEMGQSYRALSVDDVIEADSDGSTVARLDSVGEVEDGYDQTERRMV---LEKILPILS 207

Query: 499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 547
            +E+ I+   F  E+   K   E G   G+S+  V +L+ +A+ +LK++
Sbjct: 208 EREKSIIHCTF-EENLSQK---ETGERLGISQMHVSRLQRQAISKLKEA 252

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

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

 Score = 49.9 bits (120), Expect = 9e-07
 Identities = 22/60 (36%), Positives = 37/60 (61%), Gaps = 4/60 (6%)

Query: 491 RNLLTL----LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
           R LL      L+ +E+ I+ LRFG+  G+ K+  EV ++ G+S+  + +LE R + RLK+
Sbjct: 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228

Length = 234

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

 Score = 43.4 bits (103), Expect = 1e-04
 Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 1/96 (1%)

Query: 316 HSGNS-SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 374
            SG+  + E LI      V   A+ Y   G    D++QEG +GL K++  +       F 
Sbjct: 19  RSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFK 78

Query: 375 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVL 410
           S+A   + + I  AI   +R   +P N Y  L K +
Sbjct: 79  SFAELCITRQIITAIKTANRQKHIPLNSYVSLDKPI 114

Length = 208

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

 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 1/104 (0%)

Query: 306 LSCRDLKSELHSGNS-SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK 364
           L   ++      GN+ + E LIN     V   A+ Y   G    D++QEG +GL K++  
Sbjct: 4   LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRD 63

Query: 365 FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSK 408
           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|183523 PRK12427, PRK12427, flagellar biosynthesis sigma factor; Provisional

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 52/230 (22%), Positives = 98/230 (42%), Gaps = 28/230 (12%)

Query: 324 KLINANLRLVVHVAKQ--YQGRG-ISLHDLLQEGSMGLMKSVEKF-KPQAGCRFASYAYW 379
           K +NA L LV  V +Q  +Q    I   D+ Q   MGL++++ ++  P     FA+YA  
Sbjct: 19  KYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDEQ--FAAYAV- 75

Query: 380 WVRQTIRKAIFQHSRTIRL-PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 438
                IR AI    R +   P  +     K  +A R   +   H P+ E+++  + +T E
Sbjct: 76  ---HRIRGAILDELRELDWRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAE 132

Query: 439 KLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS--VQKQLM-RQHVRNLLT 495
           +                   A    +  E+ A         S  +++ ++   +++  L+
Sbjct: 133 EY----------QEYLLLENAGTLESLDELLALEAHNDILQSRDLEENIIIEDNLKQALS 182

Query: 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
            L+ +E+ I+ L +  E     SL E+  +  L++ R+ QL  +   ++K
Sbjct: 183 QLDEREQLILHLYYQHE----MSLKEIALVLDLTEARICQLNKKIAQKIK 228

Length = 231

>gnl|CDD|224511 COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 20/102 (19%), Positives = 37/102 (36%), Gaps = 4/102 (3%)

Query: 454 QQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIED 513
           ++   A  +                  +  +   + +R  L  L P++R    LR+ +E 
Sbjct: 85  RKRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRY-LEG 143

Query: 514 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 555
               S  E+  I G+S   V+    RA  +L++ L      G
Sbjct: 144 ---LSYEEIAEILGISVGTVKSRLHRARKKLREQLEEAGERG 182

Length = 182

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	561
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	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
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	100.0
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	100.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	100.0
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	100.0
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	100.0
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	100.0
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	100.0
PRK08215	258	sporulation sigma factor SigG; Reviewed	100.0
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	100.0
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	100.0
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	100.0
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	100.0
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	100.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	100.0
PRK05572	252	sporulation sigma factor SigF; Validated	100.0
PRK08583	257	RNA polymerase sigma factor SigB; Validated	100.0
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	100.0
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	100.0
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	100.0
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.96
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.93
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.93
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.92
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.91
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.9
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.89
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.89
PRK12513	194	RNA polymerase sigma factor; Provisional	99.89
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.89
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.88
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.88
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.87
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.87
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.87
PRK12519	194	RNA polymerase sigma factor; Provisional	99.87
PRK12514	179	RNA polymerase sigma factor; Provisional	99.87
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.87
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.87
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.86
PRK11922	231	RNA polymerase sigma factor; Provisional	99.86
PRK12524	196	RNA polymerase sigma factor; Provisional	99.86
PRK12537	182	RNA polymerase sigma factor; Provisional	99.86
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.86
PRK12538	233	RNA polymerase sigma factor; Provisional	99.86
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.86
PRK12534	187	RNA polymerase sigma factor; Provisional	99.85
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.85
PRK12526	206	RNA polymerase sigma factor; Provisional	99.85
PRK12515	189	RNA polymerase sigma factor; Provisional	99.85
PRK12542	185	RNA polymerase sigma factor; Provisional	99.85
PRK11924	179	RNA polymerase sigma factor; Provisional	99.85
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.84
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.84
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.84
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.84
PRK12531	194	RNA polymerase sigma factor; Provisional	99.83
PRK12543	179	RNA polymerase sigma factor; Provisional	99.83
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.83
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.83
PRK12536	181	RNA polymerase sigma factor; Provisional	99.82
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.82
PRK12522	173	RNA polymerase sigma factor; Provisional	99.82
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.82
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.82
PRK12520	191	RNA polymerase sigma factor; Provisional	99.82
PRK12539	184	RNA polymerase sigma factor; Provisional	99.82
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.82
PRK12512	184	RNA polymerase sigma factor; Provisional	99.81
PRK12533	216	RNA polymerase sigma factor; Provisional	99.81
PRK12529	178	RNA polymerase sigma factor; Provisional	99.81
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.81
PRK12518	175	RNA polymerase sigma factor; Provisional	99.81
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.8
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.8
PRK12516	187	RNA polymerase sigma factor; Provisional	99.8
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.8
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.8
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.8
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.8
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.79
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.79
PRK12528	161	RNA polymerase sigma factor; Provisional	99.78
PRK12547	164	RNA polymerase sigma factor; Provisional	99.78
PRK12532	195	RNA polymerase sigma factor; Provisional	99.78
PRK12545	201	RNA polymerase sigma factor; Provisional	99.78
PRK12541	161	RNA polymerase sigma factor; Provisional	99.78
PRK12530	189	RNA polymerase sigma factor; Provisional	99.78
PRK12544	206	RNA polymerase sigma factor; Provisional	99.78
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.78
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.77
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.77
PRK12535	196	RNA polymerase sigma factor; Provisional	99.77
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.77
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.76
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.76
PRK12540	182	RNA polymerase sigma factor; Provisional	99.76
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.76
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.75
PRK12517	188	RNA polymerase sigma factor; Provisional	99.75
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.75
PRK12546	188	RNA polymerase sigma factor; Provisional	99.74
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.73
PRK12511	182	RNA polymerase sigma factor; Provisional	99.73
PRK12525	168	RNA polymerase sigma factor; Provisional	99.72
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.7
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.69
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.66
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.64
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.63
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.51
PRK09191	261	two-component response regulator; Provisional	99.51
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.46
PF07638	185	Sigma70_ECF: ECF sigma factor	99.37
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.24
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.24
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	99.03
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	98.93
PRK06930	170	positive control sigma-like factor; Validated	98.66
PRK00118	104	putative DNA-binding protein; Validated	98.45
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.3
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.18
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.14
PRK04217	110	hypothetical protein; Provisional	98.09
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.03
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	97.98
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	97.96
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	97.93
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.8
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.65
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.62
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.6
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.59
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.54
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.48
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.31
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.28
PRK10840	216	transcriptional regulator RcsB; Provisional	97.23
PRK13870	234	transcriptional regulator TraR; Provisional	97.23
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.23
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.21
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.21
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.2
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	97.16
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	97.15
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	97.02
COG2197	211	CitB Response regulator containing a CheY-like rec	97.02
COG4566	202	TtrR Response regulator [Signal transduction mecha	96.96
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	96.96
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.95
PRK09483	217	response regulator; Provisional	96.86
PRK15369	211	two component system sensor kinase SsrB; Provision	96.75
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.74
COG3413	215	Predicted DNA binding protein [General function pr	96.67
PRK01381	99	Trp operon repressor; Provisional	96.5
PRK10651	216	transcriptional regulator NarL; Provisional	96.47
COG1356	143	tfx Transcriptional regulator [DNA replication, re	96.41
PRK09390	202	fixJ response regulator FixJ; Provisional	96.39
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.34
COG1342	99	Predicted DNA-binding proteins [General function p	96.07
PRK15320	251	transcriptional activator SprB; Provisional	95.93
PRK10403	215	transcriptional regulator NarP; Provisional	95.86
COG4941	415	Predicted RNA polymerase sigma factor containing a	95.53
PRK09935	210	transcriptional regulator FimZ; Provisional	95.44
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	95.42
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.3
PRK13558	665	bacterio-opsin activator; Provisional	95.3
PRK04841	903	transcriptional regulator MalT; Provisional	95.21
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	94.97
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	94.87
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	94.53
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	94.52
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.51
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	94.44
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	94.27
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	94.13
PRK15418	318	transcriptional regulator LsrR; Provisional	94.1
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	93.96
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	93.74
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	93.48
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	93.47
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	93.4
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	93.32
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	93.19
PRK05901	509	RNA polymerase sigma factor; Provisional	93.15
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	92.09
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	92.04
PF13730	55	HTH_36: Helix-turn-helix domain	91.76
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	91.74
PHA00675	78	hypothetical protein	91.54
PRK07598	415	RNA polymerase sigma factor SigC; Validated	91.34
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	91.02
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	90.84
PF13518	52	HTH_28: Helix-turn-helix domain	90.82
smart00351	125	PAX Paired Box domain.	90.59
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	90.07
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	89.95
PF10668	60	Phage_terminase: Phage terminase small subunit; In	89.82
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	89.79
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	89.75
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	89.49
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	89.49
PRK05932	455	RNA polymerase factor sigma-54; Reviewed	89.38
PHA02547	179	55 RNA polymerase sigma factor; Provisional	89.29
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	89.26
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	89.19
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	89.17
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	89.08
PHA02591	83	hypothetical protein; Provisional	88.98
COG3355	126	Predicted transcriptional regulator [Transcription	88.86
PRK11083	228	DNA-binding response regulator CreB; Provisional	88.54
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	88.3
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	88.29
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	88.0
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	87.82
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	87.58
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	87.47
PRK05949	327	RNA polymerase sigma factor; Validated	87.24
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	87.07
cd00131	128	PAX Paired Box domain	87.07
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	87.04
PRK07670	251	RNA polymerase sigma factor SigD; Validated	87.03
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	86.58
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	86.49
PRK12423	202	LexA repressor; Provisional	86.42
PRK15479	221	transcriptional regulatory protein TctD; Provision	86.06
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	86.04
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	86.01
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	85.91
PRK12469	481	RNA polymerase factor sigma-54; Provisional	85.86
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	85.32
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	85.29
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	85.18
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	84.99
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	84.95
PRK07405	317	RNA polymerase sigma factor SigD; Validated	84.67
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	84.62
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	84.35
PRK10046	225	dpiA two-component response regulator DpiA; Provis	84.26
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	84.25
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	84.2
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	84.09
PF12728	51	HTH_17: Helix-turn-helix domain	83.5
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	83.5
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	83.26
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	83.26
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	82.99
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	82.88
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	82.47
COG1508	444	RpoN DNA-directed RNA polymerase specialized sigma	82.26
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	82.01
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	81.87
COG3415	138	Transposase and inactivated derivatives [DNA repli	81.86
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	81.66
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	81.56
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	81.43
TIGR01764	49	excise DNA binding domain, excisionase family. An	81.33
PRK00215	205	LexA repressor; Validated	81.21
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	80.89
CHL00148	240	orf27 Ycf27; Reviewed	80.76
PRK13413	200	mpi multiple promoter invertase; Provisional	80.56
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	80.41
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	80.25

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=7.3e-65  Score=540.80  Aligned_cols=315  Identities=38%  Similarity=0.651  Sum_probs=299.0

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHhhhhCCCCcHHHHHHHc
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI  304 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~--------------------le~~~~~l~~~~g~~pt~~ewA~a~  304 (561)
                      ..|+++.||++|++.||||++||++|+++||.++.                    |++++..|++.+|++||..|||.++
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            57899999999999999999999999999999999                    8999999999999999999999554


Q ss_pred             ----------------------cCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhh
Q 008556          305 ----------------------GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV  362 (561)
Q Consensus       305 ----------------------g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAi  362 (561)
                                            ||++++|+..++.|..|+++||.+|+++|++||++|.++|++++||||||++|||+|+
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                                  5566677777788999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHH
Q 008556          363 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER  442 (561)
Q Consensus       363 ekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~  442 (561)
                      ++|||++|++|+|||+||||++|.+++++++++||+|.|+...+++++++.+.+.+++||.|+.+|||+.+|+++++|+.
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             HHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHH
Q 008556          443 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV  522 (561)
Q Consensus       443 ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EI  522 (561)
                      ++.....++|||.+++++++..+.+.+.++. .+|++.+....+...|..+|..||++||.||.|||||+||+++|++||
T Consensus       298 ~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~-~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EI  376 (415)
T PRK07598        298 VLLRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEI  376 (415)
T ss_pred             HHHHccCCcccccccCCCccccHHHhccCCC-CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHH
Confidence            9999999999999999888888888876543 578888888899999999999999999999999999999999999999


Q ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 008556          523 GNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL  560 (561)
Q Consensus       523 Ae~LGISrerVRqie~RALkKLR~~l~~~~l~~yldll  560 (561)
                      |+.||||+++||+++++|++|||+.-....+++|++.|
T Consensus       377 A~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~~~  414 (415)
T PRK07598        377 GRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLELL  414 (415)
T ss_pred             HHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999764

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=5.5e-62  Score=515.00  Aligned_cols=312  Identities=37%  Similarity=0.728  Sum_probs=299.9

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  324 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~  324 (561)
                      ..|++..||++|+++|+||++||++|+++|++++.+++++.+|+...|++|+..+||.++|++..+|..+++.|..|++.
T Consensus        61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~  140 (373)
T PRK07406         61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK  140 (373)
T ss_pred             CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556          325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  404 (561)
Q Consensus       325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~  404 (561)
                      ||..|+++|+++|++|.++|.+++||+|||+||||+|+++|||.+|++|+|||+||||++|.++|++++++||+|.|+..
T Consensus       141 Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~  220 (373)
T PRK07406        141 MVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYE  220 (373)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556          405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  484 (561)
Q Consensus       405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~  484 (561)
                      .+++++++...+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++++.. .+|++.+...
T Consensus       221 ~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~~  299 (373)
T PRK07406        221 TISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAKN  299 (373)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHHH
Confidence            999999999999999999999999999999999999999888889999999998777778888888763 4788888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 008556          485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA  557 (561)
Q Consensus       485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yl  557 (561)
                      .+...|..+|..||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+......++.|+
T Consensus       300 ~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~  372 (373)
T PRK07406        300 LLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI  372 (373)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence            8999999999999999999999999999889999999999999999999999999999999999888898886

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=2e-61  Score=504.39  Aligned_cols=311  Identities=40%  Similarity=0.676  Sum_probs=297.5

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  324 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~  324 (561)
                      ..|++..||++|+++|+||++||++|+++|+.++.+++.+..|+..+|++|+..+|+.+++|++.+|+..++.|+.|++.
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             HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556          325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  404 (561)
Q Consensus       325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~  404 (561)
                      ||..|+++|+++|++|.+++.+++|||||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
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             HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556          405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  484 (561)
Q Consensus       405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~  484 (561)
                      .+++++++.+.+..++|++|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|.. .+|++.+...
T Consensus       176 ~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~~  254 (327)
T PRK05949        176 KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQE  254 (327)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHHH
Confidence            999999999999999999999999999999999999999998899999999998777777888888765 5789889988


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556          485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  558 (561)
Q Consensus       485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld  558 (561)
                      .+...|..+|+.||++||.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+.  ...++.|+.
T Consensus       255 ~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~  326 (327)
T PRK05949        255 LLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA  326 (327)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999999999994  456777764

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

Probab=100.00  E-value=1.2e-60  Score=492.69  Aligned_cols=298  Identities=44%  Similarity=0.755  Sum_probs=285.6

Q ss_pred             hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 008556          247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  326 (561)
Q Consensus       247 d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI  326 (561)
                      |++..||++|+++|+||++||.+|+++++.++.++..+..|+.+.|++||..+||+++|+++.+|...++.|..|++.||
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             HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556          327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  406 (561)
Q Consensus       327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l  406 (561)
                      .+|+++|++||++|.++|.+++|||||||+|||+|+++|||.+|++|+|||+||||++|.+++.+++++||+|.++...+
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             HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556          407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  486 (561)
Q Consensus       407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~  486 (561)
                      ++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+.+.+. ..+|++.+...+.
T Consensus       161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~~  239 (298)
T TIGR02997       161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERESL  239 (298)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHHH
Confidence            999999999999999999999999999999999999999888999999998776666777777774 4578888998889


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ...|..+|+.||++||+||.+||||+|++++|++|||+.||||++||||++++|++|||
T Consensus       240 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr  298 (298)
T TIGR02997       240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR  298 (298)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            99999999999999999999999999989999999999999999999999999999996

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).

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=2.6e-60  Score=494.27  Aligned_cols=310  Identities=38%  Similarity=0.644  Sum_probs=296.1

Q ss_pred             ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHH
Q 008556          246 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  325 (561)
Q Consensus       246 ~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~L  325 (561)
                      +|++..||++|+++|+||++||.+|+++|++++.+++++..|+.++|++|+..+||.++++++.+|+..++.|..|+++|
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             HHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHH
Q 008556          326 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL  405 (561)
Q Consensus       326 I~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~  405 (561)
                      |..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+...
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             HHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHH
Q 008556          406 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQL  485 (561)
Q Consensus       406 l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e  485 (561)
                      +++++++...+...+|+.|+.+|||+.+|+++++|..++......+|||.+++++.+..+.++++++. ..|++.+...+
T Consensus       167 ~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~~  245 (317)
T PRK07405        167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSS  245 (317)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHHH
Confidence            99999999999999999999999999999999999999988888999999998777777888887764 57888899889


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556          486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  558 (561)
Q Consensus       486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld  558 (561)
                      +...|..+|+.||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||+.  ...+..|+.
T Consensus       246 ~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~  316 (317)
T PRK07405        246 LQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA  316 (317)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999995  456777764

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=2.9e-59  Score=508.70  Aligned_cols=301  Identities=35%  Similarity=0.613  Sum_probs=277.2

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  324 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~  324 (561)
                      ..|++..||++|+++|+||++||++|+++|+.+..++..   +.       ...+|+.   ....+|.+.++.|..|+++
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            568999999999999999999999999999875433321   11       1123442   2457788889999999999


Q ss_pred             HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556          325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  404 (561)
Q Consensus       325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~  404 (561)
                      ||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+..
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             HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556          405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  484 (561)
Q Consensus       405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~  484 (561)
                      .++++.++.+.+.+.+||.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|.....|++.+...
T Consensus       356 ~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~~~  435 (509)
T PRK05901        356 TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFT  435 (509)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999888999999999877777888999988777899999999


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556          485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  558 (561)
Q Consensus       485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld  558 (561)
                      .++..|..+|..|++|||.||.+||||++++++|++|||+.||||++|||||+.+||+|||.......|+.|++
T Consensus       436 ~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~  509 (509)
T PRK05901        436 LLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD  509 (509)
T ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999974

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

Probab=100.00  E-value=4.2e-59  Score=482.84  Aligned_cols=314  Identities=36%  Similarity=0.654  Sum_probs=289.1

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh-hhCCCCcHH---------------HHHHHccCCH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC  308 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~-~~g~~pt~~---------------ewA~a~g~~~  308 (561)
                      ..|.+..|+.+++..+++++++|.++.+.++....+......|.. ..+..|+..               +|+..+..++
T Consensus         7 ~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E   86 (342)
T COG0568           7 SADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE   86 (342)
T ss_pred             chhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence            357889999999999999999999999999887777667777776 677888876               6666555554


Q ss_pred             -HHHHHHHhhcH---HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          309 -RDLKSELHSGN---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       309 -~eL~~~l~~G~---~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                       ..|..++..|.   .|+.+||.+|+|||++||++|.|+|+++.|||||||||||+|+++|||++||+|||||+||||++
T Consensus        87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqa  166 (342)
T COG0568          87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQA  166 (342)
T ss_pred             HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHH
Confidence             66777777663   69999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      |.++|.+++|+||+|.|+...+++++++.+.+.+++|++|+.+|||+.+|+++++|..++.....++|||.|++++++..
T Consensus       167 I~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~  246 (342)
T COG0568         167 ITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSE  246 (342)
T ss_pred             HHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998889


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  543 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~-L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK  543 (561)
                      +.|++.|+...+|++.+.+..+.+.+...|.. |++||+.||++|||++|+++.|++|||+.+|||++|||||+.+|++|
T Consensus       247 l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~K  326 (342)
T COG0568         247 LGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRK  326 (342)
T ss_pred             HHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence            99999999877999999999999999999999 99999999999999999999999999999999999999999999999


Q ss_pred             HHH-HhhcCchhhhhh
Q 008556          544 LKQ-SLGGKASYGYAD  558 (561)
Q Consensus       544 LR~-~l~~~~l~~yld  558 (561)
                      ||. ......+++|++
T Consensus       327 Lr~~~~~~~~~~~~l~  342 (342)
T COG0568         327 LRRHPERSALLRSYLD  342 (342)
T ss_pred             HHHhhhhhhHHHHhhC
Confidence            994 444555677764

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=5.7e-58  Score=477.52  Aligned_cols=300  Identities=36%  Similarity=0.629  Sum_probs=275.5

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  324 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~  324 (561)
                      .+|++..||++|+++|+||++||.+|+++|+.+..++..           |...+|....  ...+|...++.|..|+++
T Consensus        24 ~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~   90 (324)
T PRK07921         24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRH   90 (324)
T ss_pred             CCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHH
Confidence            357899999999999999999999999999986655543           2223332111  456788899999999999


Q ss_pred             HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556          325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  404 (561)
Q Consensus       325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~  404 (561)
                      ||..|+++|+++|++|.++|.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+..
T Consensus        91 Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~  170 (324)
T PRK07921         91 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE  170 (324)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556          405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  484 (561)
Q Consensus       405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~  484 (561)
                      .+++++++...+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+...
T Consensus       171 ~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~  250 (324)
T PRK07921        171 QVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAG  250 (324)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999998888899999999877777888999887666888888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 008556          485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA  557 (561)
Q Consensus       485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yl  557 (561)
                      +++..|..+|..|++|||.||.+||||+||+++|++|||+.||||++|||||+.+|++|||.......++.|+
T Consensus       251 ~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~  323 (324)
T PRK07921        251 LLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA  323 (324)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence            9999999999999999999999999999989999999999999999999999999999999998888888885

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.5e-54  Score=459.37  Aligned_cols=276  Identities=36%  Similarity=0.704  Sum_probs=262.6

Q ss_pred             CCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHH
Q 008556          243 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR  322 (561)
Q Consensus       243 ~~~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Ar  322 (561)
                      ....|+++.||++|+++|+||++||.+|+.+++.                                        |+..|+
T Consensus        92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~  131 (367)
T PRK09210         92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAK  131 (367)
T ss_pred             cccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHH
Confidence            3457899999999999999999999999988764                                        345899


Q ss_pred             HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556          323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  402 (561)
Q Consensus       323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~  402 (561)
                      +.||..|+++|+++|++|.+++.+++||+|||+||||+|+++|||.+|++|+|||+||||++|.++|++++|+||+|.|+
T Consensus       132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~  211 (367)
T PRK09210        132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM  211 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHH
Q 008556          403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  482 (561)
Q Consensus       403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le  482 (561)
                      ...++++.++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.+++.+++..+.+++.|....+|++.+.
T Consensus       212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~  291 (367)
T PRK09210        212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAA  291 (367)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHH
Confidence            99999999999999999999999999999999999999999998888999999998877778899999887778999999


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556          483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  558 (561)
Q Consensus       483 ~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld  558 (561)
                      ...++..|..+|..||++||.||.+||||+||+++|++|||+.||||++||||++.+||+|||+......|+.|++
T Consensus       292 ~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~  367 (367)
T PRK09210        292 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE  367 (367)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999874

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.3e-51  Score=463.18  Aligned_cols=274  Identities=34%  Similarity=0.633  Sum_probs=252.6

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008556          248 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  327 (561)
Q Consensus       248 ~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~  327 (561)
                      .+..||.++...+.||++|+.+++++++.               |.                      .....|+++||.
T Consensus       345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~---------------g~----------------------~~~~~a~~~Li~  387 (619)
T PRK05658        345 KLQQELEAIEEETGLTIEELKEINRQISK---------------GE----------------------AKARRAKKEMVE  387 (619)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHhc---------------cc----------------------hhhhHHHHHHHH
Confidence            44556777777777777777777766654               21                      011368999999


Q ss_pred             HHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHH
Q 008556          328 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  407 (561)
Q Consensus       328 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~  407 (561)
                      +|+|||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|++++|+||+|.|+...++
T Consensus       388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~  467 (619)
T PRK05658        388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN  467 (619)
T ss_pred             HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHHH
Q 008556          408 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR  487 (561)
Q Consensus       408 ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~~  487 (561)
                      +++++...+.+++||.||.+|||+.+|+++++|..++.....++|||.|++++++..+.+++.|....+|++.+....++
T Consensus       468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~  547 (619)
T PRK05658        468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLR  547 (619)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHH
Confidence            99999999999999999999999999999999999999888999999999888888899999998777899989899999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556          488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  558 (561)
Q Consensus       488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld  558 (561)
                      ..|..+|..||+|||.||++||||+++.++|++|||+.||||++||||++.+|++|||+......|+.|+|
T Consensus       548 ~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~  618 (619)
T PRK05658        548 EATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD  618 (619)
T ss_pred             HHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence            99999999999999999999999998899999999999999999999999999999999999999999987

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

Probab=100.00  E-value=8.5e-48  Score=384.61  Aligned_cols=238  Identities=39%  Similarity=0.753  Sum_probs=227.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556          321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  400 (561)
Q Consensus       321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~  400 (561)
                      |+++||..|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+|+|.
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             hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556          401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  480 (561)
Q Consensus       401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~  480 (561)
                      ++...++++.++...+.+++|++||.+|||+.+|+++++|..++......+|||.+++.+++.++.+.+.|+...+|++.
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~  160 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY  160 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence            99999999999999999999999999999999999999999998888889999999877766678888888877788888


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556          481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  558 (561)
Q Consensus       481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld  558 (561)
                      +...++...|..+|..||++||.||.++|||++++++|++|||+.||||+++|+|++.+|++|||+.+....++.|+|
T Consensus       161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~~  238 (238)
T TIGR02393       161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD  238 (238)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhhC
Confidence            888889999999999999999999999999998899999999999999999999999999999999999999999975

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=100.00  E-value=1e-44  Score=378.52  Aligned_cols=272  Identities=35%  Similarity=0.567  Sum_probs=253.7

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  324 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~  324 (561)
                      ..|.++.|+.+|+..|+||+++|.+|+.+++.                                        |+..|++.
T Consensus        51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~   90 (325)
T PRK05657         51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR   90 (325)
T ss_pred             cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence            46788999999999999999999999987654                                        45689999


Q ss_pred             HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556          325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  404 (561)
Q Consensus       325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~  404 (561)
                      ||..|.++|+++|++|.+++.+++||+|||++|+|+++++||+.+|++|+||++||||++|.++++++.+.|++|.++..
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            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHH
Q 008556          405 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  484 (561)
Q Consensus       405 ~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~  484 (561)
                      .++++.++...+.+.+|+.|+.+|||+.+|+++++|..++.......|+|.++..+...++.+.+.+....+|+..+...
T Consensus       171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~  250 (325)
T PRK05657        171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDD  250 (325)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHH
Confidence            99988899999999999999999999999999999999998888889999998777666778888877666888888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 008556          485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY  556 (561)
Q Consensus       485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~y  556 (561)
                      +....|..+|..||+++|.||.+||||.+.+++|++|||+.||||+++|++++++|+++||+.+...++..+
T Consensus       251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~~~  322 (325)
T PRK05657        251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLSIE  322 (325)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccchh
Confidence            888999999999999999999999999888999999999999999999999999999999999998887644

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=2e-44  Score=369.84  Aligned_cols=262  Identities=27%  Similarity=0.470  Sum_probs=223.8

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  324 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~  324 (561)
                      +.+.+..|++++++.|+||.++|.+|+.+++.                                       .|+..|++.
T Consensus        12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~~   52 (284)
T PRK06596         12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAKQ   52 (284)
T ss_pred             CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHHH
Confidence            45789999999999999999999999887532                                       245689999


Q ss_pred             HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH
Q 008556          325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  404 (561)
Q Consensus       325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~  404 (561)
                      ||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.+++++++++|++|.+...
T Consensus        53 Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~  132 (284)
T PRK06596         53 LVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQ  132 (284)
T ss_pred             HHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999888999987642


Q ss_pred             --HHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh-cCCCccCCCCCCCCCC--chhhhhcccCCCCChhH
Q 008556          405 --LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI-TRMPLSMQQPVWADQD--TTFQEITADTGVEIPDI  479 (561)
Q Consensus       405 --~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~-~~~~~SLD~~v~~d~~--~~l~d~l~d~~~~~pee  479 (561)
                        ...++.+....+.  .+++|+.+|||+.+|+++++|..++.. ....+|||.+++++++  .++.+.+.|+. .+|++
T Consensus       133 ~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~~  209 (284)
T PRK06596        133 RKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPAD  209 (284)
T ss_pred             HHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCchH
Confidence              2334444444443  358999999999999999999998753 3478999999865532  45778887764 46776


Q ss_pred             HHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          480 SVQKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       480 ~le~~----e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      .++..    ++...|..+|+.||++||.||.+||+. + +++|++|||+.||||++||||++++|++|||..+..
T Consensus       210 ~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~  282 (284)
T PRK06596        210 VLEEDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA  282 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            66654    357789999999999999999999973 2 689999999999999999999999999999998754

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=2.4e-44  Score=370.14  Aligned_cols=264  Identities=26%  Similarity=0.451  Sum_probs=226.2

Q ss_pred             hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 008556          247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  326 (561)
Q Consensus       247 d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI  326 (561)
                      +.++.||++++++|+||+++|.+|+.+++.                                       .|+..|+++||
T Consensus         6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~Lv   46 (289)
T PRK07500          6 SADRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRII   46 (289)
T ss_pred             hHHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHH
Confidence            467789999999999999999999987642                                       14568999999


Q ss_pred             HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHH--
Q 008556          327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT--  404 (561)
Q Consensus       327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~--  404 (561)
                      ..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++++|+|.+...  
T Consensus        47 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~  126 (289)
T PRK07500         47 SAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKA  126 (289)
T ss_pred             HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999988654  


Q ss_pred             HHHHHHHHHHHHHH---hCCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCCccCCCCCCCCCCc--hhhhhcccCCCCChh
Q 008556          405 LLSKVLEAKRLYIQ---EGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQEITADTGVEIPD  478 (561)
Q Consensus       405 ~l~ki~ka~~~l~~---e~gr~Pt~eEIA~~lgis~e~v~~ll~-~~~~~~SLD~~v~~d~~~--~l~d~l~d~~~~~pe  478 (561)
                      ...++++....+.+   .+|+.|+.+|||+.||+++++|..+.. ....++|||.+++++++.  ++.+.+.++.. +|+
T Consensus       127 ~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~-~pe  205 (289)
T PRK07500        127 LFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP-LPD  205 (289)
T ss_pred             HHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC-Cch
Confidence            33444445444444   689999999999999999999988753 355799999998765443  57788877643 566


Q ss_pred             HHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          479 ISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       479 e~le~----~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      +.+..    .+....|..+|..||++||.||.+||+.  ++++|++|||+.||||+++|+|++++|++|||..+....
T Consensus       206 ~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~~  281 (289)
T PRK07500        206 EQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQS  281 (289)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            55443    3456779999999999999999999962  378999999999999999999999999999999987544

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=8.2e-44  Score=362.57  Aligned_cols=258  Identities=28%  Similarity=0.501  Sum_probs=217.0

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008556          248 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  327 (561)
Q Consensus       248 ~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~  327 (561)
                      ++..||++++++|+|++++|.+|+.++..                                       .++..|++.||.
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            57789999999999999999999886432                                       245689999999


Q ss_pred             HHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH--HH
Q 008556          328 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL  405 (561)
Q Consensus       328 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~--~~  405 (561)
                      .|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++.++++|+|.+..  ..
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            9999999999999999999999999999999999999999999999999999999999999999988899997653  33


Q ss_pred             HHHHHHHHHHHHHhCCCCC-CHHHHHHHhCCCHHHHHHHHHhc-CCCccCCCCCCCCCC--chhhhhcccCCCCChhHHH
Q 008556          406 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQD--TTFQEITADTGVEIPDISV  481 (561)
Q Consensus       406 l~ki~ka~~~l~~e~gr~P-t~eEIA~~lgis~e~v~~ll~~~-~~~~SLD~~v~~d~~--~~l~d~l~d~~~~~pee~l  481 (561)
                      ..++.++...+.  +++.| +.+|||+.+|+++++|..++... ....|||.+++++++  ..+.+.+.|.. .+|++.+
T Consensus       123 ~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~~  199 (270)
T TIGR02392       123 FFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDTL  199 (270)
T ss_pred             HHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHHH
Confidence            444444444432  32455 69999999999999999986533 348999999866543  25667777764 3677666


Q ss_pred             HHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          482 QKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       482 e~~----e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      +..    .+...|..+|..||++||.||.+||+.  ++++|++|||+.||||+++|+|++++|++|||..+.
T Consensus       200 ~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~  269 (270)
T TIGR02392       200 EEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA  269 (270)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence            543    356789999999999999999999962  368999999999999999999999999999998764

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=3.7e-43  Score=357.03  Aligned_cols=220  Identities=24%  Similarity=0.393  Sum_probs=200.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556          320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  399 (561)
Q Consensus       320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP  399 (561)
                      .++++||.+|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+|
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--cCCCccCCCCCCCCCCc--hhhhhcccCCCC
Q 008556          400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDT--TFQEITADTGVE  475 (561)
Q Consensus       400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~--~l~d~l~d~~~~  475 (561)
                      +++...+++++++...+.+++|+.||.+|||+.+|+++++|.+++..  ...+.|||.+++++++.  .+.+.++     
T Consensus       120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~-----  194 (264)
T PRK07122        120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLG-----  194 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccC-----
Confidence            99999999999999999999999999999999999999999998864  45689999998654322  3333332     


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      .++..++..+....|..+|..||++||.||.++|+    +++|++|||+.||||.++|++++++|+++||..+
T Consensus       195 ~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l  263 (264)
T PRK07122        195 DVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL  263 (264)
T ss_pred             CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence            34555666777888999999999999999999998    8999999999999999999999999999999876

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=2.5e-41  Score=342.01  Aligned_cols=228  Identities=25%  Similarity=0.408  Sum_probs=201.7

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCC-CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~-g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      ++..|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++++.++
T Consensus        22 gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~  101 (256)
T PRK07408         22 PSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT  101 (256)
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCe
Confidence            445899999999999999999999876 6679999999999999999999999999999999999999999999999999


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCccCCCCCCCCCCc--hhhhhccc
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT--TFQEITAD  471 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~v~~d~~~--~l~d~l~d  471 (561)
                      ||+|+++...+++++++...+.+++|++|+.+|||+.+|+++++|..++.  ......|||.++..+++.  .+.+.+++
T Consensus       102 vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d  181 (256)
T PRK07408        102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD  181 (256)
T ss_pred             eeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCC
Confidence            99999999999999999999999999999999999999999999999865  345689999987554332  45566655


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          472 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       472 ~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      +... +.  ....+....|..+|..||+++|.||.++|+    +++|++|||+.||||.++|++++++|++|||+.+...
T Consensus       182 ~~~~-~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~  254 (256)
T PRK07408        182 PRYR-SF--QLAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE  254 (256)
T ss_pred             cccc-hh--hhhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence            4322 11  123345677999999999999999999998    8999999999999999999999999999999988653

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=5.6e-41  Score=344.13  Aligned_cols=274  Identities=35%  Similarity=0.553  Sum_probs=249.3

Q ss_pred             CCCCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHH
Q 008556          241 EGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS  320 (561)
Q Consensus       241 ~~~~~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~  320 (561)
                      ......|.+++||.+|+.+|.||.++|.+|+.+++.                                        |+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~   46 (285)
T TIGR02394         7 TETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFE   46 (285)
T ss_pred             cccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHH
Confidence            334467899999999999999999999999887654                                        4568


Q ss_pred             HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556          321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  400 (561)
Q Consensus       321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~  400 (561)
                      |++.||..|.++|+++|++|.+++.+++||+|||+||||+|+++||+.+|++|+||+.|||+.+|.+++.++.+.+++|.
T Consensus        47 a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~  126 (285)
T TIGR02394        47 ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPV  126 (285)
T ss_pred             HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556          401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  480 (561)
Q Consensus       401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~  480 (561)
                      ++...++.+.+..+.+.+..|+.|+.+++|..+|++++++..++.......|+|.++..++...+.+.+.++...+|++.
T Consensus       127 ~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~  206 (285)
T TIGR02394       127 HVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESL  206 (285)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHH
Confidence            99999999888888788888999999999999999999999999888889999988766555556666666655678888


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchh
Q 008556          481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY  554 (561)
Q Consensus       481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~  554 (561)
                      +...+....|..+|..||+++|.||.++|||.+.+++|++|||+.||||.++|++++++|+++||+.+...++.
T Consensus       207 ~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~~  280 (285)
T TIGR02394       207 VQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGVD  280 (285)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            99889999999999999999999999999887779999999999999999999999999999999999865553

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).

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=100.00  E-value=8.6e-40  Score=330.04  Aligned_cols=243  Identities=27%  Similarity=0.443  Sum_probs=215.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 008556          256 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  335 (561)
Q Consensus       256 i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~s  335 (561)
                      .+++|+||++||.+|+.+++.                                        ++..|++.|+..|+++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence            468899999999998877653                                        3468999999999999999


Q ss_pred             HHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH
Q 008556          336 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  415 (561)
Q Consensus       336 IArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~  415 (561)
                      +|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .||+|+++...++++.++...
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            9999999999999999999999999999999999999999999999999999999965 889999999999999999999


Q ss_pred             HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCC--chhhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 008556          416 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDISVQKQLMRQHVRNL  493 (561)
Q Consensus       416 l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~--~~l~d~l~d~~~~~pee~le~~e~~e~L~~a  493 (561)
                      +..++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++  ..+.+.+.|+.. .++    ....+..|..+
T Consensus       129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~-~~~----~~~~~~~l~~~  203 (254)
T TIGR02850       129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN-KDS----QWLEGIALKEA  203 (254)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc-cHH----HHHhHHHHHHH
Confidence            99999999999999999999999999999888889999998754443  245666665432 122    22344578999


Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      +..|++++|.||.+||+    +++|++|||+.||||+++|++++++|++|||+.+
T Consensus       204 l~~L~~rer~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~  254 (254)
T TIGR02850       204 MKRLNEREKMILNMRFF----EGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV  254 (254)
T ss_pred             HHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence            99999999999999997    8899999999999999999999999999999853

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.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=100.00  E-value=1.2e-39  Score=330.02  Aligned_cols=227  Identities=26%  Similarity=0.391  Sum_probs=204.6

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  393 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s  393 (561)
                      ++..|+++||..|+++|+++|++|.+   .+++++||+|||+||||+|+++|||++|++|+|||.||||++|.+++++..
T Consensus        20 ~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~   99 (257)
T PRK05911         20 QEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD   99 (257)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            45589999999999999999999852   356899999999999999999999999999999999999999999999987


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCccCCCCCCC--CC--Cchhhh
Q 008556          394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--DQ--DTTFQE  467 (561)
Q Consensus       394 r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~--d~--~~~l~d  467 (561)
                      +   +|+++...++++.++...+.+++|+.|+.+|||+.+|+++++|..++....  .++|||.++..  ++  +.++.+
T Consensus       100 ~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~  176 (257)
T PRK05911        100 W---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE  176 (257)
T ss_pred             C---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence            5   899999999999999999999999999999999999999999999887553  46899987643  21  235677


Q ss_pred             hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          468 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       468 ~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      .++|.....|++.+...+....|..+|..||++||.||.++|+    +++|++|||+.||||.++|++++.+|+++||+.
T Consensus       177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~  252 (257)
T PRK05911        177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT  252 (257)
T ss_pred             hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            8888766678888888888899999999999999999999998    899999999999999999999999999999998


Q ss_pred             hhc
Q 008556          548 LGG  550 (561)
Q Consensus       548 l~~  550 (561)
                      +..
T Consensus       253 l~~  255 (257)
T PRK05911        253 LSA  255 (257)
T ss_pred             HHh
Confidence            754

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=100.00  E-value=2.1e-38  Score=320.43  Aligned_cols=243  Identities=27%  Similarity=0.463  Sum_probs=214.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 008556          256 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  335 (561)
Q Consensus       256 i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~s  335 (561)
                      ..++|+|+++|+..|+.+++.                                        ++..|+++||..|.++|++
T Consensus        13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~   52 (258)
T PRK08215         13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS   52 (258)
T ss_pred             CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence            467789999999988877653                                        4568999999999999999


Q ss_pred             HHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHH
Q 008556          336 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  415 (561)
Q Consensus       336 IArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~  415 (561)
                      +|++|.+++.+++||+|||++|||+++++|||.+|++|+||+++||+++|.++++++. .+|+|+++.....++.++...
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            9999999999999999999999999999999999999999999999999999999885 889999999999999999999


Q ss_pred             HHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCc--hhhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 008556          416 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL  493 (561)
Q Consensus       416 l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~l~d~~~~~pee~le~~e~~e~L~~a  493 (561)
                      +.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++.  ++.+.+.++.. .++    .......|..+
T Consensus       132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~~~----~~~~~~~l~~~  206 (258)
T PRK08215        132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-KDE----NWLEEIALKEA  206 (258)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-cHH----HHHhHHHHHHH
Confidence            999999999999999999999999999988877888999988655432  34555554431 222    22334578899


Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      |..||+++|.||.++|+    +++|++|||+.||||.++|++++++|++|||+.+
T Consensus       207 l~~L~~~er~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l  257 (258)
T PRK08215        207 MKKLNDREKLILNLRFF----QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI  257 (258)
T ss_pred             HHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999997    8899999999999999999999999999999876

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

Probab=100.00  E-value=1.8e-38  Score=318.03  Aligned_cols=223  Identities=27%  Similarity=0.504  Sum_probs=202.7

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCC-CHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~-~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      ++..++ .||+.|+|||.+||++|.+++. +++||+|-|+|||++|+++|||++|.+|+|||...|+++|.+++|++. .
T Consensus        21 g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~   98 (247)
T COG1191          21 GDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-S   98 (247)
T ss_pred             cCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-C
Confidence            345888 9999999999999999998877 999999999999999999999999999999999999999999999999 9


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCccCCCCCCCCCCchhhhhcccCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTG  473 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~d~~~~l~d~l~d~~  473 (561)
                      +++|+.+....+++..+...+.+++||+||.+|||+.+|++.+++..++....  ..+|+|..+..+++..     .++.
T Consensus        99 v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~  173 (247)
T COG1191          99 VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQ  173 (247)
T ss_pred             ccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhc
Confidence            99999999999999999999999999999999999999999999999887654  6788887665444333     2233


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ..+|...+++.+..+.|.+++..|++|||.|+.+||.    +++|++|||+.||||..+|+|++++|++|||..+..
T Consensus       174 ~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~  246 (247)
T COG1191         174 IENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK  246 (247)
T ss_pred             cccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence            4467778888888889999999999999999999998    999999999999999999999999999999998753

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=100.00  E-value=5.4e-37  Score=311.99  Aligned_cols=250  Identities=20%  Similarity=0.359  Sum_probs=221.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 008556          256 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  335 (561)
Q Consensus       256 i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~s  335 (561)
                      .+++|+||.++|.+|+.+++.                                       .++..+++.|+..|.++|+.
T Consensus         6 ~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~~   46 (268)
T PRK06288          6 SGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVKY   46 (268)
T ss_pred             cCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHH
Confidence            378999999999999987653                                       13468999999999999999


Q ss_pred             HHHhhh-C--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHH
Q 008556          336 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA  412 (561)
Q Consensus       336 IArrY~-~--~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka  412 (561)
                      +|++|. +  .+.+++||+|||++|||+++++||+.+|++|+||++||||+.|.+++++..   ++|+++....++++++
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 3  467899999999999999999999999999999999999999999998654   6899999999999999


Q ss_pred             HHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCccCCCCCCCCC---CchhhhhcccCCCCChhHHHHHHHHH
Q 008556          413 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMR  487 (561)
Q Consensus       413 ~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~---~~~l~d~l~d~~~~~pee~le~~e~~  487 (561)
                      ...+.+++|+.|+.+|||+.+|++.+++..++...  ....|||..+..++   ..++.+.++++...+|+..+...+..
T Consensus       124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~  203 (268)
T PRK06288        124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIK  203 (268)
T ss_pred             HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999988643  45789988763222   23466777776667888888888888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      ..|..+|..||+++|.||.++|+    +++|++|||+.||+|.++|++++.+|+++||.++...
T Consensus       204 ~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~  263 (268)
T PRK06288        204 RVIVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEI  263 (268)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999998    8999999999999999999999999999999988643

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=100.00  E-value=3e-36  Score=303.89  Aligned_cols=244  Identities=23%  Similarity=0.358  Sum_probs=215.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHh
Q 008556          260 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ  339 (561)
Q Consensus       260 ~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArr  339 (561)
                      |.||+++|.+|+.+++.                                       .++..|+++|+..|.++|+.+|++
T Consensus         8 ~~l~~~~~~~li~~~~~---------------------------------------~gd~~a~~~l~~~y~~~v~~~a~~   48 (255)
T TIGR02941         8 TNLTKEDVIQWIAEFQQ---------------------------------------NQNGEAQEKLVDHYQNLVYSIAYK   48 (255)
T ss_pred             CCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHHHhHHHHHHHHHH
Confidence            66899999888877653                                       134689999999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHh
Q 008556          340 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE  419 (561)
Q Consensus       340 Y~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e  419 (561)
                      |.+++.+++||+|||++|||+++++||+..|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+.+.
T Consensus        49 ~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~  128 (255)
T TIGR02941        49 YSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDH  128 (255)
T ss_pred             HhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC
Q 008556          420 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL  497 (561)
Q Consensus       420 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L  497 (561)
                      +|+.|+.+|+|+.+|++.+++..++...  ....|||.++..+++......+ +. ...|++.+...+....|..+|+.|
T Consensus       129 ~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~e~~~~l~~~l~~L  206 (255)
T TIGR02941       129 LQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARL-DS-VGEVEDGYDQTERRMVLEKILPIL  206 (255)
T ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccc-cc-cCCcchHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999999998887653  4578999888655443222221 11 124666677777778899999999


Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       498 ~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      |+++|.||.++|+    +++|++|||+.||||.++|++++.+|+++||+.+
T Consensus       207 ~~~~r~ii~l~~~----~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~  253 (255)
T TIGR02941       207 SEREKSIIHCTFE----ENLSQKETGERLGISQMHVSRLQRQAISKLKEAA  253 (255)
T ss_pred             CHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            9999999999998    8999999999999999999999999999999865

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

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=100.00  E-value=2.5e-36  Score=299.91  Aligned_cols=223  Identities=29%  Similarity=0.469  Sum_probs=199.1

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      .++..|+++|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .
T Consensus         7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~   85 (231)
T TIGR02885         7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-I   85 (231)
T ss_pred             cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-C
Confidence            355699999999999999999999999999999999999999999999999999999999999999999999999986 8


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCc--hhhhhcccCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTG  473 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~l~d~~  473 (561)
                      |++|+++...++++.++...+..++|+.|+.+|||+.+|++++++..++.......|||.++.++++.  ++.+.+.++.
T Consensus        86 i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~  165 (231)
T TIGR02885        86 IKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKG  165 (231)
T ss_pred             eECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCC
Confidence            89999999999999999999999999999999999999999999999988888889999888655432  3456665543


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      .  ++.   ....+..|..++..||++|++||.++|+    +++|++|||+.||||+++|++++++|++|||..|
T Consensus       166 ~--~~~---~~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l  231 (231)
T TIGR02885       166 S--EDS---DWLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL  231 (231)
T ss_pred             c--cHH---hHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence            2  222   2223557889999999999999999998    8999999999999999999999999999999864

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.

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

Probab=100.00  E-value=6.9e-36  Score=295.77  Aligned_cols=221  Identities=28%  Similarity=0.452  Sum_probs=198.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556          319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  398 (561)
Q Consensus       319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl  398 (561)
                      ..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+|+++||+.+|.+|+||++|||++.|.++++++.+.+++
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            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCC--CccCCCCCCCCCC--chhhhhcccCCC
Q 008556          399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQD--TTFQEITADTGV  474 (561)
Q Consensus       399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~--~~SLD~~v~~d~~--~~l~d~l~d~~~  474 (561)
                      |.++...+++++++...+.+.+|+.|+.+|+|+.+|++++++..++.....  ..|||.++.++++  ..+.+.+.    
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~----  157 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG----  157 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence            999999999999999999999999999999999999999999998876654  8999988763222  12223322    


Q ss_pred             CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          475 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       475 ~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                       +++..++..+....|..+|..||+++|+||.++|+    +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus       158 -~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l  226 (227)
T TIGR02980       158 -DEDDALETVEDRLALKPLLAALPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL  226 (227)
T ss_pred             -CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence             34455556667778999999999999999999998    8999999999999999999999999999999865

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.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=3.8e-35  Score=295.65  Aligned_cols=226  Identities=23%  Similarity=0.367  Sum_probs=202.3

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  393 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s  393 (561)
                      ++..|++.||..|.++|+++|++|.+   ++.+.+||+|||++|||+++++||+.+|.+|+||+++||++.|.++++++.
T Consensus        19 ~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~   98 (251)
T PRK07670         19 RDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED   98 (251)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            34589999999999999999999965   678999999999999999999999999999999999999999999999876


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCccCCCCCCCCCCc-hhhhhcc
Q 008556          394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT-TFQEITA  470 (561)
Q Consensus       394 r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~v~~d~~~-~l~d~l~  470 (561)
                         ++|.++...+++++++...+.+.+|+.|+.+|||+.+|+++++|..++.  ......|||.++.++++. .+.+.+.
T Consensus        99 ---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~  175 (251)
T PRK07670         99 ---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIR  175 (251)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhc
Confidence               6999999999999999999999999999999999999999999999976  356789999988654432 2334444


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          471 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       471 d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      +....++++.+...+....|..+|..||+++|+||.++|+    +++|++|||+.||+|.++|+++++||+++||.++.
T Consensus       176 ~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~  250 (251)
T PRK07670        176 DDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE  250 (251)
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            5555577878888888889999999999999999999998    89999999999999999999999999999999875

>PRK05572 sporulation sigma factor SigF; Validated

Probab=100.00  E-value=1.9e-34  Score=290.66  Aligned_cols=244  Identities=28%  Similarity=0.430  Sum_probs=213.1

Q ss_pred             hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHH
Q 008556          254 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV  333 (561)
Q Consensus       254 ~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV  333 (561)
                      +.-+..|.||.+++.+|..+++.                                        ++..|++.|+..|.++|
T Consensus         6 ~~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v   45 (252)
T PRK05572          6 KNKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLV   45 (252)
T ss_pred             ccCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHH
Confidence            44567899999999888766442                                        44689999999999999


Q ss_pred             HHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHH
Q 008556          334 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK  413 (561)
Q Consensus       334 ~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~  413 (561)
                      +++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||++.|.+++++.. .+++|+++....++++++.
T Consensus        46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~  124 (252)
T PRK05572         46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK  124 (252)
T ss_pred             HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999998889999999999999999999884 7899999999999999999


Q ss_pred             HHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCc--hhhhhcccCCCCChhHHHHHHHHHHHHH
Q 008556          414 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVR  491 (561)
Q Consensus       414 ~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~l~d~~~~~pee~le~~e~~e~L~  491 (561)
                      ..+..++|+.|+.+|+|+.+|++++++..++.....+.|++.++.+++..  ++.+.+.++..   +    .......|.
T Consensus       125 ~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~---~----~~~~~~~l~  197 (252)
T PRK05572        125 DELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSE---E----DWFDKIALK  197 (252)
T ss_pred             HHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCch---h----hHHHHHHHH
Confidence            99999999999999999999999999999888878889999887654322  23344433321   1    123356789


Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          492 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       492 ~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      .+|..||+++++||.++|+    +++|++|||+.+|+|.++|++++++|+++||..+.
T Consensus       198 ~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~  251 (252)
T PRK05572        198 EAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD  251 (252)
T ss_pred             HHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999998    89999999999999999999999999999998774

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=2.5e-34  Score=290.34  Aligned_cols=243  Identities=24%  Similarity=0.355  Sum_probs=213.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHh
Q 008556          260 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ  339 (561)
Q Consensus       260 ~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArr  339 (561)
                      |.|+++||.+|..+++.                                       .++..|++.||..|.++|+++|++
T Consensus         8 ~~l~~~e~~~li~~~~~---------------------------------------~gd~~a~~~l~~~~~~~v~~~a~~   48 (257)
T PRK08583          8 TKLTKEEVNKWIAEYQE---------------------------------------NQDEEAQEKLVKHYKNLVESLAYK   48 (257)
T ss_pred             CcCChHHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHHHHHH
Confidence            77999999888776543                                       134689999999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHh
Q 008556          340 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE  419 (561)
Q Consensus       340 Y~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e  419 (561)
                      |.+++.+++||+||||+|||+++++||+.+|.+|.||+++||++.|.++++++.+.+++|+++....++++++...+...
T Consensus        49 ~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~~  128 (257)
T PRK08583         49 YSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTE  128 (257)
T ss_pred             HhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999998999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCccCCCCCCCCCCc---hhhhhcccCCCCChhHHHHHHHHHHHHHHHH
Q 008556          420 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDT---TFQEITADTGVEIPDISVQKQLMRQHVRNLL  494 (561)
Q Consensus       420 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~---~l~d~l~d~~~~~pee~le~~e~~e~L~~aL  494 (561)
                      .++.|+.+++|+.+|++.+++..++...  ....|+|.+++.+++.   .+.+..     ..|+..+...+....|..+|
T Consensus       129 ~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~-----~~~e~~~~~~~~~~~l~~~l  203 (257)
T PRK08583        129 LQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIV-----GQQEDGYELTEQRMILEKIL  203 (257)
T ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhhhc-----CCcchhHHHHHHHHHHHHHH
Confidence            9999999999999999999998876643  3578888887654332   122222     24556666677778899999


Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ..||+++|+||.++|+    +++|++|||+.||||.++|++++++|+++||..+..
T Consensus       204 ~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~  255 (257)
T PRK08583        204 PVLSDREKSIIQCTFI----ENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL  255 (257)
T ss_pred             HhCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence            9999999999999998    899999999999999999999999999999998764

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

Probab=100.00  E-value=1.5e-34  Score=286.14  Aligned_cols=217  Identities=23%  Similarity=0.419  Sum_probs=195.5

Q ss_pred             HHHHHHHHHHHHHHhhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556          325 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  401 (561)
Q Consensus       325 LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~  401 (561)
                      |+..|.++|+++|++|.+   ++.+++||+|||++|||+++++|||.+|++|+||+++||++.|.+++++..   ++|.+
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   58999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCccCCCCCCCC-CCchhhhhcccCCCCChh
Q 008556          402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWAD-QDTTFQEITADTGVEIPD  478 (561)
Q Consensus       402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d-~~~~l~d~l~d~~~~~pe  478 (561)
                      ....++++.++...+.+.+|+.|+.+|+|+.+|+++++|..++..  .....|+|....++ +...+.+.++++...+|+
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE  157 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence            999999999999999999999999999999999999999999864  34567888766443 234566666655556788


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      +.+...+....|..+|..||+++|+||.++|+    +++|++|||+.||+|.++|++++++|+++||+++
T Consensus       158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l  223 (224)
T TIGR02479       158 EELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL  223 (224)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence            88888888899999999999999999999998    8999999999999999999999999999999875

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.

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=100.00  E-value=2.8e-34  Score=286.60  Aligned_cols=209  Identities=21%  Similarity=0.327  Sum_probs=179.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556          322 REKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  398 (561)
Q Consensus       322 re~LI~~nlrLV~sIArrY~~---~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl  398 (561)
                      ...|+..|+++|.++|++|.+   .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..+   +
T Consensus        17 ~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~---~   92 (231)
T PRK12427         17 EGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW---R   92 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---C
Confidence            356788899999999999875   4679999999999999999999998666 89999999999999999998653   6


Q ss_pred             chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556          399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITADTGVEI  476 (561)
Q Consensus       399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~  476 (561)
                      |+++....++++++...+.+++|+.|+.+|||+.+|+++++|.+++..  .....|||.+++++++..   .+.+   ..
T Consensus        93 ~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~~  166 (231)
T PRK12427         93 PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---RD  166 (231)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---CC
Confidence            888889999999999999999999999999999999999999998764  456899999886654322   2221   12


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      +++.   ......|..++..||+++|.||.++|+    +++|++|||+.||||.++|+|++++|++|||..
T Consensus       167 ~~~~---~~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~  230 (231)
T PRK12427        167 LEEN---IIIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF  230 (231)
T ss_pred             HHHH---HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            3322   234557899999999999999999998    899999999999999999999999999999964

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=100.00  E-value=4.1e-33  Score=278.14  Aligned_cols=225  Identities=23%  Similarity=0.406  Sum_probs=197.9

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  393 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~---~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s  393 (561)
                      .|.-++++|+..|.++|+++|++|.   +++.+++||+|||++|||+++++|||.+|.+|+||+++||++.|.++++++.
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            4678999999999999999999997   6789999999999999999999999999999999999999999999999986


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCccCCCCCCCCCCchhhhhccc
Q 008556          394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITAD  471 (561)
Q Consensus       394 r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~~l~d~l~d  471 (561)
                      +   +|.++....+++.++...+.+.+|++|+.+|||+.+|++.++|..++..  .....|++..++++++. +.. ..+
T Consensus        85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~  159 (236)
T PRK06986         85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TED  159 (236)
T ss_pred             C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccC
Confidence            4   6888888888888888999999999999999999999999999998874  34567888876554442 222 223


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          472 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       472 ~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      +...+|++.+...+....|..+|..||+++|.||.++|.    +++|++|||+.||||.++|++++.+|+++||+.+..
T Consensus       160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  234 (236)
T PRK06986        160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE  234 (236)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            334467778888888889999999999999999999998    899999999999999999999999999999998754

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.96  E-value=3.5e-28  Score=242.35  Aligned_cols=210  Identities=25%  Similarity=0.451  Sum_probs=171.1

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008556          248 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  327 (561)
Q Consensus       248 ~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~  327 (561)
                      .+..|+.+++..|+||+++|..|+..++.                                        ++..|++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence            46789999999999999999888776543                                        44689999999


Q ss_pred             HHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHH
Q 008556          328 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  407 (561)
Q Consensus       328 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~  407 (561)
                      .|.++|+++|.+|.+++.+.+||+|||++++|+++++||+++|.+|.||+++|+++.+.+++++..+..           
T Consensus        57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~-----------  125 (233)
T PRK05803         57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK-----------  125 (233)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc-----------
Confidence            999999999999999999999999999999999999999998999999999999999999998754210           


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCC---CCchhhhhcccCCCCChhHHHHHH
Q 008556          408 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQ  484 (561)
Q Consensus       408 ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d---~~~~l~d~l~d~~~~~pee~le~~  484 (561)
                                                               ...+++.....+   ....+.+...+. .+++++.+..+
T Consensus       126 -----------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  163 (233)
T PRK05803        126 -----------------------------------------KEVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVELK  163 (233)
T ss_pred             -----------------------------------------cCCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHHH
Confidence                                                     011111111111   112233333332 23567777777


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ...+.|..+|..||+++|+||.++|++++.+++|++|||+.||||.++|+++++||+++||+.+..
T Consensus       164 ~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~  229 (233)
T PRK05803        164 MEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYR  229 (233)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            777889999999999999999999977666899999999999999999999999999999998754

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.93  E-value=2.1e-24  Score=214.86  Aligned_cols=181  Identities=28%  Similarity=0.533  Sum_probs=140.0

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++..|++.|+..|.++|+.+|++|.+++.+++|++||+++++|+++++|++..+++|.||++++++|.+.++++++.+..
T Consensus        49 gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~  128 (234)
T PRK08301         49 GDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK  128 (234)
T ss_pred             cCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            44689999999999999999999999999999999999999999999999988889999999999999999998764210


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCC--CCC-chhhhhcccCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA--DQD-TTFQEITADTG  473 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~--d~~-~~l~d~l~d~~  473 (561)
                                                                          ...+++.+...  ++. ..+.+...+. 
T Consensus       129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-  155 (234)
T PRK08301        129 ----------------------------------------------------AEVSFDEPLNIDWDGNELLLSDVLGTD-  155 (234)
T ss_pred             ----------------------------------------------------cccccccccccccCCCcccHHHhccCc-
Confidence                                                                00111111100  000 1111222211 


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ...++..+........|..+|+.||+++|+||.++|+|...+++|++|||+.||||.++|+++++||+++||+.+..
T Consensus       156 ~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~  232 (234)
T PRK08301        156 NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK  232 (234)
T ss_pred             ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            11233344455556679999999999999999999965444899999999999999999999999999999998753

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.93  E-value=2.3e-24  Score=214.19  Aligned_cols=199  Identities=28%  Similarity=0.527  Sum_probs=155.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHH
Q 008556          257 ETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV  336 (561)
Q Consensus       257 ~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sI  336 (561)
                      +..+.|++.+|.+|..+++.                                        ++..|++.|+..|.++|+++
T Consensus        25 ~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~af~~l~~~y~~~v~~~   64 (227)
T TIGR02846        25 SFPQPLSEEEEKKYLDRLKE----------------------------------------GDEEARNVLIERNLRLVAHI   64 (227)
T ss_pred             hCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHHH
Confidence            45567888888888776543                                        44689999999999999999


Q ss_pred             HHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHH
Q 008556          337 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLY  416 (561)
Q Consensus       337 ArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l  416 (561)
                      |.+|.++..+++||+||+++++|+++++|+++++.+|.||+++|+++.|.+++++..+..+                   
T Consensus        65 ~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~-------------------  125 (227)
T TIGR02846        65 VKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKG-------------------  125 (227)
T ss_pred             HHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhcccc-------------------
Confidence            9999999999999999999999999999999888899999999999999999987642100                   


Q ss_pred             HHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCC---CCchhhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 008556          417 IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQLMRQHVRNL  493 (561)
Q Consensus       417 ~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d---~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~a  493 (561)
                                                       ..+++.....+   ....+.+...+. ...+++.+...+..+.|..+
T Consensus       126 ---------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~~  171 (227)
T TIGR02846       126 ---------------------------------EVSLQDPIGVDKEGNEISLIDILGSD-GDSVIEQVELNLEIKKLYKK  171 (227)
T ss_pred             ---------------------------------ceeccccccCCcccCcccHHHHhcCC-CCChHHHHHHHHHHHHHHHH
Confidence                                             00111111000   011122222221 23456666666666789999


Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      |+.||+++|+||.++|.++..+++|++|||+.||+|.++|++++++|+++||+.+
T Consensus       172 i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~  226 (227)
T TIGR02846       172 LSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL  226 (227)
T ss_pred             HHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999765557899999999999999999999999999999865

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.

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.92  E-value=1.5e-23  Score=209.30  Aligned_cols=181  Identities=30%  Similarity=0.540  Sum_probs=141.2

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++..|++.|+..|.+.|+.+|++|.+++.+.+|++||+++++|+++++|++..+++|.||++.++++.+.++++++.+..
T Consensus        49 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~  128 (234)
T TIGR02835        49 GDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTR  128 (234)
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence            45689999999999999999999999999999999999999999999999988889999999999999999998765310


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCC---CCCCchhhhhcccCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW---ADQDTTFQEITADTG  473 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~---~d~~~~l~d~l~d~~  473 (561)
                                                                          ...+++..+.   .+......+.. ++.
T Consensus       129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~-~~~  155 (234)
T TIGR02835       129 ----------------------------------------------------SEVSFDEPLNVDWDGNELLLSDVL-GTD  155 (234)
T ss_pred             ----------------------------------------------------CcccccccccCCCCCCcchHHHhc-CCC
Confidence                                                                0011111110   00001111111 111


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      .+.++..+........|..+|+.||+++|+||.++|++.+++++|++|||+.||||..+|+++.+||+++||+.+..
T Consensus       156 ~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~  232 (234)
T TIGR02835       156 SDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR  232 (234)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            12333444555566789999999999999999999976555899999999999999999999999999999998754

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.91  E-value=1.2e-22  Score=197.55  Aligned_cols=195  Identities=22%  Similarity=0.329  Sum_probs=149.5

Q ss_pred             CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      ++++.|...++.| ..|++.|+..|.++|+.+|++|.+++.+++|++||++++||+++.+||+.+|.+|.||++.++++.
T Consensus         9 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~   88 (208)
T PRK08295          9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQ   88 (208)
T ss_pred             CChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHH
Confidence            4556666666544 599999999999999999999999999999999999999999999999988789999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCC-CCCc
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT  463 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~-d~~~  463 (561)
                      +.+++++..+..+.+.                                               ....|.+.++.. +.+.
T Consensus        89 ~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~  121 (208)
T PRK08295         89 IITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDR  121 (208)
T ss_pred             HHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccch
Confidence            9998876432111100                                               011233332221 1222


Q ss_pred             hhhhhcccCCCCChhHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          464 TFQEITADTGVEIPDISVQKQLMRQHV-RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       464 ~l~d~l~d~~~~~pee~le~~e~~e~L-~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                      .+.+.+.++...+|+..+...+....+ ..++..||+++|+||.+ |.    +++|++|||+.||||.++|+..+.||++
T Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~----e~~s~~EIA~~lgis~~tV~~~l~rar~  196 (208)
T PRK08295        122 TLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YL----DGKSYQEIAEELNRHVKSIDNALQRVKR  196 (208)
T ss_pred             hHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HH----ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            344444444444677666555555555 45679999999999999 77    8999999999999999999999999999


Q ss_pred             HHHHHhhcCc
Q 008556          543 RLKQSLGGKA  552 (561)
Q Consensus       543 KLR~~l~~~~  552 (561)
                      +||+++....
T Consensus       197 ~Lr~~l~~~~  206 (208)
T PRK08295        197 KLEKYLENRE  206 (208)
T ss_pred             HHHHHHHhhc
Confidence            9999886543

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.90  E-value=4e-22  Score=191.19  Aligned_cols=176  Identities=16%  Similarity=0.250  Sum_probs=143.5

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      ++++.|+..+..|+ .|++.|+..|.++|+.+|++|.+++.+.+|++||+++++|+++.+|++. +..|.+|++..+++.
T Consensus         5 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~   83 (186)
T PRK05602          5 DPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNL   83 (186)
T ss_pred             ccHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHH
Confidence            45666777665555 9999999999999999999999999999999999999999999999986 457999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      +.++++++...                                                        +.+. .       
T Consensus        84 ~~d~~R~~~~~--------------------------------------------------------~~~~-~-------   99 (186)
T PRK05602         84 CYDRLRRRREV--------------------------------------------------------PVED-A-------   99 (186)
T ss_pred             HHHHHHhcCCC--------------------------------------------------------Cccc-c-------
Confidence            99998765310                                                        0000 0       


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                       .+ ..+. ...++..+...+....+..+|..||+++|+||.++|.    +++|++|||+.||+|..+|++.++||+++|
T Consensus       100 -~~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~L  172 (186)
T PRK05602        100 -PD-VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVDALESLLARGRRAL  172 (186)
T ss_pred             -cc-cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence             00 0011 1134555555666678999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCch
Q 008556          545 KQSLGGKAS  553 (561)
Q Consensus       545 R~~l~~~~l  553 (561)
                      |+.+...+.
T Consensus       173 r~~l~~~~~  181 (186)
T PRK05602        173 RAQLADLPG  181 (186)
T ss_pred             HHHHHhccc
Confidence            999876553

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.89  E-value=8.6e-22  Score=189.83  Aligned_cols=191  Identities=23%  Similarity=0.325  Sum_probs=145.1

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      |++..|+..+..|+ .|++.|+..|.+.|+.+|+++.++..+++||+||+++++|+++.+|++..+..|.||++.+|++.
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            45667777776665 99999999999999999999999999999999999999999999999988779999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCC-CCCc
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT  463 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~-d~~~  463 (561)
                      +.++++...+..+.+                                               .....|++.+... +++.
T Consensus        84 ~~~~~r~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~  116 (198)
T TIGR02859        84 IITAIKTATRQKHIP-----------------------------------------------LNSYVSLNKPIYDEESDR  116 (198)
T ss_pred             HHHHHHHHHHhcccc-----------------------------------------------hhhhcCcccccccccccc
Confidence            988886532110000                                               0011233322211 1122


Q ss_pred             hhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          464 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       464 ~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L-~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                      ++.+.+.+....+|+..+...+....|.++|..| ++.++.|+. +|.    +++|++|||+.||+|.++|+..++||++
T Consensus       117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~  191 (198)
T TIGR02859       117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SYL----DGKSYQEIACDLNRHVKSIDNALQRVKR  191 (198)
T ss_pred             hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2333333222346777777777778899999995 566666665 566    8999999999999999999999999999


Q ss_pred             HHHHHh
Q 008556          543 RLKQSL  548 (561)
Q Consensus       543 KLR~~l  548 (561)
                      +||+.+
T Consensus       192 ~L~~~l  197 (198)
T TIGR02859       192 KLEKYL  197 (198)
T ss_pred             HHHHhc
Confidence            999875

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.

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.89  E-value=1e-21  Score=190.16  Aligned_cols=175  Identities=17%  Similarity=0.196  Sum_probs=139.1

Q ss_pred             HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHH
Q 008556          308 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  386 (561)
Q Consensus       308 ~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~  386 (561)
                      ...|+..+..| ..++++|+..|.++|+++|.+|.++..+.+|++||+++++|+++++||+.+| .|.+|++..+++.+.
T Consensus        17 ~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~   95 (194)
T PRK09646         17 LDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAV   95 (194)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHH
Confidence            44555655544 5999999999999999999999999999999999999999999999998766 699999999999999


Q ss_pred             HHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh
Q 008556          387 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  466 (561)
Q Consensus       387 ~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~  466 (561)
                      ++++++.+..+.                                                   ...    ... .     
T Consensus        96 d~~r~~~~~~~~---------------------------------------------------~~~----~~~-~-----  114 (194)
T PRK09646         96 DRVRSEQAASQR---------------------------------------------------EVR----YGA-R-----  114 (194)
T ss_pred             HHHHhhcccccc---------------------------------------------------ccc----ccc-c-----
Confidence            999876421100                                                   000    000 0     


Q ss_pred             hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          467 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       467 d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +.  +.....+++.+...+..+.|..+|..||+++|+||.++|.    +++|++|||+.||+|..+|+++++||+++||.
T Consensus       115 ~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~  188 (194)
T PRK09646        115 NV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPLGTVKTRMRDGLIRLRD  188 (194)
T ss_pred             cc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence            00  0001123344444555678999999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhhc
Q 008556          547 SLGG  550 (561)
Q Consensus       547 ~l~~  550 (561)
                      .+..
T Consensus       189 ~l~~  192 (194)
T PRK09646        189 CLGV  192 (194)
T ss_pred             Hhcc
Confidence            8854

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=8.2e-22  Score=190.25  Aligned_cols=181  Identities=19%  Similarity=0.254  Sum_probs=145.5

Q ss_pred             CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      ++++.++..+..| ..|++.|+..|.+.|+++|+++.++..+.+|++||+++++|+++++|++..  .|.+|++.++++.
T Consensus        11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~   88 (194)
T PRK12513         11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNL   88 (194)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHH
Confidence            3456666666655 599999999999999999999999999999999999999999999999753  6999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      +.+++++..+....+                                                     .+.    +.  .
T Consensus        89 ~~~~~R~~~~~~~~~-----------------------------------------------------~~~----~~--~  109 (194)
T PRK12513         89 LIDHWRRHGARQAPS-----------------------------------------------------LDA----DE--Q  109 (194)
T ss_pred             HHHHHHHhccccccc-----------------------------------------------------ccc----ch--h
Confidence            999998765321110                                                     000    00  0


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                      . ....+ ....|+..++..+....|..+|+.||+++|.||.++|.    +++|++|||+.||||.++|++++.||+++|
T Consensus       110 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~L  183 (194)
T PRK12513        110 L-HALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREH----GDLELEEIAELTGVPEETVKSRLRYALQKL  183 (194)
T ss_pred             h-hhcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            0 00011 12256666666677788999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCch
Q 008556          545 KQSLGGKAS  553 (561)
Q Consensus       545 R~~l~~~~l  553 (561)
                      |..+...++
T Consensus       184 r~~l~~~~~  192 (194)
T PRK12513        184 RELLAEEVA  192 (194)
T ss_pred             HHHHHHhhc
Confidence            999876554

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.89  E-value=1.5e-21  Score=186.20  Aligned_cols=180  Identities=15%  Similarity=0.234  Sum_probs=141.4

Q ss_pred             HHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHH
Q 008556          308 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  386 (561)
Q Consensus       308 ~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~  386 (561)
                      .+.|+..++.|+ .+++.|+..|.++|+++|+++.++..+++|++||++++||+++.+|++..  .|.+|++..+++.+.
T Consensus         5 ~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~   82 (187)
T PRK09641          5 IKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTI   82 (187)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHH
Confidence            344555555554 99999999999999999999999999999999999999999999999853  699999999999999


Q ss_pred             HHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh
Q 008556          387 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  466 (561)
Q Consensus       387 ~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~  466 (561)
                      ++++++.+..                                                       +++.....++.....
T Consensus        83 d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~  107 (187)
T PRK09641         83 DRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLTMY  107 (187)
T ss_pred             HHHHhcCccc-------------------------------------------------------cccccccCCcchhhh
Confidence            9988754210                                                       000000011111111


Q ss_pred             hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          467 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       467 d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +.+.+. ..+|++.+...+....+..+|..||+++|+||.++|.    ++++++|||+.||||.++|++.++||+++||+
T Consensus       108 ~~~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~  182 (187)
T PRK09641        108 SQLAAD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSLKEISEILDLPVGTVKTRIHRGREALRK  182 (187)
T ss_pred             cccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            111111 2246666777777788999999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhh
Q 008556          547 SLG  549 (561)
Q Consensus       547 ~l~  549 (561)
                      .+.
T Consensus       183 ~l~  185 (187)
T PRK09641        183 QLR  185 (187)
T ss_pred             HHh
Confidence            875

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.88  E-value=1.4e-21  Score=186.52  Aligned_cols=178  Identities=16%  Similarity=0.241  Sum_probs=139.0

Q ss_pred             HHHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008556          310 DLKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  388 (561)
Q Consensus       310 eL~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~  388 (561)
                      .|+..+. ++..++++|+..|.++|+.+|++|.+++.+++|++||+++++|+++.+|++..  .|.+|++..+++.+.++
T Consensus         7 ~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~~   84 (187)
T TIGR02948         7 KRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTIDR   84 (187)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHH
Confidence            3444444 45599999999999999999999999999999999999999999999999865  59999999999999999


Q ss_pred             HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhh
Q 008556          389 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI  468 (561)
Q Consensus       389 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~  468 (561)
                      +++..+...                                                       ++.....++.....+.
T Consensus        85 ~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~~  109 (187)
T TIGR02948        85 LRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMESQ  109 (187)
T ss_pred             HHhhccccc-------------------------------------------------------ccccccCccccccccc
Confidence            876431100                                                       0000000000011111


Q ss_pred             cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          469 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       469 l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      ..+. .+.|++.+...+....+..+|..||+++|.||.++|.    +++|++|||+.||+|.++|++.+.||+++||..+
T Consensus       110 ~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l  184 (187)
T TIGR02948       110 LAAD-EAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQL  184 (187)
T ss_pred             cccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            1111 1256666666677778999999999999999999998    8999999999999999999999999999999987


Q ss_pred             h
Q 008556          549 G  549 (561)
Q Consensus       549 ~  549 (561)
                      .
T Consensus       185 ~  185 (187)
T TIGR02948       185 R  185 (187)
T ss_pred             h
Confidence            5

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

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.88  E-value=2.9e-21  Score=185.68  Aligned_cols=171  Identities=23%  Similarity=0.325  Sum_probs=137.4

Q ss_pred             HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          310 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       310 eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~----g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      .|+..+..| ..|+++|+..|.+.|+.+|.++.++    +.+++|++||+++++|+++.+|++. +..|.+|++..+++.
T Consensus        13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~   91 (189)
T PRK09648         13 ALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHK   91 (189)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHH
Confidence            355555545 5999999999999999999998765    3689999999999999999999864 457999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      +.++++++.+....+                                                     .+.         
T Consensus        92 ~~d~~r~~~r~~~~~-----------------------------------------------------~~~---------  109 (189)
T PRK09648         92 VADAHRAAGRDKAVP-----------------------------------------------------TEE---------  109 (189)
T ss_pred             HHHHHHHhCCCcccc-----------------------------------------------------ccc---------
Confidence            999988765311000                                                     000         


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                      ..+...  ...+|++.+...+..+.|..+|..||+++|+||.++|+    +++|++|||+.||||..+|++.++||+++|
T Consensus       110 ~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L  183 (189)
T PRK09648        110 VPERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGSTPGAVRVAQHRALARL  183 (189)
T ss_pred             cccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            000000  11256666666777788999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhh
Q 008556          545 KQSLG  549 (561)
Q Consensus       545 R~~l~  549 (561)
                      |+.+.
T Consensus       184 r~~l~  188 (189)
T PRK09648        184 RAEIE  188 (189)
T ss_pred             HHHhc
Confidence            99764

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

Probab=99.87  E-value=7.2e-21  Score=178.68  Aligned_cols=164  Identities=20%  Similarity=0.343  Sum_probs=134.8

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      .++..|++.|+..|.+.+++++.++.++..+++|++||+++++|+++++|+...+ .|.+|++.++++.+.++++++.+.
T Consensus         7 ~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~   85 (170)
T TIGR02952         7 DREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRH   85 (170)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCC
Confidence            3456999999999999999999999998899999999999999999999997555 799999999999999999876521


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  475 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~  475 (561)
                      ...                                                     +.+.         ..+...  ...
T Consensus        86 ~~~-----------------------------------------------------~~~~---------~~~~~~--~~~  101 (170)
T TIGR02952        86 PLF-----------------------------------------------------SLDV---------FKELLS--NEP  101 (170)
T ss_pred             CCC-----------------------------------------------------cHHH---------HhhcCC--CCC
Confidence            100                                                     0000         000000  112


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      .|++.+...+..+.+..+|..|||++|+||.++|.    +|+|++|||+.||||..+|++.+.||+++||+.+
T Consensus       102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l  170 (170)
T TIGR02952       102 NPEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFRAIKKLARQM  170 (170)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            45666666667788999999999999999999998    8999999999999999999999999999999864

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.

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.87  E-value=7.5e-21  Score=179.47  Aligned_cols=172  Identities=19%  Similarity=0.236  Sum_probs=136.9

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      .++..|+++|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+  .+.+|.+|++.++++.+.+++++..+.
T Consensus         6 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~   83 (182)
T PRK09652          6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRR   83 (182)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCC
Confidence            455699999999999999999999999999999999999999999999999  445899999999999999998775421


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  475 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~  475 (561)
                      ...+                                                    +++  ..+.++....+...+  ..
T Consensus        84 ~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~~--~~  107 (182)
T PRK09652         84 PPAS----------------------------------------------------DVD--AEEAEDFDLADALRD--IS  107 (182)
T ss_pred             CCcc----------------------------------------------------ccc--ccccccccccccccc--cc
Confidence            1000                                                    000  000000011111111  12


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      +|+..+...+....+..+|..||+++|+||.++|.    .++|++|||+.||+|..+|++.+.||+++||+.+.
T Consensus       108 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~  177 (182)
T PRK09652        108 TPENELLSAELEQRVRAAIESLPEELRTAITLREI----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ  177 (182)
T ss_pred             ChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            46666666677788999999999999999999998    89999999999999999999999999999999875

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.87  E-value=7.1e-21  Score=182.15  Aligned_cols=176  Identities=19%  Similarity=0.286  Sum_probs=135.1

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556          307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  385 (561)
Q Consensus       307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  385 (561)
                      ++..+...+..| ..|++.|+..|.+.|+.++++|.+++.+++|++||+++++|+++++|++..+ .|.+|++..+++.+
T Consensus         9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~   87 (186)
T PRK13919          9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAA   87 (186)
T ss_pred             CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHH
Confidence            456666666544 5999999999999999999999999899999999999999999999997643 69999999999999


Q ss_pred             HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556          386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  465 (561)
Q Consensus       386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  465 (561)
                      .+++++..+..+                                                    ....+     ......
T Consensus        88 ~d~~rk~~~~~~----------------------------------------------------~~~~~-----~~~~~~  110 (186)
T PRK13919         88 VDHVRRRAARPQ----------------------------------------------------PLEPD-----EREPEA  110 (186)
T ss_pred             HHHHHhhhcccc----------------------------------------------------ccccc-----cccccc
Confidence            999976542100                                                    00000     000000


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .+ ..     .+..........+.|..+|..||+++|+||.++|.    +++|++|||+.||||..+|+..++||+++||
T Consensus       111 ~~-~~-----~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr  180 (186)
T PRK13919        111 FD-LP-----GPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYY----QGYTHREAAQLLGLPLGTLKTRARRALSRLK  180 (186)
T ss_pred             cc-CC-----CccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            00 00     11111122233456899999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhhc
Q 008556          546 QSLGG  550 (561)
Q Consensus       546 ~~l~~  550 (561)
                      ..+..
T Consensus       181 ~~l~~  185 (186)
T PRK13919        181 EVLRE  185 (186)
T ss_pred             HHhcC
Confidence            98753

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=7.2e-21  Score=183.49  Aligned_cols=175  Identities=22%  Similarity=0.276  Sum_probs=137.6

Q ss_pred             CHHHHHHHHhh-cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556          307 SCRDLKSELHS-GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  385 (561)
Q Consensus       307 ~~~eL~~~l~~-G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  385 (561)
                      ++.+|...+.. +..+++.|+..|.+.|+.+++++.++..+.+|++||+++++|+. ..|++..+ .|.||++.++++.+
T Consensus        15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~   92 (194)
T PRK12519         15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA   92 (194)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence            34556665554 45999999999999999999999999899999999999999976 67887655 79999999999999


Q ss_pred             HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556          386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  465 (561)
Q Consensus       386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  465 (561)
                      .++++++.+..+..                           .+.                        +        .  
T Consensus        93 ~d~~Rk~~~~~~~~---------------------------~~~------------------------~--------~--  111 (194)
T PRK12519         93 IDRLRSRRSRQRLL---------------------------ERW------------------------Q--------Q--  111 (194)
T ss_pred             HHHHHhcccccchh---------------------------hhh------------------------h--------h--
Confidence            99998764210000                           000                        0        0  


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                       +...+.....+++.+...+....|..+|..||+++++||.++|.    +++|++|||+.||+|..+|++++.||+++||
T Consensus       112 -~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr  186 (194)
T PRK12519        112 -ELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGIPLGTVKARARQGLLKLR  186 (194)
T ss_pred             -hhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence             00000011245555555666677999999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhh
Q 008556          546 QSLG  549 (561)
Q Consensus       546 ~~l~  549 (561)
                      +.+.
T Consensus       187 ~~l~  190 (194)
T PRK12519        187 ELLQ  190 (194)
T ss_pred             HHHH
Confidence            9874

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=9.8e-21  Score=180.28  Aligned_cols=173  Identities=14%  Similarity=0.146  Sum_probs=137.6

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556          307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  385 (561)
Q Consensus       307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  385 (561)
                      +...|+..+..| ..++..|+..|.+.|+.+|.+|.++..+.+|++||+++++|+++++|++..+ .|.||++..++|.+
T Consensus         5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~   83 (179)
T PRK12514          5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHA   83 (179)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHH
Confidence            344555555444 5899999999999999999999999999999999999999999999997544 69999999999999


Q ss_pred             HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556          386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  465 (561)
Q Consensus       386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  465 (561)
                      .++++++.+.. .+                                                     ++      .   .
T Consensus        84 ~d~~R~~~~~~-~~-----------------------------------------------------~~------~---~  100 (179)
T PRK12514         84 IDRLRARKAVA-VD-----------------------------------------------------ID------E---A  100 (179)
T ss_pred             HHHHHhcCCcc-cc-----------------------------------------------------cc------c---c
Confidence            99998654210 00                                                     00      0   0


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .+ ..+. ...|++.+...+....|..+|..||+++|+||.++|.    +|+|++|||+.||||..+|++.+.||+++||
T Consensus       101 ~~-~~~~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr  174 (179)
T PRK12514        101 HD-LADP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPLNTMRTWLRRSLLKLR  174 (179)
T ss_pred             hh-cccc-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence            00 0011 1245555554555567899999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhh
Q 008556          546 QSLG  549 (561)
Q Consensus       546 ~~l~  549 (561)
                      +++.
T Consensus       175 ~~l~  178 (179)
T PRK12514        175 ECLS  178 (179)
T ss_pred             HHhc
Confidence            9874

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.87  E-value=1.2e-20  Score=181.84  Aligned_cols=174  Identities=14%  Similarity=0.192  Sum_probs=141.1

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCC---CCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHH
Q 008556          306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV  381 (561)
Q Consensus       306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g---~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wI  381 (561)
                      ++++.|+..+..|+ .|++.|+..|.+.|+.++.++.+++   .+++|++||+++++|+++++|++..+ .|.||++..+
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            56677777777665 8999999999999999999998863   46899999999999999999997655 7999999999


Q ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCC
Q 008556          382 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ  461 (561)
Q Consensus       382 RqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~  461 (561)
                      ++.+.++++++.+....                                                    .+.+.      
T Consensus        82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------  103 (189)
T PRK06811         82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------  103 (189)
T ss_pred             HHHHHHHHHHhcccccc----------------------------------------------------ccchh------
Confidence            99999999876521100                                                    00000      


Q ss_pred             CchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          462 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       462 ~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                            ... ....++++.+...+....|..+|..||+++|.||.++|.    +++|++|||+.||+|..+|++.+.||+
T Consensus       104 ------~~~-~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~~V~~~l~Ra~  172 (189)
T PRK06811        104 ------FIL-ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKKLGLTRSAIDNRLSRGR  172 (189)
T ss_pred             ------hhh-cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence                  000 011245566666677778999999999999999999998    899999999999999999999999999


Q ss_pred             HHHHHHhh
Q 008556          542 YRLKQSLG  549 (561)
Q Consensus       542 kKLR~~l~  549 (561)
                      ++||...-
T Consensus       173 ~~Lr~~~~  180 (189)
T PRK06811        173 KKLQKNKL  180 (189)
T ss_pred             HHHHHccc
Confidence            99998643

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.87  E-value=1.5e-20  Score=179.84  Aligned_cols=181  Identities=16%  Similarity=0.210  Sum_probs=140.9

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556          307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  385 (561)
Q Consensus       307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  385 (561)
                      ++..|+..+..| ..+++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++.+|++.  ..|.+|++...++.+
T Consensus         6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~   83 (190)
T TIGR02939         6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA   83 (190)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence            455666666655 48999999999999999999999999999999999999999999999975  369999999999999


Q ss_pred             HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556          386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  465 (561)
Q Consensus       386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  465 (561)
                      .++++++.+.....                                                  ..+.+.      ....
T Consensus        84 ~~~~r~~~r~~~~~--------------------------------------------------~~~~~~------~~~~  107 (190)
T TIGR02939        84 KNHLVAQGRRPPTS--------------------------------------------------DVEIED------AEHF  107 (190)
T ss_pred             HHHHHHhccCCCcc--------------------------------------------------cccccc------hhhh
Confidence            99887554211000                                                  000000      0000


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .+........+|++.+...+....|..+|..||+++|+||.++|.    ++++++|||+.||+|..+|++.++||+++||
T Consensus       108 ~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr  183 (190)
T TIGR02939       108 EGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLREL----EGLSYEDIARIMDCPVGTVRSRIFRAREAIA  183 (190)
T ss_pred             cccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            000000011246666666777788999999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhh
Q 008556          546 QSLG  549 (561)
Q Consensus       546 ~~l~  549 (561)
                      +++.
T Consensus       184 ~~l~  187 (190)
T TIGR02939       184 IRLR  187 (190)
T ss_pred             HHhh
Confidence            9885

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.

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.86  E-value=6.8e-21  Score=176.52  Aligned_cols=151  Identities=21%  Similarity=0.253  Sum_probs=123.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556          319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  398 (561)
Q Consensus       319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl  398 (561)
                      ..|++.|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.+|++..+++.+.++++++.+..  
T Consensus         3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~--   78 (154)
T PRK06759          3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ--   78 (154)
T ss_pred             cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc--
Confidence            4689999999999999999886 56678999999999999999999998776 6999999999999999998753100  


Q ss_pred             chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556          399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  478 (561)
Q Consensus       399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe  478 (561)
                                            .                                 ... .+              +.|+
T Consensus        79 ----------------------~---------------------------------~~~-~~--------------~~~~   88 (154)
T PRK06759         79 ----------------------E---------------------------------KCV-CV--------------GEYE   88 (154)
T ss_pred             ----------------------c---------------------------------ccc-cc--------------CCCc
Confidence                                  0                                 000 00              0111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      +.+...+....|..+|..||+++|+||.++|+    +++|.+|||+.||+|..+|++++.||+++||+.
T Consensus        89 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~  153 (154)
T PRK06759         89 DHFHFEDVEMKVKDFMSVLDEKEKYIIFERFF----VGKTMGEIALETEMTYYQVRWIYRQALEKMRNS  153 (154)
T ss_pred             ccccHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence            12223334567999999999999999999998    899999999999999999999999999999974

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.3e-20  Score=187.71  Aligned_cols=173  Identities=19%  Similarity=0.245  Sum_probs=137.9

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++..|++.|+..|.+.|+++|+++.+++.+++|++||+++++|+++++|++.  ..|.+|++..+++.+.+++++..+..
T Consensus        27 gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~  104 (231)
T PRK11922         27 GDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLV  104 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccc
Confidence            4568999999999999999999999999999999999999999999999986  36999999999999999988765321


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  476 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~  476 (561)
                      .++.                            .                      ..+. ... ++  ...... ....+
T Consensus       105 ~~~~----------------------------~----------------------~~~~-~~~-~~--~~~~~~-~~~~~  129 (231)
T PRK11922        105 NLAE----------------------------M----------------------VMAS-TIA-GG--ERTPLA-DPAED  129 (231)
T ss_pred             cchh----------------------------c----------------------cccc-ccc-cc--cccccC-cccCC
Confidence            1100                            0                      0000 000 00  000001 11235


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      |++.+...+..+.|..+|..||+++|+||.++|.    +++|++|||+.||+|.++|++++.||+++||+.+..
T Consensus       130 ~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~  199 (231)
T PRK11922        130 PERAAARREIRALLERAIDALPDAFRAVFVLRVV----EELSVEETAQALGLPEETVKTRLHRARRLLRESLAR  199 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            6677777778888999999999999999999987    899999999999999999999999999999998864

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.7e-20  Score=181.90  Aligned_cols=177  Identities=19%  Similarity=0.206  Sum_probs=142.8

Q ss_pred             CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      +++..|+..+..| ..|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.+|++..+++.
T Consensus        11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~   89 (196)
T PRK12524         11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL   89 (196)
T ss_pred             cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence            4566777776665 499999999999999999999999999999999999999999999998533 46999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      +.++++++.+..                                                      ..++. . .     
T Consensus        90 ~~d~~Rk~~~~~------------------------------------------------------~~~~~-~-~-----  108 (196)
T PRK12524         90 CTDRLRRRRRAS------------------------------------------------------VDLDD-A-P-----  108 (196)
T ss_pred             HHHHHHhhcCCC------------------------------------------------------CCccc-c-c-----
Confidence            999987653100                                                      00000 0 0     


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                        +. .+. ...+++.+...+....|..+|..||+++|+||.|+|.    ++++++|||+.||||..+|+++++||+++|
T Consensus       109 --~~-~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L  180 (196)
T PRK12524        109 --EP-ADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRHI----EGLSNPEIAEVMEIGVEAVESLTARGKRAL  180 (196)
T ss_pred             --cc-ccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence              00 011 1235555666677778999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCc
Q 008556          545 KQSLGGKA  552 (561)
Q Consensus       545 R~~l~~~~  552 (561)
                      |.++...+
T Consensus       181 r~~l~~~~  188 (196)
T PRK12524        181 AALLAGQR  188 (196)
T ss_pred             HHHHHhcc
Confidence            99987543

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.7e-20  Score=179.58  Aligned_cols=172  Identities=14%  Similarity=0.177  Sum_probs=137.0

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556          307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  385 (561)
Q Consensus       307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  385 (561)
                      +...|+..+.+| ..|++.|+..|.+.++.++.++.++..+.+|++||+++.+|+.+++|++..+ .|.+|++..+++.+
T Consensus         9 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~   87 (182)
T PRK12537          9 DYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLA   87 (182)
T ss_pred             hHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHH
Confidence            445566666555 4999999999999999999999999999999999999999999999986443 69999999999999


Q ss_pred             HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556          386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  465 (561)
Q Consensus       386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  465 (561)
                      .+++++..+...+                                                       +.     ..   
T Consensus        88 ~d~~r~~~~~~~~-------------------------------------------------------~~-----~~---  104 (182)
T PRK12537         88 LNVLRDTRREVVL-------------------------------------------------------DD-----DA---  104 (182)
T ss_pred             HHHHHhccccCcc-------------------------------------------------------cc-----ch---
Confidence            9999876421100                                                       00     00   


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .+...+  ...+++..+..+....|..+|+.||+++|+||.++|.    +++|++|||+.||||.++|+..+.||+++||
T Consensus       105 ~~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr  178 (182)
T PRK12537        105 EETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYV----DGCSHAEIAQRLGAPLGTVKAWIKRSLKALR  178 (182)
T ss_pred             hhhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence            000000  1123333444455667899999999999999999998    8999999999999999999999999999999


Q ss_pred             HHh
Q 008556          546 QSL  548 (561)
Q Consensus       546 ~~l  548 (561)
                      .++
T Consensus       179 ~~l  181 (182)
T PRK12537        179 ECM  181 (182)
T ss_pred             HHh
Confidence            876

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.86  E-value=2.9e-20  Score=179.09  Aligned_cols=180  Identities=15%  Similarity=0.203  Sum_probs=140.2

Q ss_pred             HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHH
Q 008556          308 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  386 (561)
Q Consensus       308 ~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~  386 (561)
                      ++.|+..++.| ..+++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++..  .|.+|++..+++.+.
T Consensus         7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~   84 (193)
T PRK11923          7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK   84 (193)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence            44555555554 599999999999999999999999989999999999999999999999874  499999999999999


Q ss_pred             HHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh
Q 008556          387 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  466 (561)
Q Consensus       387 ~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~  466 (561)
                      ++++++.+....                                                  ....++.....++.    
T Consensus        85 d~~rk~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~----  110 (193)
T PRK11923         85 NHLVSRGRRPPD--------------------------------------------------SDVSSEDAEFYDGD----  110 (193)
T ss_pred             HHHHHhcCCCcc--------------------------------------------------ccccccchhhhccc----
Confidence            998765421100                                                  00000000000000    


Q ss_pred             hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          467 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       467 d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ..+.  ....|+..+...+..+.+..+|..||+++|+||.++|.    +|+|++|||+.||+|..+|++.+.||+++||.
T Consensus       111 ~~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~  184 (193)
T PRK11923        111 HALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF----DGLSYEDIASVMQCPVGTVRSRIFRAREAIDK  184 (193)
T ss_pred             cccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            0011  12356666666777788999999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhh
Q 008556          547 SLG  549 (561)
Q Consensus       547 ~l~  549 (561)
                      ++.
T Consensus       185 ~l~  187 (193)
T PRK11923        185 ALQ  187 (193)
T ss_pred             HHH
Confidence            885

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.7e-20  Score=187.70  Aligned_cols=174  Identities=15%  Similarity=0.223  Sum_probs=139.9

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556          307 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  385 (561)
Q Consensus       307 ~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  385 (561)
                      ++..|+..+..| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+++++|++..+ .|.+|++..+++.+
T Consensus        49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~  127 (233)
T PRK12538         49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC  127 (233)
T ss_pred             cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence            455666666555 5899999999999999999999999999999999999999999999987554 79999999999999


Q ss_pred             HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556          386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  465 (561)
Q Consensus       386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  465 (561)
                      .++++++.+. .                                                       ++. . .      
T Consensus       128 id~~Rk~~~~-~-------------------------------------------------------~~~-~-~------  143 (233)
T PRK12538        128 IDLRRKPRTE-N-------------------------------------------------------VDA-V-P------  143 (233)
T ss_pred             HHHHHhhccc-c-------------------------------------------------------ccc-c-c------
Confidence            9988753210 0                                                       000 0 0      


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                       +. .+ ....+++.+...+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|+++++||+++||
T Consensus       144 -~~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr  216 (233)
T PRK12538        144 -EV-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVAAVESLLKRGRQQLR  216 (233)
T ss_pred             -cc-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence             00 00 01133444555666678999999999999999999998    9999999999999999999999999999999


Q ss_pred             HHhhcCc
Q 008556          546 QSLGGKA  552 (561)
Q Consensus       546 ~~l~~~~  552 (561)
                      +.+...+
T Consensus       217 ~~l~~~~  223 (233)
T PRK12538        217 DLLRRHE  223 (233)
T ss_pred             HHHHHhh
Confidence            9987544

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.86  E-value=1.1e-20  Score=181.84  Aligned_cols=173  Identities=20%  Similarity=0.286  Sum_probs=136.5

Q ss_pred             cCCHHHHHHHHhh----cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHH
Q 008556          305 GLSCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW  380 (561)
Q Consensus       305 g~~~~eL~~~l~~----G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~w  380 (561)
                      .++++.|+..++.    +..|++.|+..|.+.|+++|.+|.++..+.+|++||+++.+|+++++|++.  ..|.+|++.+
T Consensus         7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~i   84 (188)
T PRK09640          7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSI   84 (188)
T ss_pred             CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHH
Confidence            4667778777763    569999999999999999999999999999999999999999999999963  4699999999


Q ss_pred             HHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCC
Q 008556          381 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD  460 (561)
Q Consensus       381 IRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d  460 (561)
                      +++.+.+++++..+....                                                     ..+..    
T Consensus        85 a~n~~~d~~R~~~~~~~~-----------------------------------------------------~~~~~----  107 (188)
T PRK09640         85 TYNECITQYRKERRKRRL-----------------------------------------------------MDALS----  107 (188)
T ss_pred             HHHHHHHHHHHhcccccC-----------------------------------------------------cchhh----
Confidence            999999999864321000                                                     00000    


Q ss_pred             CCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          461 QDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       461 ~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                           .+...++.    +......+....|..+|..||+++|+||.++|.    +++|++|||+.||||..+|+..+.||
T Consensus       108 -----~~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra  174 (188)
T PRK09640        108 -----LDPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIMHMGLSATKMRYKRA  174 (188)
T ss_pred             -----hccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence                 00000000    001112234456899999999999999999998    89999999999999999999999999


Q ss_pred             HHHHHHHhh
Q 008556          541 LYRLKQSLG  549 (561)
Q Consensus       541 LkKLR~~l~  549 (561)
                      +++||+.+.
T Consensus       175 ~~~Lr~~l~  183 (188)
T PRK09640        175 LDKLREKFA  183 (188)
T ss_pred             HHHHHHHHH
Confidence            999999874

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=3e-20  Score=178.20  Aligned_cols=172  Identities=15%  Similarity=0.160  Sum_probs=136.2

Q ss_pred             HHHHH-HhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008556          310 DLKSE-LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  388 (561)
Q Consensus       310 eL~~~-l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~  388 (561)
                      .+... ..++..+++.|+..|.++|+.+|+++.++..+.+|++||+++++|+++++|++.++ .|.+|++..+++.+.++
T Consensus        14 ~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~   92 (187)
T PRK12534         14 RLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDH   92 (187)
T ss_pred             HHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHH
Confidence            34444 34555999999999999999999999999999999999999999999999998655 58899999999999999


Q ss_pred             HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhh
Q 008556          389 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI  468 (561)
Q Consensus       389 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~  468 (561)
                      ++++.+...                                                    ..+.+.         ..+.
T Consensus        93 ~R~~~~~~~----------------------------------------------------~~~~~~---------~~~~  111 (187)
T PRK12534         93 LRANAPQRR----------------------------------------------------NVALDD---------AGEL  111 (187)
T ss_pred             HHhcccccc----------------------------------------------------cccccc---------hhhh
Confidence            876542100                                                    000000         0000


Q ss_pred             cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          469 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       469 l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      . ++ ..++++.....+....|..+|..||+++++||.++|.    +++|++|||+.||||..+|+++++||+++||..+
T Consensus       112 ~-~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l  185 (187)
T PRK12534        112 R-AA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPIGTVKSWIRRGLAKLKACL  185 (187)
T ss_pred             c-cc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence            0 00 1123344455566778999999999999999999998    8999999999999999999999999999999987


Q ss_pred             h
Q 008556          549 G  549 (561)
Q Consensus       549 ~  549 (561)
                      .
T Consensus       186 ~  186 (187)
T PRK12534        186 E  186 (187)
T ss_pred             c
Confidence            4

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

Probab=99.85  E-value=7.8e-20  Score=174.51  Aligned_cols=180  Identities=18%  Similarity=0.203  Sum_probs=138.1

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhC----CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  392 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~----~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~  392 (561)
                      ++..|++.|+..|.+.|+.+|++|.+    +..+.+|++||+++.+|+++.+|++..+..|.+|++..+++.+.+++++.
T Consensus         4 ~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~   83 (189)
T TIGR02984         4 GDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH   83 (189)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence            45699999999999999999999853    56789999999999999999999986666899999999999999998764


Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCC-CCCCchhhhhccc
Q 008556          393 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW-ADQDTTFQEITAD  471 (561)
Q Consensus       393 sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~-~d~~~~l~d~l~d  471 (561)
                      .+.                 .+       +.+                       ....+++.... .+....+.+.+.+
T Consensus        84 ~~~-----------------~~-------r~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~~  116 (189)
T TIGR02984        84 LGA-----------------QK-------RDI-----------------------RREQSLDAGGRLDESSVRLAAQLAA  116 (189)
T ss_pred             HHH-----------------Hh-------hhc-----------------------ccccCCCcccccCCcchhHHHHccC
Confidence            200                 00       000                       00112221111 1111123333333


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          472 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       472 ~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      . ..+|++.+...+....|..+|..||+++|+||.++|.    +|++++|||+.||||.++|++.++||+++||+.+
T Consensus       117 ~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l  188 (189)
T TIGR02984       117 D-GPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL  188 (189)
T ss_pred             C-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            2 2356777777777788999999999999999999998    8999999999999999999999999999999876

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).

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=5.7e-20  Score=179.96  Aligned_cols=171  Identities=12%  Similarity=0.165  Sum_probs=133.2

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      .++..++++|+..|.+.|+.++.++.++..+++|++||+++.+|+++.+|++.++ .|.||++.++++.+.++++++.+.
T Consensus        34 ~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~  112 (206)
T PRK12526         34 SRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAK  112 (206)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccc
Confidence            3556999999999999999999999999889999999999999999999998765 599999999999999999876421


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  475 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~  475 (561)
                      ....                                                     .+     ++...+.+.+.+. ..
T Consensus       113 ~~~~-----------------------------------------------------~~-----~~~~~~~~~~~~~-~~  133 (206)
T PRK12526        113 KEQN-----------------------------------------------------LG-----DDIWPIEQALAES-QS  133 (206)
T ss_pred             cccc-----------------------------------------------------cc-----cccchhhhhcccc-cC
Confidence            1000                                                     00     0000000111111 11


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      .+. ..........|..+|..||+++|+||.++|+    +++|++|||+.||||..+|+..++||+++||+.+...
T Consensus       134 ~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~  204 (206)
T PRK12526        134 ESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ  204 (206)
T ss_pred             chH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            122 2223334457899999999999999999998    8999999999999999999999999999999998654

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=7.9e-20  Score=175.89  Aligned_cols=177  Identities=19%  Similarity=0.266  Sum_probs=142.9

Q ss_pred             CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      ++++.|...+..| ..|++.|+..|.+.++.++.++.++..+.+|++||+++.+|+++++|++.  ..|.+|++..+++.
T Consensus         7 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~   84 (189)
T PRK12515          7 TTDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFK   84 (189)
T ss_pred             cCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHH
Confidence            4666777766655 58999999999999999999999999999999999999999999999964  36999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      +.+++++..+..                                                        +..    +.   
T Consensus        85 ~~d~~r~~~~~~--------------------------------------------------------~~~----~~---  101 (189)
T PRK12515         85 ALSALRRRKHEE--------------------------------------------------------IDD----EA---  101 (189)
T ss_pred             HHHHHHccCCCC--------------------------------------------------------Ccc----cc---
Confidence            999987643100                                                        000    00   


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                       .....+ ...+++......+....+..+|+.||+++|+||.++|.    ++++++|||+.||||..+|++++.||+++|
T Consensus       102 -~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~Rar~~L  175 (189)
T PRK12515        102 -AAAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIPESTVKTRMFYARKKL  175 (189)
T ss_pred             -ccccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence             000111 12245555566666778999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCch
Q 008556          545 KQSLGGKAS  553 (561)
Q Consensus       545 R~~l~~~~l  553 (561)
                      |..+...+.
T Consensus       176 r~~l~~~~~  184 (189)
T PRK12515        176 AELLKAAGV  184 (189)
T ss_pred             HHHHHHhcc
Confidence            999876543

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=3.3e-20  Score=177.95  Aligned_cols=175  Identities=17%  Similarity=0.201  Sum_probs=138.7

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      .++..|++.|+..|.+.++.+|.++.++..+++|++||+++.+|+++++|++..+..|.||++..+++.+.++++++.+.
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            35569999999999999999999999999999999999999999999999875445799999999999999999876421


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  475 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~  475 (561)
                      ...                  .                                    +. .   ..    +.... ..+
T Consensus        85 ~~~------------------~------------------------------------~~-~---~~----~~~~~-~~~  101 (185)
T PRK12542         85 ETF------------------L------------------------------------EE-Y---ER----ESIEA-VDE  101 (185)
T ss_pred             hhh------------------h------------------------------------hh-c---cc----cchhh-hhc
Confidence            000                  0                                    00 0   00    00000 001


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhh
Q 008556          476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG  555 (561)
Q Consensus       476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~  555 (561)
                      .+++.....+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|+..+.||+++||+.+.......
T Consensus       102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~  177 (185)
T PRK12542        102 NIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDE  177 (185)
T ss_pred             cHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            23333334444567999999999999999999998    89999999999999999999999999999999998877766


Q ss_pred             hh
Q 008556          556 YA  557 (561)
Q Consensus       556 yl  557 (561)
                      |+
T Consensus       178 ~~  179 (185)
T PRK12542        178 FK  179 (185)
T ss_pred             HH
Confidence            64

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=7.8e-20  Score=172.08  Aligned_cols=168  Identities=16%  Similarity=0.176  Sum_probs=138.7

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      .++..|++.|+..|.+.|+++|+++.+++.+.+|++||++++||+++++|+  .+..|.+|++..+++.+.+++++..+.
T Consensus         9 ~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~~   86 (179)
T PRK11924          9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRRE   86 (179)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhcccc
Confidence            455699999999999999999999999999999999999999999999998  345799999999999999998765421


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  475 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~  475 (561)
                      ...                                                     ..+ ..        .+...+....
T Consensus        87 ~~~-----------------------------------------------------~~~-~~--------~~~~~~~~~~  104 (179)
T PRK11924         87 KAV-----------------------------------------------------LSD-DA--------LEPEFAETAE  104 (179)
T ss_pred             ccc-----------------------------------------------------Ccc-cc--------cccccCCccC
Confidence            100                                                     000 00        0000000223


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      +|+..+...+....|..+|..||+++++||.++|.    ++++.+|||+.||+|+.+|++.+.||+++||+.+...
T Consensus       105 ~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~  176 (179)
T PRK11924        105 TPEAALLAKDDLARIDRCLDALPVKQREVFLLRYV----EGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ  176 (179)
T ss_pred             CHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            67777888888889999999999999999999998    8999999999999999999999999999999988654

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.84  E-value=8.6e-20  Score=172.97  Aligned_cols=172  Identities=13%  Similarity=0.188  Sum_probs=134.2

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      |++..+...+..|+ .|++.|+..|.+.|+.+|++|.++..+.+|++||+++++|+++++|++.  .+|.+|++..+++.
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            45566666655554 9999999999999999999999998999999999999999999999874  47999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      +.+++++..+.....                           +.+                       .+.         
T Consensus        81 ~~d~~r~~~~~~~~~---------------------------~~~-----------------------~~~---------  101 (176)
T PRK09638         81 YKDHLRKQKREKLRL---------------------------QRA-----------------------KEE---------  101 (176)
T ss_pred             HHHHHHHhccccchh---------------------------hhc-----------------------ccc---------
Confidence            999998754211000                           000                       000         


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                          ..+  .... +..........|..+|..||+++|+||.++|.    +|++++|||+.||+|..+|++.+.||+++|
T Consensus       102 ----~~~--~~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~~V~~~l~ra~~~l  170 (176)
T PRK09638        102 ----TLR--KEKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNIPEGTVKSRVHHGIKQL  170 (176)
T ss_pred             ----cCC--ccch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence                000  0000 11122233456889999999999999999988    899999999999999999999999999999


Q ss_pred             HHHhh
Q 008556          545 KQSLG  549 (561)
Q Consensus       545 R~~l~  549 (561)
                      |+.+.
T Consensus       171 ~~~l~  175 (176)
T PRK09638        171 RKEWG  175 (176)
T ss_pred             HHHhc
Confidence            99763

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.84  E-value=1.5e-19  Score=174.97  Aligned_cols=172  Identities=17%  Similarity=0.174  Sum_probs=138.5

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          306 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       306 ~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      +++..+...+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+++.+|+++++|++..  .|.+|++..+++.
T Consensus        12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~   89 (192)
T PRK09643         12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNA   89 (192)
T ss_pred             cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHH
Confidence            35666666665554 99999999999999999999999999999999999999999999999753  5999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      +.+++++..+..+.                                                     +++     +..  
T Consensus        90 ~~d~~Rk~~~~~~~-----------------------------------------------------~~~-----~~~--  109 (192)
T PRK09643         90 CLDRLRRAKARPTV-----------------------------------------------------PLD-----DVY--  109 (192)
T ss_pred             HHHHHHccccCCCC-----------------------------------------------------Ccc-----ccc--
Confidence            99999875421100                                                     000     000  


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                        +. .    ..+++.+...+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|+..+.||+++|
T Consensus       110 --~~-~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~~tV~~rl~rar~~L  178 (192)
T PRK09643        110 --PV-A----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAEGTVKSRCARGRARL  178 (192)
T ss_pred             --cc-c----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence              00 0    012223444455667999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhc
Q 008556          545 KQSLGG  550 (561)
Q Consensus       545 R~~l~~  550 (561)
                      |+.+..
T Consensus       179 r~~l~~  184 (192)
T PRK09643        179 AELLGY  184 (192)
T ss_pred             HHHHHH
Confidence            998864

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

Probab=99.84  E-value=1.2e-19  Score=171.19  Aligned_cols=167  Identities=18%  Similarity=0.230  Sum_probs=132.1

Q ss_pred             CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          306 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       306 ~~~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      |+++.+...+..| ..|++.++..|.+.|++++.++.++..+++|++||+++.+|+++++|++..  .|.||++..+++.
T Consensus         1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~   78 (169)
T TIGR02954         1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE   78 (169)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence            3455666665555 599999999999999999999999999999999999999999999999753  6999999999999


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      +.+++++..+..  |                                                     ++.....+    
T Consensus        79 ~~d~~R~~~~~~--~-----------------------------------------------------~~~~~~~~----   99 (169)
T TIGR02954        79 CIDLLKKKKKVI--P-----------------------------------------------------FDPNTSIE----   99 (169)
T ss_pred             HHHHHHhcCCcC--c-----------------------------------------------------cccccccc----
Confidence            999987654210  0                                                     00000000    


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                            +.   .++  ... .....+..+|..||+++|+||.++|.    +|+|.+|||+.||||..+|+..+.||+++|
T Consensus       100 ------~~---~~~--~~~-~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L  163 (169)
T TIGR02954       100 ------KG---ECE--THA-DSRLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVKTYLHRALKKL  163 (169)
T ss_pred             ------cc---hhh--hch-HHHHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                  00   000  001 11236889999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhh
Q 008556          545 KQSLG  549 (561)
Q Consensus       545 R~~l~  549 (561)
                      |..+.
T Consensus       164 r~~l~  168 (169)
T TIGR02954       164 KKRLE  168 (169)
T ss_pred             HHHhc
Confidence            99874

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.

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

Probab=99.84  E-value=2.1e-19  Score=162.50  Aligned_cols=157  Identities=24%  Similarity=0.383  Sum_probs=131.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556          321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  400 (561)
Q Consensus       321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~  400 (561)
                      |++.++..|.++|.++++++.+++.+.+|++|||++++|++++.|++.  .+|.+|+.+++++.+.++++++.+ .  +.
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~-~--~~   76 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR-L--RR   76 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc-C--Cc
Confidence            789999999999999999999999999999999999999999999998  589999999999999999987763 1  10


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556          401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  480 (561)
Q Consensus       401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~  480 (561)
                      ..                                                   .      ..    ... ......++..
T Consensus        77 ~~---------------------------------------------------~------~~----~~~-~~~~~~~~~~   94 (158)
T TIGR02937        77 EL---------------------------------------------------D------LL----EEL-LDSDPSPEEE   94 (158)
T ss_pred             ch---------------------------------------------------h------hh----hhc-ccccCCHHHH
Confidence            00                                                   0      00    000 0111245556


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      .........|..++..||++++.||.++|+    .|+|..|||+.+|+|+.+|+++..+++++||+.+
T Consensus        95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l  158 (158)
T TIGR02937        95 LEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL  158 (158)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            666677788999999999999999999987    7899999999999999999999999999999754

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.

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=1.4e-19  Score=175.29  Aligned_cols=176  Identities=11%  Similarity=0.145  Sum_probs=133.8

Q ss_pred             HHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHH
Q 008556          311 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  389 (561)
Q Consensus       311 L~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~I  389 (561)
                      ++..+. ++..+++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++.++ .|.+|++..++|.+.+++
T Consensus        17 li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~   95 (194)
T PRK12531         17 CMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLL   95 (194)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHH
Confidence            445554 445999999999999999999999999889999999999999999999997554 699999999999999999


Q ss_pred             HhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhc
Q 008556          390 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT  469 (561)
Q Consensus       390 r~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l  469 (561)
                      ++..+....                         .                           ..+... .+..  ....+
T Consensus        96 Rk~~~~~~~-------------------------~---------------------------~~~~~~-~~~~--~~~~~  120 (194)
T PRK12531         96 RKQKGKDLH-------------------------I---------------------------HADDIW-PSDY--YPPDL  120 (194)
T ss_pred             HHhcccccc-------------------------c---------------------------chhhcc-cccc--ccccc
Confidence            875421000                         0                           000000 0000  00000


Q ss_pred             ccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          470 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       470 ~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      .+  ...++..    ...+.+..+|..||+++|+||.++|.    +++|.+|||+.||||.++|+..++||+++||..+.
T Consensus       121 ~~--~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~  190 (194)
T PRK12531        121 VD--HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYL----EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD  190 (194)
T ss_pred             cc--ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence            00  0122221    23356889999999999999999998    89999999999999999999999999999999987


Q ss_pred             cCc
Q 008556          550 GKA  552 (561)
Q Consensus       550 ~~~  552 (561)
                      ...
T Consensus       191 ~~~  193 (194)
T PRK12531        191 AES  193 (194)
T ss_pred             hcc
Confidence            654

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=1.9e-19  Score=172.00  Aligned_cols=165  Identities=16%  Similarity=0.196  Sum_probs=132.8

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++..|++.|+..|.+.|+.++++|.++..+.+|++||+++.+|+++.+|++..  .|.+|++..+++.+.++++...+..
T Consensus         4 ~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~   81 (179)
T PRK12543          4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRF   81 (179)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccc
Confidence            44589999999999999999999999999999999999999999999999864  5999999999999988876543110


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  476 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~  476 (561)
                      +.                                                      ++...  +    ..+   ......
T Consensus        82 ~~------------------------------------------------------~~~~~--~----~~~---~~~~~~   98 (179)
T PRK12543         82 RI------------------------------------------------------FEKAE--E----QRK---PVSIDF   98 (179)
T ss_pred             cc------------------------------------------------------ccccc--c----ccc---cccccC
Confidence            00                                                      00000  0    000   001113


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      |+. +...+....|..+|..||+++|+||.++|.    +++|++|||+.||||..+|+..++||+++||+.+...
T Consensus        99 ~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~  168 (179)
T PRK12543         99 SED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE  168 (179)
T ss_pred             hHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            444 556666778999999999999999999998    8999999999999999999999999999999988654

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

Probab=99.83  E-value=1.9e-19  Score=166.26  Aligned_cols=160  Identities=18%  Similarity=0.183  Sum_probs=129.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556          321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  400 (561)
Q Consensus       321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~  400 (561)
                      |+++|+..|.+.|+++++++.++..+.+|++||+++++|+++.+|++.  .+|.+|++.++++.+.+++++..+...   
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~---   76 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEK---   76 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhH---
Confidence            789999999999999999999998999999999999999999999874  369999999999999999876542100   


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556          401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  480 (561)
Q Consensus       401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~  480 (561)
                                 ..             ..+                        .    .+..       .......+++.
T Consensus        77 -----------~~-------------~~~------------------------~----~~~~-------~~~~~~~~~~~   97 (161)
T TIGR02985        77 -----------YQ-------------EEI------------------------L----EIEV-------DELSENDPEEE   97 (161)
T ss_pred             -----------HH-------------HHH------------------------H----hhcc-------cccCCCCcHHH
Confidence                       00             000                        0    0000       00011245555


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      +...+....|..++..||+++++||.++|.    +++|..|||+.||+|+++|++++.+|+++||+.|
T Consensus        98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l  161 (161)
T TIGR02985        98 LEAKELQLIIYKAIEKLPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISKALKELRKEL  161 (161)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            666677778999999999999999999998    8999999999999999999999999999999864

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.

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.83  E-value=3.1e-19  Score=168.92  Aligned_cols=165  Identities=14%  Similarity=0.133  Sum_probs=131.2

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++..+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+..
T Consensus         6 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~   84 (173)
T PRK09645          6 AEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARP   84 (173)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence            35689999999999999999999999888999999999999999999997533 36999999999999999998654210


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  476 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~  476 (561)
                      ..                                                     ..+      +..   +. .+.   .
T Consensus        85 ~~-----------------------------------------------------~~~------~~~---~~-~~~---~   98 (173)
T PRK09645         85 VE-----------------------------------------------------GGD------DVL---GV-PEQ---S   98 (173)
T ss_pred             cc-----------------------------------------------------ccc------ccc---cC-CCC---C
Confidence            00                                                     000      000   00 000   1


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      +++.+........|..+|+.||+++|+||.|+|.    +++|++|||+.||+|..+|+..++||+++||+.+...+
T Consensus        99 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  170 (173)
T PRK09645         99 APDEVDRALDRLLVADALAQLSPEHRAVLVRSYY----RGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG  170 (173)
T ss_pred             CchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence            2222333344457899999999999999999998    89999999999999999999999999999999987544

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=2.5e-19  Score=171.50  Aligned_cols=169  Identities=15%  Similarity=0.128  Sum_probs=129.9

Q ss_pred             HHHHHH-hhcHHHHHHHHHHHHHHHHHHHHhhhC-CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHH
Q 008556          310 DLKSEL-HSGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  387 (561)
Q Consensus       310 eL~~~l-~~G~~Are~LI~~nlrLV~sIArrY~~-~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~  387 (561)
                      .++..+ .++..|++.|+..|.+.|+.++.++.+ ...+.+|++||+++.||+.++.|++.  ..|.+|++..++|.+.+
T Consensus        10 ~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d   87 (181)
T PRK12536         10 ALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMD   87 (181)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHH
Confidence            344444 455699999999999999999998764 57899999999999999999999974  36999999999999999


Q ss_pred             HHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhh
Q 008556          388 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE  467 (561)
Q Consensus       388 ~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d  467 (561)
                      +++++.+....                                                   ..+++    .     ..+
T Consensus        88 ~~Rk~~~~~~~---------------------------------------------------~~~~~----~-----~~~  107 (181)
T PRK12536         88 FLRSRARREAL---------------------------------------------------HDPLD----D-----ESE  107 (181)
T ss_pred             HHHHHhccccc---------------------------------------------------cCCcc----c-----hhh
Confidence            99875421000                                                   00000    0     000


Q ss_pred             hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          468 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       468 ~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      ...+.   .++.    .+....+..+|..||+++|.||.++|.    +++|.+|||+.||||.++|+..++||+++||+.
T Consensus       108 ~~~~~---~~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~  176 (181)
T PRK12536        108 LFATS---DDEA----AEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK  176 (181)
T ss_pred             hcCCC---Ccch----HHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            00011   1111    123446899999999999999999998    899999999999999999999999999999998


Q ss_pred             hhcC
Q 008556          548 LGGK  551 (561)
Q Consensus       548 l~~~  551 (561)
                      +...
T Consensus       177 l~~~  180 (181)
T PRK12536        177 IRGE  180 (181)
T ss_pred             hcCC
Confidence            7643

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.82  E-value=4.1e-19  Score=169.80  Aligned_cols=164  Identities=16%  Similarity=0.180  Sum_probs=133.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008556          318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  397 (561)
Q Consensus       318 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IR  397 (561)
                      +..|+++|+..|.+.|+++|.++.++..+.+|++||+++.+|+++++|++.  ..|.+|++..+++.+.+++++..+...
T Consensus        14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~   91 (179)
T PRK09415         14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKV   91 (179)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhccccc
Confidence            358999999999999999999999999999999999999999999999874  369999999999999999876431100


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCCh
Q 008556          398 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  477 (561)
Q Consensus       398 lP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~p  477 (561)
                      .                                                     ..+.        ......  ....+|
T Consensus        92 ~-----------------------------------------------------~~~~--------~~~~~~--~~~~~~  108 (179)
T PRK09415         92 I-----------------------------------------------------VTED--------IFTYME--SQKESV  108 (179)
T ss_pred             c-----------------------------------------------------cccc--------cccccc--ccccCc
Confidence            0                                                     0000        000000  011245


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          478 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       478 ee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ++.+...+....|..+|..||+++|+||.++|.    +|+|++|||+.||||.++|++.+.||+++||+.+..
T Consensus       109 e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~  177 (179)
T PRK09415        109 EEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----EELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE  177 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            666666677778999999999999999999998    899999999999999999999999999999998764

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=5.3e-19  Score=167.69  Aligned_cols=167  Identities=16%  Similarity=0.193  Sum_probs=130.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556          320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  399 (561)
Q Consensus       320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP  399 (561)
                      ..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++..  +|.+|++..+++.+.++++++.+....+
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~   80 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI   80 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            45899999999999999999999999999999999999999999999754  6999999999999999998765311000


Q ss_pred             hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556          400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  479 (561)
Q Consensus       400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee  479 (561)
                      ...                                                  .+      .+ ...+.........++.
T Consensus        81 ~~~--------------------------------------------------~~------~~-~~~~~~~~~~~~~~~~  103 (173)
T PRK12522         81 LDL--------------------------------------------------FH------KE-DGGEIEFADDVNISEE  103 (173)
T ss_pred             ccc--------------------------------------------------cc------hh-hhhhhccccCCCChHH
Confidence            000                                                  00      00 0000000001112333


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       480 ~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                       ....+..+.|..+|..||+++++||.|+|.    ++++++|||+.||||.++|+..+.||+++||+.+..
T Consensus       104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~  169 (173)
T PRK12522        104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYY----EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG  169 (173)
T ss_pred             -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence             444556778999999999999999999998    899999999999999999999999999999998753

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

Probab=99.82  E-value=3.1e-19  Score=166.03  Aligned_cols=158  Identities=18%  Similarity=0.214  Sum_probs=125.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556          321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  400 (561)
Q Consensus       321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~  400 (561)
                      +++.++..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++..  .|.+|++..+++.+.++++++.+.-.. .
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~   78 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F   78 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence            7899999999999999999999999999999999999999999999764  599999999999999999876521100 0


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556          401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  480 (561)
Q Consensus       401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~  480 (561)
                                               .++                                    ..+.+.+..  .+.+.
T Consensus        79 -------------------------~~~------------------------------------~~~~~~~~~--~~~~~   95 (159)
T TIGR02989        79 -------------------------DDE------------------------------------LLEALAAEA--EATEA   95 (159)
T ss_pred             -------------------------CHH------------------------------------HHHHHHhhc--ccchH
Confidence                                     000                                    000000000  11112


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      ....+....|..+++.||++++.||.++|.    +|++.+|||+.||||..+|+..++||+++||+++
T Consensus        96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~  159 (159)
T TIGR02989        96 DRSEDELQALEGCLEKLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV  159 (159)
T ss_pred             hhHHHHHHHHHHHHHHCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence            222334567899999999999999999998    8999999999999999999999999999999853

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).

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

Probab=99.82  E-value=5.4e-19  Score=178.18  Aligned_cols=181  Identities=16%  Similarity=0.201  Sum_probs=141.6

Q ss_pred             ccCCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHH-------hhhhcCCCCCCchhH
Q 008556          304 IGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFAS  375 (561)
Q Consensus       304 ~g~~~~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLir-------AiekFDp~kG~rFST  375 (561)
                      ++.++..|...+++|+ .|++.|+..|.+.|+.+++++.++..+++|++||.|+.+|.       .+.+|++.  ..|.|
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            4456777888877666 99999999999999999999999999999999999999994       78889864  36999


Q ss_pred             HHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCC
Q 008556          376 YAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQ  455 (561)
Q Consensus       376 YA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~  455 (561)
                      |++.+++|.+.++++++.+...+                                                       + 
T Consensus       100 WL~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~-  123 (244)
T TIGR03001       100 WVRIVATRIALELQAQERRHSPV-------------------------------------------------------E-  123 (244)
T ss_pred             HHHHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c-
Confidence            99999999999999765421000                                                       0 


Q ss_pred             CCCCCCCchhhhhcccCCCCChhHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHH
Q 008556          456 PVWADQDTTFQEITADTGVEIPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE  531 (561)
Q Consensus       456 ~v~~d~~~~l~d~l~d~~~~~pee~le~----~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISre  531 (561)
                         .+.  ...+. .+. ...|++.+..    .+..+.|..+|+.||+++|+||.|+|.    +++|++|||++||||.+
T Consensus       124 ---~~~--~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~----eg~S~~EIA~~Lgis~~  192 (244)
T TIGR03001       124 ---EPT--ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV----DGLSMDRIGAMYQVHRS  192 (244)
T ss_pred             ---ccc--ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHH
Confidence               000  00000 011 1133433332    235567999999999999999999998    89999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhcCch
Q 008556          532 RVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       532 rVRqie~RALkKLR~~l~~~~l  553 (561)
                      +|+..+.||+++||+.+.....
T Consensus       193 TVk~rl~RAr~~Lr~~l~~~~~  214 (244)
T TIGR03001       193 TVSRWVAQARERLLERTRRRLA  214 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999876543

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.

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=4.4e-19  Score=170.97  Aligned_cols=182  Identities=16%  Similarity=0.178  Sum_probs=136.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556          321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  400 (561)
Q Consensus       321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~  400 (561)
                      +++.|+..|.+.|+.+|+++.++..+.+|++||.++.+|+.+++|++..  +|.+|++..++|.+.++++++.+......
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            6899999999999999999999999999999999999999999998643  69999999999999999987653211100


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556          401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  480 (561)
Q Consensus       401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~  480 (561)
                      ..                  .......++                       ++. ... .+. .....++. ..+|++.
T Consensus        81 ~~------------------~~~~~~~~~-----------------------~~~-~~~-~~~-~~~~~~~~-~~~~~~~  115 (191)
T PRK12520         81 DD------------------ADEQSDDDL-----------------------FDA-LFA-ADG-HYREPPSD-WGDPDAA  115 (191)
T ss_pred             cc------------------cccchhhhh-----------------------hhh-hcc-ccc-ccccCccc-cCCHHHH
Confidence            00                  000000000                       000 000 000 00001111 2356666


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      +...+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|++.+.||+++||+++...+.
T Consensus       116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~  184 (191)
T PRK12520        116 LSRREFFEVLQACVDRLPPRTGRVFMMREW----LELETEEICQELQITATNAWVLLYRARMRLRECLDLHWF  184 (191)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            777777788999999999999999999998    899999999999999999999999999999999987653

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=7.3e-19  Score=168.66  Aligned_cols=169  Identities=15%  Similarity=0.157  Sum_probs=130.1

Q ss_pred             HHHHHHHHhh-cHHHHHHHHHHHHHHHHHHHHh----hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHH
Q 008556          308 CRDLKSELHS-GNSSREKLINANLRLVVHVAKQ----YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  382 (561)
Q Consensus       308 ~~eL~~~l~~-G~~Are~LI~~nlrLV~sIArr----Y~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR  382 (561)
                      ...|+..+.. +..|++.|+..|.+.|+.+|++    +.++..+.+|++||+++.+|++++.|++..  .|.+|++..++
T Consensus         8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~   85 (184)
T PRK12539          8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIAR   85 (184)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHH
Confidence            3445555544 4599999999999999999874    557788999999999999999999999753  59999999999


Q ss_pred             HHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCC
Q 008556          383 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD  462 (561)
Q Consensus       383 qaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~  462 (561)
                      +.+.+++++..+.. .                                                   ....+      +.
T Consensus        86 n~~~d~~R~~~~~~-~---------------------------------------------------~~~~~------~~  107 (184)
T PRK12539         86 YKLIDHLRRTRASL-A---------------------------------------------------DVPID------DA  107 (184)
T ss_pred             HHHHHHHHHHhccc-c---------------------------------------------------ccChh------hh
Confidence            99999988653100 0                                                   00000      00


Q ss_pred             chhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          463 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       463 ~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                      .   ...       +.+.....+....|..++..||+++|+||.++|.    +|++++|||+.||||..+|+..+.||++
T Consensus       108 ~---~~~-------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~  173 (184)
T PRK12539        108 D---ELV-------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRGLK  173 (184)
T ss_pred             c---ccc-------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            0   000       0001112233457899999999999999999998    8999999999999999999999999999


Q ss_pred             HHHHHhhc
Q 008556          543 RLKQSLGG  550 (561)
Q Consensus       543 KLR~~l~~  550 (561)
                      +||+.+..
T Consensus       174 ~Lr~~l~~  181 (184)
T PRK12539        174 ALAALIGR  181 (184)
T ss_pred             HHHHHHhh
Confidence            99998754

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

Probab=99.82  E-value=7.9e-19  Score=167.39  Aligned_cols=171  Identities=19%  Similarity=0.264  Sum_probs=125.2

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCC-----CHHHHHHHHHHHHHH-hhhhcCCCCCCchhHHHHHHH
Q 008556          309 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWWV  381 (561)
Q Consensus       309 ~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~-----~~eDLIQEG~IGLir-AiekFDp~kG~rFSTYA~~wI  381 (561)
                      ..|+..+..|+ .|++.|+..|.+.++.+|++|.++..     +.+|++||+|+.+|+ ...+|++.  ..|.+|++.++
T Consensus         5 ~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~   82 (183)
T TIGR02999         5 TELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAM   82 (183)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHH
Confidence            34555555554 89999999999999999999998877     899999999999998 78889754  36999999999


Q ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCC
Q 008556          382 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ  461 (561)
Q Consensus       382 RqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~  461 (561)
                      ++.+.++++++.+..+.                      .                             ...+..     
T Consensus        83 ~n~~~d~~R~~~~~~~~----------------------~-----------------------------~~~~~~-----  106 (183)
T TIGR02999        83 RRILVDHARRRRAQKRG----------------------G-----------------------------GAVRVP-----  106 (183)
T ss_pred             HHHHHHHHHHHHHHhcc----------------------C-----------------------------Cccccc-----
Confidence            99999998764311000                      0                             000000     


Q ss_pred             CchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          462 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       462 ~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                         +.+..++.   .++.. +.....+.+...|..||+++|+||.|+|.    +|+|++|||+.||||..+|+..+.||+
T Consensus       107 ---~~~~~~~~---~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar  175 (183)
T TIGR02999       107 ---LDEVLPDA---EADLD-EELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIAELLGVSVRTVERDWRFAR  175 (183)
T ss_pred             ---cccccCCC---CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence               00000000   11111 11111223444567799999999999998    999999999999999999999999999


Q ss_pred             HHHHHHh
Q 008556          542 YRLKQSL  548 (561)
Q Consensus       542 kKLR~~l  548 (561)
                      ++||+.+
T Consensus       176 ~~Lr~~l  182 (183)
T TIGR02999       176 AWLADEL  182 (183)
T ss_pred             HHHHHHh
Confidence            9999876

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.

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.3e-18  Score=166.40  Aligned_cols=166  Identities=19%  Similarity=0.239  Sum_probs=128.4

Q ss_pred             HHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHH
Q 008556          311 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  385 (561)
Q Consensus       311 L~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~----g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  385 (561)
                      +...+. ++..|++.|+..|.+.|+.+|+++.++    ..+++|++||+++.+|...++|+..  ..|.+|++..+++.+
T Consensus        12 l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~   89 (184)
T PRK12512         12 LMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKL   89 (184)
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHH
Confidence            334443 556999999999999999999998753    3689999999999999999999874  469999999999999


Q ss_pred             HHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchh
Q 008556          386 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  465 (561)
Q Consensus       386 ~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  465 (561)
                      .++++++.+...+                                                     .++.         +
T Consensus        90 ~d~~Rr~~~~~~~-----------------------------------------------------~~~~---------~  107 (184)
T PRK12512         90 IDALRRRGRRVFV-----------------------------------------------------DIDD---------F  107 (184)
T ss_pred             HHHHHhhcccccC-----------------------------------------------------Cchh---------c
Confidence            9998765421110                                                     0000         0


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       466 ~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .+.+++.   .+..    ....+.+..+|..||+++|+||.++|.    +++|++|||+.||+|..+|+..+.||+++||
T Consensus       108 ~~~~~~~---~~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr  176 (184)
T PRK12512        108 AETLPAE---PATE----TLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVRVALHRGLAALA  176 (184)
T ss_pred             ccccccc---chhh----HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence            0001110   0001    122346788999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhhcC
Q 008556          546 QSLGGK  551 (561)
Q Consensus       546 ~~l~~~  551 (561)
                      ..+...
T Consensus       177 ~~l~~~  182 (184)
T PRK12512        177 AKFRSE  182 (184)
T ss_pred             HHhhcC
Confidence            988754

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.6e-18  Score=171.74  Aligned_cols=172  Identities=18%  Similarity=0.165  Sum_probs=136.7

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      .....+++.|+..|.+.++.+++++.++..+.+|++||+++.+|+.+++|++.   .|.+|++.+++|.+.++++++.+.
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            34568999999999999999999999999999999999999999999999853   499999999999999998875421


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  475 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~  475 (561)
                      ....                                                     .......+  ..... . ++...
T Consensus        91 ~~~~-----------------------------------------------------~~~~~~~~--~~~~~-~-~~~~~  113 (216)
T PRK12533         91 HEVA-----------------------------------------------------APDTLDDA--DSLDD-W-QPAGE  113 (216)
T ss_pred             cccc-----------------------------------------------------cccccccc--ccccc-c-ccCCC
Confidence            0000                                                     00000000  00000 0 11123


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      +|++.+...+....|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|+++++||+++||+.+...
T Consensus       114 ~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~  185 (216)
T PRK12533        114 DPLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA  185 (216)
T ss_pred             CHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence            56667777777788999999999999999999998    8999999999999999999999999999999998653

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.2e-18  Score=166.60  Aligned_cols=166  Identities=9%  Similarity=0.032  Sum_probs=130.2

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHhhhC--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556          316 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  393 (561)
Q Consensus       316 ~~G~~Are~LI~~nlrLV~sIArrY~~--~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s  393 (561)
                      .++..+++.|+..|.+.|+.++.++.+  +..+++|++||.|+.+|+..++|++.....|.||++.++++.+.++++++.
T Consensus         9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~   88 (178)
T PRK12529          9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS   88 (178)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence            456699999999999999998766665  357899999999999999999998544457999999999999999887542


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCC
Q 008556          394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG  473 (561)
Q Consensus       394 r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~  473 (561)
                      +..                  ..                                    .+.         ..+. .+..
T Consensus        89 ~~~------------------~~------------------------------------~~~---------~~~~-~~~~  104 (178)
T PRK12529         89 LEL------------------AW------------------------------------LEA---------LATL-PEPL  104 (178)
T ss_pred             HHh------------------hh------------------------------------hhH---------hhhc-cCcC
Confidence            100                  00                                    000         0000 0011


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      ..+|++.+...+....|..+|..||+++|.||.|+|.    +++|++|||+.||||.++|+..+.||+.+|++.+.
T Consensus       105 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~~  176 (178)
T PRK12529        105 HPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATL----DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLMP  176 (178)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhCC
Confidence            1245655665666678999999999999999999998    89999999999999999999999999999998753

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

Probab=99.81  E-value=2.2e-18  Score=165.26  Aligned_cols=171  Identities=20%  Similarity=0.286  Sum_probs=136.3

Q ss_pred             HHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhc
Q 008556          313 SELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  392 (561)
Q Consensus       313 ~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~  392 (561)
                      ....++..+++.++..|.+.++.+|+++.++..+.+||+||+++.+|+++..| ... ..|.||++.+++|.+.+++++.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~-~~~~~wl~~Ia~n~~iD~~R~~   85 (182)
T COG1595           8 EALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGR-SSFKAWLYRIARNLAIDRLRKR   85 (182)
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CCC-CchHHHHHHHHHHHHHHHHHHh
Confidence            34456679999999999999999999999988899999999999999999999 433 4799999999999999999876


Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccC
Q 008556          393 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADT  472 (561)
Q Consensus       393 sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~  472 (561)
                      .+....                                                      .+     +.+  ..+...+.
T Consensus        86 ~r~~~~------------------------------------------------------~~-----~~~--~~~~~~~~  104 (182)
T COG1595          86 KRRRAR------------------------------------------------------VE-----EAD--LLPEEADP  104 (182)
T ss_pred             cccccc------------------------------------------------------cc-----ccc--ccccccCc
Confidence            643211                                                      00     000  00000011


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          473 GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       473 ~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      ..+.. +.+...+....|..+|..||+++|+||.|+|.    +|+|++|||+.||||.++|+..++||+++||+.+...
T Consensus       105 ~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~  178 (182)
T COG1595         105 APDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA  178 (182)
T ss_pred             ccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            10011 24555667788999999999999999999999    9999999999999999999999999999999988754

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.1e-18  Score=165.34  Aligned_cols=166  Identities=17%  Similarity=0.153  Sum_probs=128.0

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          316 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       316 ~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      .++..+++.|+..|.+.|+.+++++.+ ..+++|++||+++.+|+.++.|++.  ..|.+|++..+++.+.+++++..+.
T Consensus         7 ~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~   83 (175)
T PRK12518          7 RGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQR   83 (175)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcc
Confidence            455699999999999999999999875 3689999999999999999999974  4699999999999999998764311


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  475 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~  475 (561)
                      -..                                                      .+... ...     . ....   
T Consensus        84 ~~~------------------------------------------------------~~~~~-~~~-----~-~~~~---   99 (175)
T PRK12518         84 PSR------------------------------------------------------IQDDS-LND-----Q-PSRP---   99 (175)
T ss_pred             ccc------------------------------------------------------hhccc-ccc-----c-ccCC---
Confidence            000                                                      00000 000     0 0000   


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          476 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       476 ~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      .++......+....+..+|+.||+++|+||.++|.    +|+|++|||+.||+|..+|++.+.||+++||+.+...+
T Consensus       100 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~  172 (175)
T PRK12518        100 SDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG  172 (175)
T ss_pred             CCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence            11112222334456889999999999999999998    89999999999999999999999999999999987644

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.80  E-value=1.4e-18  Score=167.20  Aligned_cols=169  Identities=17%  Similarity=0.111  Sum_probs=128.2

Q ss_pred             HHHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008556          310 DLKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  388 (561)
Q Consensus       310 eL~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~  388 (561)
                      .|+..+. ++..|++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+.+++|++.  ..|.+|++.++++.+.++
T Consensus        13 ~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~   89 (185)
T PRK09649         13 ALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADH   89 (185)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHH
Confidence            3444444 4559999999999999999995 67888899999999999999999999964  369999999999999999


Q ss_pred             HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhh
Q 008556          389 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI  468 (561)
Q Consensus       389 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~  468 (561)
                      +++..+..+.                                                     +.+.     .    .+.
T Consensus        90 ~Rk~~~~~~~-----------------------------------------------------~~~~-----~----~~~  107 (185)
T PRK09649         90 IRHVRSRPRT-----------------------------------------------------TRGA-----R----PEH  107 (185)
T ss_pred             HHHhcccccc-----------------------------------------------------cccc-----c----hhh
Confidence            9875421000                                                     0000     0    000


Q ss_pred             cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          469 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       469 l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      ..+.     +......+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|++.+.||+++||+.+
T Consensus       108 ~~~~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~  178 (185)
T PRK09649        108 LIDG-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDALLADA  178 (185)
T ss_pred             ccCh-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            0000     000011112245788999999999999999998    8999999999999999999999999999999966


Q ss_pred             hcCc
Q 008556          549 GGKA  552 (561)
Q Consensus       549 ~~~~  552 (561)
                      ....
T Consensus       179 ~~~~  182 (185)
T PRK09649        179 EPDD  182 (185)
T ss_pred             Cccc
Confidence            5443

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.80  E-value=1.3e-18  Score=162.55  Aligned_cols=157  Identities=13%  Similarity=0.041  Sum_probs=125.8

Q ss_pred             HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556          327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  406 (561)
Q Consensus       327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l  406 (561)
                      ..|.+.|+.+|.++.++..+++|++||+++.+|+++++|++.   .|.+|++..++|.+.++++++.+..+.        
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~--------   70 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE--------   70 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc--------
Confidence            568999999999999999999999999999999999999963   499999999999999999875421000        


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556          407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  486 (561)
Q Consensus       407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~  486 (561)
                                                                  ..+.     +.   ..+...  ...++++.+...+.
T Consensus        71 --------------------------------------------~~~~-----~~---~~~~~~--~~~~~~~~~~~~e~   96 (160)
T PRK09642         71 --------------------------------------------LSLC-----KE---TEENIK--SSHNIEDLLLTKEQ   96 (160)
T ss_pred             --------------------------------------------cccc-----hh---hhhhcc--CCCChHHHHHHHHH
Confidence                                                        0000     00   000000  11245556666677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      ...|..+|..||+++|+||.|+|.    +|+|++|||+.||||..+|++++.||+++||+.+....
T Consensus        97 ~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~  158 (160)
T PRK09642         97 KLLIAQKLRELPENYRDVVLAHYL----EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEE  158 (160)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhhc
Confidence            778999999999999999999998    99999999999999999999999999999999986543

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=1.9e-18  Score=167.06  Aligned_cols=162  Identities=20%  Similarity=0.193  Sum_probs=128.8

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++..++..|+..|.+.++.+|.++.++..+.+|++||.++.+|+..++|+...  .|.+|++..++|.+.++++++.+..
T Consensus         7 ~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~   84 (187)
T PRK12516          7 EGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREV   84 (187)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCc
Confidence            34689999999999999999999999999999999999999999999998643  5999999999999999988754210


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  476 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~  476 (561)
                      ..                                                      .+..        +.+....    .
T Consensus        85 ~~------------------------------------------------------~~~~--------~~~~~~~----~   98 (187)
T PRK12516         85 QD------------------------------------------------------TDGM--------FTEQLAV----H   98 (187)
T ss_pred             cc------------------------------------------------------cccc--------cccccCC----C
Confidence            00                                                      0000        0000000    0


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      ++.  ........|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|+.++.||+++||+.+...+
T Consensus        99 ~~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~  168 (187)
T PRK12516         99 PSQ--YGTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG  168 (187)
T ss_pred             cch--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            110  11122346889999999999999999998    89999999999999999999999999999999987654

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

Probab=99.80  E-value=1e-18  Score=168.69  Aligned_cols=172  Identities=18%  Similarity=0.199  Sum_probs=130.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556          319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  398 (561)
Q Consensus       319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl  398 (561)
                      ..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+.+|++.  ..|.+|++..++|.+.++++++.+....
T Consensus        10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~   87 (193)
T TIGR02947        10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ   87 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence            48999999999999999999999998999999999999999999999864  3699999999999999999876521100


Q ss_pred             chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556          399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  478 (561)
Q Consensus       399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe  478 (561)
                      .                         ..+++.           ..        .+.    ....      ........++
T Consensus        88 ~-------------------------~~~~~~-----------~~--------~~~----~~~~------~~~~~~~~~e  113 (193)
T TIGR02947        88 S-------------------------DDDDIE-----------DW--------QLA----KAAS------HTSNGLRSAE  113 (193)
T ss_pred             c-------------------------cchhhh-----------hh--------hhc----cccc------cccccccchh
Confidence            0                         000000           00        000    0000      0000011233


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ......+....|..+|..||+++|+||.|+|.    +++|++|||+.||||..+|+.++.||+++||+.+..
T Consensus       114 ~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~  181 (193)
T TIGR02947       114 LEALDGLPDQDIKDALQGLPEEFRQAVYLADV----EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD  181 (193)
T ss_pred             HHHHhhhhHHHHHHHHHhCCHHHhhheeehhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            33333344567899999999999999999998    899999999999999999999999999999998864

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.

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.80  E-value=4e-18  Score=167.09  Aligned_cols=166  Identities=20%  Similarity=0.287  Sum_probs=135.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008556          318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  397 (561)
Q Consensus       318 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IR  397 (561)
                      +..++++|+..|.+.++.++.++.++..+.+|++||+++.+|+...+|++  + .|.+|++..+|+.+.+++++..+ .+
T Consensus        26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~~  101 (203)
T PRK09647         26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-IR  101 (203)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-Cc
Confidence            45899999999999999999999999999999999999999999999985  3 59999999999999999987542 00


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCCh
Q 008556          398 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  477 (561)
Q Consensus       398 lP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~p  477 (561)
                      .                                                    ..++     ++   + +.... ...+|
T Consensus       102 ~----------------------------------------------------~~~~-----~~---~-~~~~~-~~~~~  119 (203)
T PRK09647        102 M----------------------------------------------------EALP-----ED---Y-DRVPG-DEPNP  119 (203)
T ss_pred             c----------------------------------------------------cccc-----cc---c-cccCC-CCCCH
Confidence            0                                                    0000     00   0 00011 12245


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          478 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       478 ee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      +..+...+....|..+|..||+++|+||.|+|.    ++++++|||+.||||..+|++.+.||+++||+.+...+-
T Consensus       120 ~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~~  191 (203)
T PRK09647        120 EQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAP  191 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhch
Confidence            556666777778999999999999999999998    899999999999999999999999999999999876543

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.80  E-value=2.5e-18  Score=163.11  Aligned_cols=163  Identities=14%  Similarity=0.092  Sum_probs=127.7

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++..++..|+..|.+.|+.+|.++.++..+.+|++||+++.+|+. ..|+..  ..|.+|++.+++|.+.++++++.+..
T Consensus         7 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~   83 (172)
T PRK12523          7 PHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQ   83 (172)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            334999999999999999999999999999999999999999987 446543  36999999999999999998753100


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  476 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~  476 (561)
                                        ...         .++                        .            . ........
T Consensus        84 ------------------~~~---------~~~------------------------~------------~-~~~~~~~~   99 (172)
T PRK12523         84 ------------------AYL---------AEL------------------------A------------L-VPEAEQPS   99 (172)
T ss_pred             ------------------HHH---------HHH------------------------h------------h-cccccCCC
Confidence                              000         000                        0            0 00000113


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      |+......+....|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|++.+.||+++||..+..
T Consensus       100 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~  169 (172)
T PRK12523        100 PEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG  169 (172)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            4444444444567999999999999999999998    899999999999999999999999999999998754

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.80  E-value=2.8e-18  Score=161.49  Aligned_cols=158  Identities=15%  Similarity=0.107  Sum_probs=130.2

Q ss_pred             HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556          322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  401 (561)
Q Consensus       322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~  401 (561)
                      ++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++.   .|.+|++..+++.+.+++++..+....   
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~---   76 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV---   76 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc---
Confidence            57899999999999999999999999999999999999999999863   599999999999999999875421100   


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556          402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  481 (561)
Q Consensus       402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l  481 (561)
                                             ..+++                                     +.+.+   ..|++.+
T Consensus        77 -----------------------~~~~~-------------------------------------~~~~~---~~~~~~~   93 (165)
T PRK09644         77 -----------------------GTDEI-------------------------------------EAIQA---ESTEEYV   93 (165)
T ss_pred             -----------------------chhHH-------------------------------------hhhcc---cChHHHH
Confidence                                   00000                                     00000   1345555


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      ...+....|..+|..||+++|+||.++|.    ++++++|||+.||+|.++|+..+.||+++||+.+....
T Consensus        94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~  160 (165)
T PRK09644         94 VAKNSYEKLIQIIHTLPVIEAQAILLCDV----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK  160 (165)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHhHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence            55666678999999999999999999998    89999999999999999999999999999999987543

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

Probab=99.79  E-value=2.6e-18  Score=160.69  Aligned_cols=158  Identities=19%  Similarity=0.211  Sum_probs=127.8

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      |+..+++.|+..|.+.|+.+|.++.++..+.+|++||+++.+|++.++|+.  ...|.+|++..+++.+.+++++..+. 
T Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~-   79 (162)
T TIGR02983         3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL-   79 (162)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-
Confidence            566999999999999999999999999999999999999999999999964  34799999999999999998765410 


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  476 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~  476 (561)
                      .+                                                     . +...            .+..   
T Consensus        80 ~~-----------------------------------------------------~-~~~~------------~~~~---   90 (162)
T TIGR02983        80 EL-----------------------------------------------------P-TREL------------PDAA---   90 (162)
T ss_pred             cc-----------------------------------------------------c-cccc------------Cccc---
Confidence            00                                                     0 0000            0000   


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      +.......+..+.|..+|..||+++|+||.|+|.    +++|.+|||+.||+|.++|++.+.||+++||+.+..
T Consensus        91 ~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~  160 (162)
T TIGR02983        91 APDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE  160 (162)
T ss_pred             CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            0001122344567889999999999999999998    899999999999999999999999999999998754

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.

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.79  E-value=7.5e-18  Score=167.16  Aligned_cols=118  Identities=18%  Similarity=0.265  Sum_probs=104.0

Q ss_pred             HhhcHHHHHHHHHHHHHHHHHHHHhhhCCC--CCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhc
Q 008556          315 LHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  392 (561)
Q Consensus       315 l~~G~~Are~LI~~nlrLV~sIArrY~~~g--~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~  392 (561)
                      ++.|+..+++||..|.|+|.++|++|.++.  .+.+|++|+|+||||+|+++|||++|.+|.|||.+||++.|.+++|+.
T Consensus         4 ~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~   83 (218)
T TIGR02895         4 IQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKN   83 (218)
T ss_pred             hhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            345554599999999999999999998765  589999999999999999999999999999999999999999999988


Q ss_pred             c---cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHH
Q 008556          393 S---RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR  432 (561)
Q Consensus       393 s---r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~  432 (561)
                      .   +.+++|.........+..+...+..+.++.|+.+||+..
T Consensus        84 ~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~  126 (218)
T TIGR02895        84 QKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY  126 (218)
T ss_pred             ccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence            7   577899766666667777778888899999999999754

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).

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=7e-18  Score=158.00  Aligned_cols=157  Identities=15%  Similarity=0.099  Sum_probs=124.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556          320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  399 (561)
Q Consensus       320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP  399 (561)
                      .|+++|+..|.+.|+.++.++.++..+.+|++||+++.+|+..+.|++   ..|.+|.+.++++.+.+++++..+.    
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~----   76 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLE----   76 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHH----
Confidence            689999999999999999999999999999999999999999988864   2599999999999999998764310    


Q ss_pred             hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556          400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  479 (561)
Q Consensus       400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee  479 (561)
                                    ...         ..++                        +            + ..+.....++.
T Consensus        77 --------------~~~---------~~~~------------------------~------------~-~~~~~~~~~~~   96 (161)
T PRK12528         77 --------------RAY---------LEAL------------------------A------------Q-LPERVAPSEEE   96 (161)
T ss_pred             --------------Hhh---------HHHh------------------------h------------c-cccccCCCHHH
Confidence                          000         0000                        0            0 00000112333


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       480 ~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      .....+....|..+|..||+++|+||.|+|.    +|+|++|||+.||+|.++|+..+.||+++||..
T Consensus        97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~  160 (161)
T PRK12528         97 RAIILETLVELDQLLDGLPPLVKRAFLLAQV----DGLGYGEIATELGISLATVKRYLNKAAMRCYFA  160 (161)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence            3333344567899999999999999999998    899999999999999999999999999999864

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=8.9e-18  Score=158.27  Aligned_cols=159  Identities=16%  Similarity=0.158  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556          319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  398 (561)
Q Consensus       319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl  398 (561)
                      ...+..++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|++..  .|.+|++..++|.+.+++++..+....
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~   82 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQD   82 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            468899999999999999999999999999999999999999999998643  599999999999999998865421000


Q ss_pred             chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556          399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  478 (561)
Q Consensus       399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe  478 (561)
                                                                            .+...  ..     .  .+   ..++
T Consensus        83 ------------------------------------------------------~~~~~--~~-----~--~~---~~~~   96 (164)
T PRK12547         83 ------------------------------------------------------SDGVF--TA-----R--VA---VHPA   96 (164)
T ss_pred             ------------------------------------------------------ccccc--cc-----c--CC---CCch
Confidence                                                                  00000  00     0  00   0111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      .  ........|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|++.+.||+++||..+.-.
T Consensus        97 ~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  163 (164)
T PRK12547         97 Q--YGSLDLQDFKKALNLLSADQREAIILIGA----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD  163 (164)
T ss_pred             h--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence            1  11122456889999999999999999998    8999999999999999999999999999999987643

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=8.4e-18  Score=162.59  Aligned_cols=181  Identities=18%  Similarity=0.160  Sum_probs=132.2

Q ss_pred             HHHHHHHHHHHHHHHHhhhCCCCC-HHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556          323 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  401 (561)
Q Consensus       323 e~LI~~nlrLV~sIArrY~~~g~~-~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~  401 (561)
                      +..+..|.+.|+.+|+++.++..+ .+|++||+++.+|+++++|++.  ..|.+|++..+++.+.++++++.+.......
T Consensus         8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~   85 (195)
T PRK12532          8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL   85 (195)
T ss_pred             hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence            456778999999999999998888 9999999999999999999864  3799999999999999999876532110000


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556          402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  481 (561)
Q Consensus       402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l  481 (561)
                      .                      ..+.+           ....      ...   ...+ .....+... ....+|+..+
T Consensus        86 ~----------------------~~~~~-----------~~~~------~~~---~~~~-~~~~~~~~~-~~~~~~e~~~  121 (195)
T PRK12532         86 L----------------------DDELL-----------DEAF------ESH---FSQN-GHWTPEGQP-QHWNTPEKSL  121 (195)
T ss_pred             c----------------------ccccc-----------chhh------hhh---hccc-cccccccCc-cccCCHHHHH
Confidence            0                      00000           0000      000   0000 000000000 1123567777


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      ...+....+..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|++.++||+++||+++....+
T Consensus       122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~  189 (195)
T PRK12532        122 NNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF  189 (195)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            77777788999999999999999999998    899999999999999999999999999999999876543

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=9e-18  Score=163.83  Aligned_cols=181  Identities=14%  Similarity=0.141  Sum_probs=130.6

Q ss_pred             HHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH
Q 008556          324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  403 (561)
Q Consensus       324 ~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~  403 (561)
                      .++..|.+.++.+|+++.++..+.+|++||.|+.+|+.+++|++..  .|.+|++.+++|.+.++++++.+...++..  
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~--   87 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSAL--   87 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence            4588999999999999999999999999999999999999999753  599999999999999999876532111000  


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHH
Q 008556          404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  483 (561)
Q Consensus       404 ~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~  483 (561)
                                            ..++.      .            ...++............+..++ ....++.....
T Consensus        88 ----------------------~~~~~------~------------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  126 (201)
T PRK12545         88 ----------------------DAELD------G------------EALLDRELFKDNGHWAAHAKPR-PWPKPETILQQ  126 (201)
T ss_pred             ----------------------ccccc------h------------hhhhhhhhhcccccccccccCc-CCCCHHHHHHH
Confidence                                  00000      0            0000000000000000000011 11245555555


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          484 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       484 ~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      .+....|..+|..||+++|+||.|+|+    +++|++|||+.||+|.++|+..+.||+++||+++...++
T Consensus       127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~  192 (201)
T PRK12545        127 QQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL  192 (201)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            566677899999999999999999998    899999999999999999999999999999999975544

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=1.2e-17  Score=156.52  Aligned_cols=157  Identities=15%  Similarity=0.120  Sum_probs=124.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008556          318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  397 (561)
Q Consensus       318 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IR  397 (561)
                      ...+++.++..|.+.|+.+|.++.++..+++|++||+++.+|+..++|++.   .|.||++..+++.+.+++++..+...
T Consensus         3 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~   79 (161)
T PRK12541          3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKT   79 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccc
Confidence            357899999999999999999999999999999999999999999999863   49999999999999999987652100


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCCh
Q 008556          398 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  477 (561)
Q Consensus       398 lP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~p  477 (561)
                      +                                                     ..+            +.........+
T Consensus        80 ~-----------------------------------------------------~~~------------~~~~~~~~~~~   94 (161)
T PRK12541         80 T-----------------------------------------------------TIE------------EFHLPNVPSTE   94 (161)
T ss_pred             c-----------------------------------------------------chh------------hhhccCCCCcH
Confidence            0                                                     000            00000000112


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          478 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       478 ee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      +......+. ..+..+|..||+++|.||.|+|.    +++|++|||+.||+|..+|++.+.||+++||+.
T Consensus        95 ~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541         95 HEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDY----YGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             HHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            222222233 34567899999999999999998    899999999999999999999999999999974

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=1.1e-17  Score=161.68  Aligned_cols=176  Identities=16%  Similarity=0.118  Sum_probs=130.7

Q ss_pred             HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556          323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  402 (561)
Q Consensus       323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~  402 (561)
                      +.-|..|.+.++.+|.++.++..+++|++||.|+.+|+.+++|++..  +|.+|++..++|.+.++++++.+...... .
T Consensus        10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~-~   86 (189)
T PRK12530         10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESE-L   86 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCccc-c
Confidence            34577889999999999999989999999999999999999998653  69999999999999999987653211000 0


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHH
Q 008556          403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  482 (561)
Q Consensus       403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le  482 (561)
                                        .     .+.                   .+....    +.......+.........|+..+.
T Consensus        87 ------------------~-----~~~-------------------~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~  120 (189)
T PRK12530         87 ------------------I-----EED-------------------SPNSFF----DEKGHWKPEYYEPSEWQEVENTVY  120 (189)
T ss_pred             ------------------c-----ccc-------------------cchhhh----cccccccccccCCccccCHHHHHH
Confidence                              0     000                   000000    000000000000111235666677


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       483 ~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      ..+....|..+|+.||+++|+||.|+|.    +++|++|||+.||+|.++|+.+++||+++||+++...
T Consensus       121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~  185 (189)
T PRK12530        121 KEEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTSNLHVLLYRARLQLQACLSKN  185 (189)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            7777788999999999999999999998    8999999999999999999999999999999998654

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=1.7e-17  Score=162.94  Aligned_cols=180  Identities=18%  Similarity=0.215  Sum_probs=133.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556          322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  401 (561)
Q Consensus       322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~  401 (561)
                      -..++..|.+.|+.+|+++.++..+.+|++||+++.+|+.+.+|++.  .+|.+|++.++++.+.+++++..+....+..
T Consensus        20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~   97 (206)
T PRK12544         20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL   97 (206)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence            46789999999999999999999999999999999999999999864  4699999999999999999876532111100


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556          402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  481 (561)
Q Consensus       402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l  481 (561)
                      .                  .  ....         ...+..+.              + ................|+..+
T Consensus        98 ~------------------~--~~~~---------~~~~~~~~--------------~-~~~~~~~~~~~~~~~~~e~~~  133 (206)
T PRK12544         98 L------------------R--DEEE---------EEDFEELF--------------D-ESGHWQKDERPQAWGNPEESL  133 (206)
T ss_pred             c------------------c--ccch---------hhHHHHhh--------------c-ccccccccccccccCCHHHHH
Confidence            0                  0  0000         00000000              0 000000000001113566667


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      ...+....+..+|..||+++|+||.|+|.    ++++++|||+.||+|..+|++.+.||+++||+.+...
T Consensus       134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~  199 (206)
T PRK12544        134 EQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK  199 (206)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777778999999999999999999998    8999999999999999999999999999999998754

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

Probab=99.78  E-value=1e-17  Score=161.89  Aligned_cols=178  Identities=12%  Similarity=0.132  Sum_probs=132.7

Q ss_pred             HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556          323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  402 (561)
Q Consensus       323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~  402 (561)
                      .+.+..|.+.|+.+|+++.++..+.+|++||+++.+|+...+|++.  .+|.+|++..+++.+.++++++.+....+. +
T Consensus         5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~-~   81 (188)
T TIGR02943         5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSD-L   81 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccc-c
Confidence            4578889999999999999999999999999999999999999965  479999999999999999987653211100 0


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHH
Q 008556          403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  482 (561)
Q Consensus       403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le  482 (561)
                                        .     .+.                   ..-.++... ...+....+...+ ....|+..+.
T Consensus        82 ------------------~-----~~~-------------------~~~~~~~~~-~~~~~~~~~~~~~-~~~~~e~~~~  117 (188)
T TIGR02943        82 ------------------D-----DEL-------------------DDEAFNALF-TQNGHWAQHGQPQ-HWNTPEKQLE  117 (188)
T ss_pred             ------------------c-----ccc-------------------ccchhhhhh-ccccchhcccccc-ccCCHHHHHH
Confidence                              0     000                   000000000 0000000011111 1235666777


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       483 ~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      ..+....+..+|..||+++|+||.++|.    ++++++|||+.||+|.++|++++.||+++||+++...
T Consensus       118 ~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~  182 (188)
T TIGR02943       118 NKEFWEVFEACLYHLPEQTARVFMMREV----LGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN  182 (188)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            7777788999999999999999999998    8999999999999999999999999999999998754

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.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.77  E-value=1.4e-17  Score=174.48  Aligned_cols=187  Identities=18%  Similarity=0.211  Sum_probs=135.3

Q ss_pred             HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008556          310 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  388 (561)
Q Consensus       310 eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~  388 (561)
                      +|+..+..| ..++++|+..|.+.|+.+|+++.++..+.+|++||.++.+|+.+++|++.  ..|.+|++.+++|.+.++
T Consensus         8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~   85 (339)
T PRK08241          8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDA   85 (339)
T ss_pred             HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHH
Confidence            455555544 59999999999999999999999998999999999999999999999853  369999999999999999


Q ss_pred             HHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhh
Q 008556          389 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI  468 (561)
Q Consensus       389 Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~  468 (561)
                      ++++.+.. .+..                  .+ .+.                         .........+......+.
T Consensus        86 ~Rk~~~~~-~~~~------------------~~-~~~-------------------------~~~~~~~~~~~~~~~~~~  120 (339)
T PRK08241         86 LEGRARRP-LPTD------------------LG-APA-------------------------ADPVDELVERPEVPWLEP  120 (339)
T ss_pred             HHhhcccc-Cccc------------------cC-CCc-------------------------CcccccccccccccccCC
Confidence            98754210 0000                  00 000                         000000000000000011


Q ss_pred             cccC----CCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008556          469 TADT----GVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  543 (561)
Q Consensus       469 l~d~----~~~~pee~le~~e-~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK  543 (561)
                      +.+.    ...+|++.+...+ ....|..+|..||+++|+||.|+|.    +++|++|||++||+|..+|++++.||+++
T Consensus       121 ~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~  196 (339)
T PRK08241        121 YPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDV----LGWSAAEVAELLDTSVAAVNSALQRARAT  196 (339)
T ss_pred             CCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHh----hCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            1110    1235665555444 3456899999999999999999998    89999999999999999999999999999


Q ss_pred             HHHH
Q 008556          544 LKQS  547 (561)
Q Consensus       544 LR~~  547 (561)
                      ||+.
T Consensus       197 Lr~~  200 (339)
T PRK08241        197 LAER  200 (339)
T ss_pred             Hhhc
Confidence            9983

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.77  E-value=1.8e-17  Score=155.37  Aligned_cols=160  Identities=19%  Similarity=0.183  Sum_probs=128.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556          319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  398 (561)
Q Consensus       319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl  398 (561)
                      +.+++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|++  .|+.  +..|.+|++..+++.+.+++++..+..+.
T Consensus         2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~   77 (166)
T PRK09639          2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR   77 (166)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence            3689999999999999999999999999999999999999999  6764  34699999999999999999875421100


Q ss_pred             chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556          399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  478 (561)
Q Consensus       399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe  478 (561)
                      .                                                      +.      .....+.  + ....|+
T Consensus        78 ~------------------------------------------------------~~------~~~~~~~--~-~~~~~e   94 (166)
T PRK09639         78 I------------------------------------------------------LG------EFQWQEV--D-NEPSPE   94 (166)
T ss_pred             c------------------------------------------------------cc------hhhhhhc--c-CCCChH
Confidence            0                                                      00      0000000  1 122566


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      +.....+....|..+|..||+++|.||.++|     +|++++|||+.||+|..+|+..+.||+++||+.+..
T Consensus        95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~  161 (166)
T PRK09639         95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ  161 (166)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            6666666777899999999999999999999     479999999999999999999999999999998864

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=1.8e-17  Score=161.40  Aligned_cols=169  Identities=17%  Similarity=0.099  Sum_probs=128.8

Q ss_pred             HHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHH
Q 008556          311 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  389 (561)
Q Consensus       311 L~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~I  389 (561)
                      |+..+. ++..+++.|+..|.+.++.+++ +.++..+.+|++||.++.+|+..++|++.  ..|.+|++..+++.+.+++
T Consensus        15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~   91 (196)
T PRK12535         15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNI   91 (196)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHH
Confidence            444443 4559999999999999999975 57888899999999999999999999864  3699999999999999999


Q ss_pred             HhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhc
Q 008556          390 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT  469 (561)
Q Consensus       390 r~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l  469 (561)
                      +++.+..+.                                                     ..+ .. .    ...+  
T Consensus        92 Rk~~~~~~~-----------------------------------------------------~~~-~~-~----~~~~--  110 (196)
T PRK12535         92 RHDMARPRK-----------------------------------------------------SAT-EY-E----DAAA--  110 (196)
T ss_pred             HhhccCCCc-----------------------------------------------------ccc-cc-c----cccc--
Confidence            875421100                                                     000 00 0    0000  


Q ss_pred             ccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          470 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       470 ~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                        .. ..++..... .....|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|++.+.||+++||+.+.
T Consensus       111 --~~-~~~~~~~~~-~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~  182 (196)
T PRK12535        111 --TT-ASNETTGSW-SEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTIRSRVARARADLIAATA  182 (196)
T ss_pred             --cc-CCcchhHHH-HHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence              00 111111111 12346889999999999999999998    89999999999999999999999999999999886


Q ss_pred             cC
Q 008556          550 GK  551 (561)
Q Consensus       550 ~~  551 (561)
                      ..
T Consensus       183 ~~  184 (196)
T PRK12535        183 TG  184 (196)
T ss_pred             cc
Confidence            54

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

Probab=99.77  E-value=1.7e-17  Score=172.46  Aligned_cols=183  Identities=16%  Similarity=0.171  Sum_probs=134.2

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      |+..+++.|+..|.+.++.+|.++.++..+.+|++||.++.+|+.+++|++.  ..|.+|++.+++|.+.++++++.+..
T Consensus         2 gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~   79 (324)
T TIGR02960         2 VDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRP   79 (324)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCc
Confidence            3468999999999999999999999999999999999999999999999964  36999999999999999998764211


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcc------
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA------  470 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~------  470 (561)
                      ....                  ... .                         ........ ..+......+.+.      
T Consensus        80 ~~~~------------------~~~-~-------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~  114 (324)
T TIGR02960        80 RPVG------------------LGA-P-------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDL  114 (324)
T ss_pred             Cccc------------------cCC-C-------------------------CCcccccc-cccccccccCCCCcccccc
Confidence            0000                  000 0                         00000000 0000000000000      


Q ss_pred             -cCCCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          471 -DTGVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       471 -d~~~~~pee~le~~e-~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                       .....+|++.+...+ +...+..+|..||+++|+||.|+|.    +++|++|||+.||||.++|++++.||+++||+++
T Consensus       115 ~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  190 (324)
T TIGR02960       115 DDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----LGWRAAETAELLGTSTASVNSALQRARATLDEVG  190 (324)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence             011124565555444 4557889999999999999999998    8999999999999999999999999999999988


Q ss_pred             hc
Q 008556          549 GG  550 (561)
Q Consensus       549 ~~  550 (561)
                      ..
T Consensus       191 ~~  192 (324)
T TIGR02960       191 PS  192 (324)
T ss_pred             cc
Confidence            74

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.

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.76  E-value=7e-18  Score=156.10  Aligned_cols=152  Identities=18%  Similarity=0.206  Sum_probs=122.4

Q ss_pred             HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556          327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  406 (561)
Q Consensus       327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l  406 (561)
                      ..|.+.|+.++.++.++..+.+|++||+++.+|+++++|++   .+|.+|++..+++.+.++++++.+.....       
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~-------   71 (154)
T TIGR02950         2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID-------   71 (154)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc-------
Confidence            57899999999999998889999999999999999999997   37999999999999999987654210000       


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556          407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  486 (561)
Q Consensus       407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~  486 (561)
                                         .+.                                    +.+... .....|++.+...+.
T Consensus        72 -------------------~~~------------------------------------~~~~~~-~~~~~~~~~~~~~~~   95 (154)
T TIGR02950        72 -------------------DDA------------------------------------IGDLEQ-HPVESPEHHLLIKIE   95 (154)
T ss_pred             -------------------Hhh------------------------------------hhhccc-cccCChhHHHHHHHH
Confidence                               000                                    000000 011245555565666


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      ...|..+|..||+++++||.++|+    +|+|++|||+.||||..+|++.+.||+++||+.+
T Consensus        96 ~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l  153 (154)
T TIGR02950        96 QEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL  153 (154)
T ss_pred             HHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            678999999999999999999998    8999999999999999999999999999999865

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.

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.76  E-value=2.8e-17  Score=153.88  Aligned_cols=159  Identities=14%  Similarity=0.214  Sum_probs=125.2

Q ss_pred             HHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH
Q 008556          324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  403 (561)
Q Consensus       324 ~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~  403 (561)
                      .++..|.+.++.+|.++.++..+.+|++||+++++|+....|++.   .|.+|++..+++.+.++++++.+....     
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~-----   73 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKY-----   73 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcccccc-----
Confidence            367789999999999999999999999999999999998877753   488999999999999999875421000     


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHH
Q 008556          404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  483 (561)
Q Consensus       404 ~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~  483 (561)
                                                                      .      ..+.... +. .+. ..+++..+..
T Consensus        74 ------------------------------------------------~------~~~~~~~-~~-~~~-~~~~~~~~~~   96 (163)
T PRK07037         74 ------------------------------------------------H------GDEEDGL-DV-PSP-EASPEAALIN   96 (163)
T ss_pred             ------------------------------------------------c------ccccccc-cc-CCC-CCCHHHHHHH
Confidence                                                            0      0000000 00 011 1245555555


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          484 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       484 ~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      .+..+.|..+|..||+++|+||.++|.    +++|.+|||+.||||.++|+..+.||+++||+.+...
T Consensus        97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~~  160 (163)
T PRK07037         97 RDTLRHVADALSELPARTRYAFEMYRL----HGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC  160 (163)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence            666678999999999999999999998    8999999999999999999999999999999988654

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=2.9e-17  Score=158.10  Aligned_cols=160  Identities=18%  Similarity=0.222  Sum_probs=126.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556          320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  399 (561)
Q Consensus       320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP  399 (561)
                      .++..++..|.+.|+.+|.++.++..+++|++||.++.+|+..++|++..  .|.+|++..++|.+.++++++.+.... 
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~-   81 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVED-   81 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccc-
Confidence            46788999999999999999999999999999999999999999998653  599999999999999998765421000 


Q ss_pred             hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556          400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  479 (561)
Q Consensus       400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee  479 (561)
                                                                           .+.        ...+.. +.   .++.
T Consensus        82 -----------------------------------------------------~~~--------~~~~~~-~~---~~~~   96 (182)
T PRK12540         82 -----------------------------------------------------ADG--------SYAKTL-KS---QPGQ   96 (182)
T ss_pred             -----------------------------------------------------ccc--------cccccc-cC---CCch
Confidence                                                                 000        000000 00   1111


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       480 ~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      ..  ......|..+|..||+++|+||.|+|.    +++|++|||+.||||..+|++.++||+++||+.+.....
T Consensus        97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~  164 (182)
T PRK12540         97 NA--HLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA  164 (182)
T ss_pred             HH--HHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            11  112346899999999999999999998    899999999999999999999999999999999986553

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.76  E-value=2.6e-17  Score=153.81  Aligned_cols=155  Identities=12%  Similarity=0.100  Sum_probs=123.9

Q ss_pred             HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556          327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  406 (561)
Q Consensus       327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l  406 (561)
                      ..|.+.++.++.++.++..+.+|++||.++.+|+..+.|++.   +|.||++..+++.+.++++++.+...         
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~---------   69 (159)
T PRK12527          2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQA---------   69 (159)
T ss_pred             hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence            568889999999999988899999999999999999998752   69999999999999999876531000         


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556          407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  486 (561)
Q Consensus       407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~  486 (561)
                                                                  ..++. . .+.        .......|++.+..++.
T Consensus        70 --------------------------------------------~~~~~-~-~~~--------~~~~~~~~~~~~~~~~~   95 (159)
T PRK12527         70 --------------------------------------------EPLEV-L-DEE--------ERLHSPSPQTRLDLGQR   95 (159)
T ss_pred             --------------------------------------------cchhh-h-hcc--------ccccCCCHHHHHHHHHH
Confidence                                                        00000 0 000        00011246666666677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      ...|..+|..||+++++||.|+|+    +++|.+|||+.||+|.++|+..+.||+++||+.+...
T Consensus        96 ~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~  156 (159)
T PRK12527         96 LALLQRALAELPPACRDSFLLRKL----EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW  156 (159)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            778999999999999999999998    8999999999999999999999999999999998753

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.75  E-value=5.4e-17  Score=154.26  Aligned_cols=164  Identities=16%  Similarity=0.094  Sum_probs=126.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccc
Q 008556          318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  397 (561)
Q Consensus       318 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IR  397 (561)
                      +..|++.++..|.+.++.++.++.++..+.+|++||.++.+|+. ..|++-.  .|.+|++..+++.+.++++++.+.. 
T Consensus         8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~-   83 (172)
T PRK09651          8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEK-   83 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence            35899999999999999999999999999999999999999998 3565433  5899999999999999987643100 


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCCh
Q 008556          398 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  477 (561)
Q Consensus       398 lP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~p  477 (561)
                                       ..         ...+                        +            + +.+....+|
T Consensus        84 -----------------~~---------~~~~------------------------~------------~-~~~~~~~~~  100 (172)
T PRK09651         84 -----------------AY---------LEML------------------------A------------L-MPEGGAPSP  100 (172)
T ss_pred             -----------------hh---------hhHH------------------------h------------h-ccccCCCCh
Confidence                             00         0000                        0            0 000011133


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          478 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       478 ee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      +......+....|..+|..||+++|+||.++|+    +++|++|||+.||+|.++|+..+.||+++|+...-..|
T Consensus       101 ~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~~  171 (172)
T PRK09651        101 EERESQLETLQLLDSMLDGLNGKTREAFLLSQL----DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEYG  171 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhc----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence            344444455567999999999999999999998    89999999999999999999999999999998765443

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=4.3e-17  Score=157.55  Aligned_cols=161  Identities=19%  Similarity=0.162  Sum_probs=125.7

Q ss_pred             HhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccc
Q 008556          315 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  394 (561)
Q Consensus       315 l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr  394 (561)
                      +..+..+++.++..|.+.|+.+|+++.++..+++|++||.|+.+|+.++.|++.  ..|.+|++..+++.+.+.++++.+
T Consensus        18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~   95 (188)
T PRK12517         18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQF   95 (188)
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhcc
Confidence            345679999999999999999999999999999999999999999999999865  369999999999876655432210


Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCC
Q 008556          395 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV  474 (561)
Q Consensus       395 ~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~  474 (561)
                      .                                                      ....+       .    +...+...
T Consensus        96 ~------------------------------------------------------~~~~~-------~----~~~~~~~~  110 (188)
T PRK12517         96 D------------------------------------------------------LVDIE-------D----DSIEDDAS  110 (188)
T ss_pred             C------------------------------------------------------ccCcc-------c----ccccCccc
Confidence            0                                                      00000       0    00011111


Q ss_pred             CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          475 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       475 ~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ..++..    ...+.|..+|..||+++|.||.++|.    ++++++|||+.||||..+|+.++.||+++||..+..
T Consensus       111 ~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  178 (188)
T PRK12517        111 HSSEEE----MEQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEK  178 (188)
T ss_pred             cChhHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            123322    22356899999999999999999998    899999999999999999999999999999999864

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.75  E-value=7.4e-17  Score=155.05  Aligned_cols=154  Identities=21%  Similarity=0.194  Sum_probs=125.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556          322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  401 (561)
Q Consensus       322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~  401 (561)
                      ++.|+..|.+.|+.+|.++.++..+++|++||.++.+|+.+..|++.  ..|.+|++..+++.+.++++++.+...++  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~--   78 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP--   78 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence            57899999999999999999999999999999999999999999853  47999999999999999998764211000  


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556          402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  481 (561)
Q Consensus       402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l  481 (561)
                                                                               .+      +...+    .+++..
T Consensus        79 ---------------------------------------------------------~~------~~~~~----~~~~~~   91 (181)
T PRK09637         79 ---------------------------------------------------------DD------LLFED----EEREEN   91 (181)
T ss_pred             ---------------------------------------------------------hh------hhccC----CChhHH
Confidence                                                                     00      00000    111222


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ...+....+..+|..||+++|+||.++|.    +|++.+|||+.||+|..+|+..+.||+++||+.+..
T Consensus        92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  156 (181)
T PRK09637         92 AKKELAPCLRPFIDALPEKYAEALRLTEL----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG  156 (181)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            33445667899999999999999999998    899999999999999999999999999999998764

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.74  E-value=1.1e-16  Score=155.16  Aligned_cols=156  Identities=19%  Similarity=0.200  Sum_probs=121.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556          320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  399 (561)
Q Consensus       320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP  399 (561)
                      .+++.|.. |.+.|+.+|+++.++..+.+|++||.++.+|+.+..|+..  ..|.+|++..++|.+.+++++..+...  
T Consensus         8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~--   82 (188)
T PRK12546          8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVP--   82 (188)
T ss_pred             hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccccc--
Confidence            56666766 7799999999999999999999999999999999999864  369999999999999998877542100  


Q ss_pred             hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556          400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  479 (561)
Q Consensus       400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee  479 (561)
                                                                          ..+.        ...+...+..  ..+ 
T Consensus        83 ----------------------------------------------------~~~~--------~~~~~~~~~~--~~~-   99 (188)
T PRK12546         83 ----------------------------------------------------DPEG--------VHAASLAVKP--AHD-   99 (188)
T ss_pred             ----------------------------------------------------Cccc--------ccccccccCC--cch-
Confidence                                                                0000        0000000000  011 


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       480 ~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                         .......+..+|..||+++|+||.|+|.    +++|.+|||+.||||..+|+..+.||+++||+.+..
T Consensus       100 ---~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~  163 (188)
T PRK12546        100 ---GRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL  163 (188)
T ss_pred             ---hHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence               1122346889999999999999999998    899999999999999999999999999999998865

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.73  E-value=1.1e-16  Score=152.05  Aligned_cols=148  Identities=21%  Similarity=0.220  Sum_probs=120.6

Q ss_pred             HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHH
Q 008556          327 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  406 (561)
Q Consensus       327 ~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l  406 (561)
                      ..|.+.++.++.++.++..+++|++||+++.+|+++++|++.  .+|.+|++..+++.+.+++++..+...++       
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~-------   72 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP-------   72 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence            468889999999999999999999999999999999999963  47999999999999999998765211000       


Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHH
Q 008556          407 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  486 (561)
Q Consensus       407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~  486 (561)
                                                                     +     +       ....   ..+++.....+.
T Consensus        73 -----------------------------------------------~-----~-------~~~~---~~~~~~~~~~e~   90 (170)
T TIGR02959        73 -----------------------------------------------E-----S-------LLAA---DSAREETFVKEL   90 (170)
T ss_pred             -----------------------------------------------h-----h-------hccc---CCccHHHHHHHH
Confidence                                                           0     0       0000   011222333445


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      ...|..+|..||+++|+||.++|.    ++++++|||+.||+|..+|++.+.||+++||..+.
T Consensus        91 ~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  149 (170)
T TIGR02959        91 SQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE  149 (170)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999999998    89999999999999999999999999999999885

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=1.2e-16  Score=153.84  Aligned_cols=157  Identities=13%  Similarity=0.167  Sum_probs=122.4

Q ss_pred             HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556          322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  401 (561)
Q Consensus       322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~  401 (561)
                      .+..+..+++.|+.+|.++.++..+.+|++||.|+.+|+.+..|++.  ..|.+|++.++++.+.++++++.+.....  
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~--   81 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA--   81 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc--
Confidence            45557889999999999999998999999999999999999999864  36999999999999999998764211000  


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556          402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  481 (561)
Q Consensus       402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l  481 (561)
                                               +++                                    .+. .+.....+.   
T Consensus        82 -------------------------~~~------------------------------------~~~-~~~~~~~~~---   96 (182)
T PRK12511         82 -------------------------DEL------------------------------------AVL-ADASLPAAQ---   96 (182)
T ss_pred             -------------------------cch------------------------------------hhc-cccCCCcch---
Confidence                                     000                                    000 000000111   


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      ........|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|++.+.||+++||..+...
T Consensus        97 ~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~  162 (182)
T PRK12511         97 EHAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT  162 (182)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence            11223456889999999999999999998    8999999999999999999999999999999988754

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=3.2e-16  Score=148.29  Aligned_cols=160  Identities=14%  Similarity=0.116  Sum_probs=126.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccccc
Q 008556          319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  398 (561)
Q Consensus       319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRl  398 (561)
                      ..++.+++..|.+.++.+|.++.++..+.+|++||.++.+|+..+.++.   ..|.+|++..++|.+.+++++...    
T Consensus         8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~----   80 (168)
T PRK12525          8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL----   80 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH----
Confidence            3789999999999999999999999999999999999999986665542   269999999999999998875320    


Q ss_pred             chhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChh
Q 008556          399 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  478 (561)
Q Consensus       399 P~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pe  478 (561)
                              .+      ...         ..+                        +            + ........|+
T Consensus        81 --------~~------~~~---------~~~------------------------~------------~-~~~~~~~~~~  100 (168)
T PRK12525         81 --------ER------AYL---------QSL------------------------A------------E-APEAVQPSPE  100 (168)
T ss_pred             --------HH------HHH---------HHH------------------------h------------c-ccccccCChH
Confidence                    00      000         000                        0            0 0000112455


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          479 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       479 e~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      ......+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|+..+.+|+++||..+.
T Consensus       101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~  167 (168)
T PRK12525        101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQL----EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ  167 (168)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence            55555666678999999999999999999998    99999999999999999999999999999998764

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.70  E-value=4.3e-16  Score=145.18  Aligned_cols=156  Identities=17%  Similarity=0.183  Sum_probs=113.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCC
Q 008556          342 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGN  421 (561)
Q Consensus       342 ~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~g  421 (561)
                      ++..+++|++||+|+.+|+..+. ++  +..|.+|++..++|.+.++++++.+..+...                     
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~-~~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~---------------------   57 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGD-RP--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVS---------------------   57 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhh-cc--cCchHHHHHHHHHHHHHHHHHhhcccccccc---------------------
Confidence            34457899999999999999886 33  3469999999999999999987542110000                     


Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCC--CCChhHHHHHHHHHHHHHHHHhcCCH
Q 008556          422 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG--VEIPDISVQKQLMRQHVRNLLTLLNP  499 (561)
Q Consensus       422 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~--~~~pee~le~~e~~e~L~~aL~~L~e  499 (561)
                                                 ...++.... .+++....+.+.+..  ...|+..+...+....|..+|..||+
T Consensus        58 ---------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~  109 (161)
T PRK09047         58 ---------------------------LFSSFSDDD-DDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA  109 (161)
T ss_pred             ---------------------------ccccccccc-ccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence                                       000000000 000111112222211  23577777777788889999999999


Q ss_pred             HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          500 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       500 rER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      ++|+||.|+|+    +++|++|||+.||||..+|+.++.||+++||+++...++
T Consensus       110 ~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~  159 (161)
T PRK09047        110 RQREAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGI  159 (161)
T ss_pred             HHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcCc
Confidence            99999999998    899999999999999999999999999999999976553

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.69  E-value=6.9e-16  Score=159.04  Aligned_cols=160  Identities=16%  Similarity=0.120  Sum_probs=123.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556          320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  399 (561)
Q Consensus       320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP  399 (561)
                      ....+++..|.+.++.+|+++.++..+.+|++||.++. |.....|+.   ..|.+|++..++|.+.+++++..+.... 
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~-   78 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRET-   78 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence            34678999999999999999999999999999999999 666677762   4699999999999999999865310000 


Q ss_pred             hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556          400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  479 (561)
Q Consensus       400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee  479 (561)
                                      .   .+                             ..+..+            ..+.. ..|++
T Consensus        79 ----------------~---~~-----------------------------~~~~e~------------~~~~~-~~~~~   97 (293)
T PRK09636         79 ----------------Y---VG-----------------------------PWLPEP------------VVEEL-DDPLE   97 (293)
T ss_pred             ----------------c---cC-----------------------------CcCCcC------------CCCCC-CChHH
Confidence                            0   00                             000000            00111 12333


Q ss_pred             H-HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          480 S-VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       480 ~-le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      . .........+..+|+.|||++|.||.|+|.    ++++++|||+.||+|..+|+++++||+++||+.+.
T Consensus        98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~  164 (293)
T PRK09636         98 AVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRARKHVRAARP  164 (293)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence            3 334455567899999999999999999998    89999999999999999999999999999999765

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.66  E-value=3.6e-15  Score=149.15  Aligned_cols=158  Identities=19%  Similarity=0.189  Sum_probs=122.5

Q ss_pred             HHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHH
Q 008556          311 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  390 (561)
Q Consensus       311 L~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir  390 (561)
                      |.+.+.++..+++.+++.| +.++.+|.++.++..+.+||+||.++.+|+.   |+..  ..|.+|++.+++|.+.++++
T Consensus         9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~R   82 (228)
T PRK06704          9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIK   82 (228)
T ss_pred             HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHh
Confidence            4445556668888888877 7899999999999999999999999999986   5543  24999999999999999988


Q ss_pred             hcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcc
Q 008556          391 QHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA  470 (561)
Q Consensus       391 ~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~  470 (561)
                      ++.+.-.                               +                       .+     +  ...     
T Consensus        83 k~k~~~~-------------------------------~-----------------------~~-----~--~~~-----   96 (228)
T PRK06704         83 SKSVHEK-------------------------------I-----------------------RD-----Q--ITF-----   96 (228)
T ss_pred             ccccccc-------------------------------c-----------------------cc-----c--ccc-----
Confidence            6542000                               0                       00     0  000     


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          471 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       471 d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                          ..+....  .+..+.+..+|..||+++|.||.|+|.    +++|++|||+.||+|.++|++.+.||+++||+.+..
T Consensus        97 ----~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~  166 (228)
T PRK06704         97 ----EEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE  166 (228)
T ss_pred             ----CChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence                0111111  123356889999999999999999998    899999999999999999999999999999998865

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

Probab=99.64  E-value=4.7e-15  Score=152.26  Aligned_cols=156  Identities=22%  Similarity=0.164  Sum_probs=118.8

Q ss_pred             HHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHH
Q 008556          324 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  403 (561)
Q Consensus       324 ~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~  403 (561)
                      +++..|.+.++.+|+++.++..+.+|++||+++.+++.  .|+..  ..|.+|++.+++|.+.+++++..+.-..     
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~-----   71 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREV-----   71 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence            37889999999999999999999999999999997775  45432  3699999999999999999764310000     


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHHH
Q 008556          404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  483 (561)
Q Consensus       404 ~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~  483 (561)
                                  +   .+                             .-+..+            ..+. ...|++.+..
T Consensus        72 ------------~---~~-----------------------------~~~~e~------------~~~~-~~~~~~~~~~   94 (281)
T TIGR02957        72 ------------Y---VG-----------------------------PWLPEP------------LLTT-SADPAESVEL   94 (281)
T ss_pred             ------------c---CC-----------------------------CCCCcc------------cCCC-CCChHHHHHH
Confidence                        0   00                             000000            0000 1234444433


Q ss_pred             -HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          484 -QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       484 -~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                       +.+...+..+|+.||++||.||.|+|.    .++|++|||+.||+|..+|+++++||+++||+...
T Consensus        95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~  157 (281)
T TIGR02957        95 AESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP  157 (281)
T ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence             345567889999999999999999998    89999999999999999999999999999999754

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.

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.63  E-value=7.3e-15  Score=151.80  Aligned_cols=161  Identities=17%  Similarity=0.133  Sum_probs=123.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccc
Q 008556          320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  399 (561)
Q Consensus       320 ~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP  399 (561)
                      ..+..++..|.+.++.+|+++.++..+.||++||.++.+|++...+ .   ..|.+|++...+|.+.+++++..+.-.. 
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~-   79 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRER-   79 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcC-
Confidence            5678899999999999999999999999999999999999987543 1   2599999999999999999864310000 


Q ss_pred             hhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhH
Q 008556          400 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  479 (561)
Q Consensus       400 ~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee  479 (561)
                                                                        ....+.  +..+     +...+  ..+|++
T Consensus        80 --------------------------------------------------~~~~~~--~~~~-----~~~~~--~~~~~~  100 (290)
T PRK09635         80 --------------------------------------------------PQDIAA--WHDG-----DASVS--SVDPAD  100 (290)
T ss_pred             --------------------------------------------------cccccc--cCcc-----ccCCC--CCCcHH
Confidence                                                              000000  0000     00001  112333


Q ss_pred             -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          480 -SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       480 -~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                       .....+....+..+|..|||++|.||.|+|.    .+++++|||+.||+|..+|+++++||+++||+..
T Consensus       101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~  166 (290)
T PRK09635        101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAHRARRKINESR  166 (290)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence             3345556678999999999999999999998    8999999999999999999999999999999864

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.51  E-value=2e-13  Score=125.43  Aligned_cols=136  Identities=12%  Similarity=0.130  Sum_probs=99.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhh-----cCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiek-----FDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++.++..|.++++.+|++|...    +| +||.++.+|..+.+     |++.  ..|.||++..++|.+.++++++.+..
T Consensus         1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~   73 (142)
T TIGR03209         1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK   73 (142)
T ss_pred             ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            3679999999999999999662    34 49999999999875     5543  46999999999999999998654110


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  476 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~  476 (561)
                      +.                 . .       ..++                        +     +           .. ..
T Consensus        74 ~~-----------------~-~-------~~~~------------------------~-----~-----------~~-~~   87 (142)
T TIGR03209        74 KI-----------------I-Y-------NSEI------------------------T-----D-----------IK-LS   87 (142)
T ss_pred             hh-----------------h-h-------hhhh------------------------h-----c-----------cc-cc
Confidence            00                 0 0       0000                        0     0           00 01


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR  534 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVR  534 (561)
                      +.+.+...+....|..+|+.||+++|+||.|+|.    +++|++|||+.||||.++|+
T Consensus        88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFF----EDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHhhc
Confidence            1122333344557889999999999999999998    99999999999999999997

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.

>PRK09191 two-component response regulator; Provisional

Probab=99.51  E-value=1.4e-13  Score=137.13  Aligned_cols=137  Identities=16%  Similarity=0.124  Sum_probs=111.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccch
Q 008556          321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  400 (561)
Q Consensus       321 Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~  400 (561)
                      ++..|+..|.+.++.+|.++.++..+.+|++||+++.+|+...+|++.  ..|.+|++.++++.....    .       
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~----~-------   68 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA----G-------   68 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc----c-------
Confidence            578999999999999999999999999999999999999999999874  358999998765321100    0       


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556          401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  480 (561)
Q Consensus       401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~  480 (561)
                                                                              .  +..        ..  ..+.. 
T Consensus        69 --------------------------------------------------------~--~~~--------~~--~~~~~-   79 (261)
T PRK09191         69 --------------------------------------------------------A--NDP--------EP--GSPFE-   79 (261)
T ss_pred             --------------------------------------------------------c--cCC--------CC--CCCch-
Confidence                                                                    0  000        00  01111 


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       481 le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                             ..+..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|+.+..+|+++||..+..
T Consensus        80 -------~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~  138 (261)
T PRK09191         80 -------ARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVAT  138 (261)
T ss_pred             -------HHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCC
Confidence                   15889999999999999999998    899999999999999999999999999999987653

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.46  E-value=4.3e-12  Score=127.72  Aligned_cols=88  Identities=20%  Similarity=0.354  Sum_probs=77.7

Q ss_pred             HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCC--CHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          308 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       308 ~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~--~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      .+.++..++.| ..|++.|+..|.++|+++|.++.++..  +.+|++|||++++|+++++|++.+|..|.+|+..+|++.
T Consensus         5 ~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~   84 (237)
T PRK08311          5 LEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRR   84 (237)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence            34455555555 589999999999999999999998765  589999999999999999999999888999999999999


Q ss_pred             HHHHHHhcccc
Q 008556          385 IRKAIFQHSRT  395 (561)
Q Consensus       385 I~~~Ir~~sr~  395 (561)
                      +.++++++.+.
T Consensus        85 ~iDylRk~~~~   95 (237)
T PRK08311         85 LIDYFRKESKH   95 (237)
T ss_pred             HHHHHHHhhcc
Confidence            99999987664

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.37  E-value=3.7e-11  Score=116.22  Aligned_cols=174  Identities=20%  Similarity=0.300  Sum_probs=118.3

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCC---CCCHHH--HHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHH
Q 008556          309 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  382 (561)
Q Consensus       309 ~eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~---g~~~eD--LIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR  382 (561)
                      .+|+..++.|+ .|.+.|+..|++-++.+|+++.+.   +.+.+|  |++|.++.+++.-...+...-..|-.|+...++
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            34555665555 999999999999999999987633   334554  477888877774333233333458888899999


Q ss_pred             HHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCC
Q 008556          383 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD  462 (561)
Q Consensus       383 qaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~  462 (561)
                      +.+.++.+++.+..                      .+|..                         ...+|+...     
T Consensus        85 r~lid~~R~~~a~K----------------------Rg~~~-------------------------~~~~l~~~~-----  112 (185)
T PF07638_consen   85 RKLIDHARRRQAQK----------------------RGGDQ-------------------------VRVELDERA-----  112 (185)
T ss_pred             HHHHHHHHHHHHHh----------------------cCCCC-------------------------cccchhhhh-----
Confidence            88888887654211                      11100                         001111111     


Q ss_pred             chhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          463 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       463 ~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                             .+...+.|+..+   ++.+.+..+.. |+|++++||.++|.    .|+|.+|||+.||||..+|++....|..
T Consensus       113 -------~~~~~~~~~~~~---~l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~~lgiS~~tV~r~l~~aR~  177 (185)
T PF07638_consen  113 -------DSGDEPSPEELL---ELEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAERLGISERTVRRRLRRARA  177 (185)
T ss_pred             -------ccccCCCHHHHH---HHHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                   011112444433   23445555555 99999999999998    8999999999999999999999999999


Q ss_pred             HHHHHhh
Q 008556          543 RLKQSLG  549 (561)
Q Consensus       543 KLR~~l~  549 (561)
                      +|+..+.
T Consensus       178 ~l~~~l~  184 (185)
T PF07638_consen  178 WLRRELR  184 (185)
T ss_pred             HHHHHhc
Confidence            9998764

>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=99.24  E-value=2.5e-11  Score=97.69  Aligned_cols=70  Identities=23%  Similarity=0.432  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccc
Q 008556          325 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  394 (561)
Q Consensus       325 LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr  394 (561)
                      |++.|.++|+++|++|.+++.+.+|++||++++||+++++||+++|..|.+|++..+++.+.++++++.|
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            6899999999999999999999999999999999999999999999899999999999999999998764

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 ....

>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=99.24  E-value=2.4e-11  Score=93.11  Aligned_cols=50  Identities=36%  Similarity=0.628  Sum_probs=46.3

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       493 aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +|+.||++||+||.++|+    +++|++|||+.||+|+++|+++..+|++|||+
T Consensus         1 Al~~L~~~er~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen    1 ALDQLPPREREVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             HHCTS-HHHHHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             ChhhCCHHHHHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            588999999999999998    99999999999999999999999999999985

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 ....

>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=99.03  E-value=6.5e-10  Score=92.47  Aligned_cols=77  Identities=30%  Similarity=0.491  Sum_probs=66.1

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHH
Q 008556          404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  480 (561)
Q Consensus       404 ~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~  480 (561)
                      +.+++|.+++..|.+++||.||.+|||+.|||++++|..++...+..+||+.+++.+++.++.+++.|+...+|++.
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~   77 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE   77 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence            35789999999999999999999999999999999999999999999999999998888899999999988788764

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 ....

>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=98.93  E-value=3e-09  Score=82.42  Aligned_cols=54  Identities=30%  Similarity=0.440  Sum_probs=46.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          487 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       487 ~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                      ++.|..+|..||+++|.||.++|.    +++|++|||+.+|+|.++|++.+.+|+++|
T Consensus         1 r~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L   54 (54)
T PF08281_consen    1 REALQQALAQLPERQREIFLLRYF----QGMSYAEIAEILGISESTVKRRLRRARKKL   54 (54)
T ss_dssp             HHHHHHHHHCS-HHHHHHHHHHHT----S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHH----HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence            357899999999999999999999    899999999999999999999999999987

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.

>PRK06930 positive control sigma-like factor; Validated

Probab=98.66  E-value=1.1e-07  Score=91.26  Aligned_cols=71  Identities=18%  Similarity=0.285  Sum_probs=62.3

Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      +.+.....+....|..++..||+++|+||.++|+    +++|++|||+.||+|..+|++++.||+++|+..+...
T Consensus        95 ~~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~----eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~  165 (170)
T PRK06930         95 EPESVISEWDKIRIEDALSVLTEREKEVYLMHRG----YGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES  165 (170)
T ss_pred             ChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            3334444556678999999999999999999998    8999999999999999999999999999999988644

>PRK00118 putative DNA-binding protein; Validated

Probab=98.45  E-value=8.8e-07  Score=78.51  Aligned_cols=61  Identities=21%  Similarity=0.146  Sum_probs=55.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       489 ~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      .+.-+...||+++++|+.++|.    +++|..|||+.+|+|+.+|++++.||+++||+++..-++
T Consensus        10 l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~   70 (104)
T PRK00118         10 LFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL   70 (104)
T ss_pred             HHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            4455668999999999999998    899999999999999999999999999999999876543

>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=98.30  E-value=2.2e-06  Score=64.30  Aligned_cols=54  Identities=37%  Similarity=0.589  Sum_probs=49.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      +.+..++..|++.++.++.++|.    +++|..+||+.+|+|..+|+++..++..+||
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            35778899999999999999997    7899999999999999999999999988874

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

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.18  E-value=3.8e-06  Score=77.99  Aligned_cols=57  Identities=19%  Similarity=0.269  Sum_probs=49.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY  556 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~y  556 (561)
                      ..|+++|++||.+++     +|+|++|||+.||+|+.+|++++++|+++|+.......+-.+
T Consensus         5 ~~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~   61 (137)
T TIGR00721         5 TFLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKF   61 (137)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHH
Confidence            359999999999975     799999999999999999999999999999986554444443

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=98.14  E-value=5.6e-06  Score=77.22  Aligned_cols=51  Identities=24%  Similarity=0.399  Sum_probs=46.8

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ..|+++|++||.+++     +++|++|||+.||+|+.+|++++++|+++||+...-
T Consensus         5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t   55 (141)
T PRK03975          5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARET   55 (141)
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999965     799999999999999999999999999999987644

>PRK04217 hypothetical protein; Provisional

Probab=98.09  E-value=7.1e-06  Score=73.47  Aligned_cols=56  Identities=20%  Similarity=0.134  Sum_probs=51.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchh
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY  554 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~  554 (561)
                      ..|++.|++||.++|.    +++|++|||+.||||+.+|++++.+|+++|++.+......
T Consensus        41 ~~Lt~eereai~l~~~----eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~   96 (110)
T PRK04217         41 IFMTYEEFEALRLVDY----EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGREL   96 (110)
T ss_pred             ccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccce
Confidence            5689999999999998    8999999999999999999999999999999998765543

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.03  E-value=1.5e-06  Score=62.93  Aligned_cols=34  Identities=41%  Similarity=0.464  Sum_probs=30.1

Q ss_pred             ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH
Q 008556          246 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR  279 (561)
Q Consensus       246 ~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~  279 (561)
                      +|+++.||++|+++|+||++||++|+++|+.+..
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            3789999999999999999999999999998554

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=97.98  E-value=0.0022  Score=73.37  Aligned_cols=34  Identities=32%  Similarity=0.493  Sum_probs=31.5

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI  278 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~  278 (561)
                      .+||+++||++|+..||||+|+|+++|++|..+.
T Consensus       102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~  135 (619)
T PRK05658        102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE  135 (619)
T ss_pred             CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999998743

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=97.96  E-value=3.4e-05  Score=68.00  Aligned_cols=58  Identities=28%  Similarity=0.350  Sum_probs=45.1

Q ss_pred             HHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          489 HVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       489 ~L~~aL-~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      .|.++. .-|+++|++++.++|.    +++|+.|||+.+|||+..|...++||.++|...=..
T Consensus         9 ~L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k   67 (101)
T PF04297_consen    9 LLFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK   67 (101)
T ss_dssp             HHHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            344444 4599999999999998    999999999999999999999999999999775433

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=97.93  E-value=4.4e-05  Score=70.59  Aligned_cols=62  Identities=18%  Similarity=0.264  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      ...+.|..+|+.|++.+|.||.++|+  .+..+|..+||..||+|+.+|.++..+|+.+|+..+
T Consensus        71 ~~~~~I~~~l~~Ld~~er~II~~rY~--~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l  132 (134)
T TIGR01636        71 RNRDAIENCLNEADEQTRVIIQELYM--KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL  132 (134)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc--cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            44577899999999999999999996  223469999999999999999999999999999865

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.80  E-value=4.7e-05  Score=58.07  Aligned_cols=46  Identities=26%  Similarity=0.400  Sum_probs=41.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|+.|+.+.+     .+++.+|||+.+|||+.+|+++..++++||+
T Consensus         2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~   47 (58)
T smart00421        2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLG   47 (58)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            468999999997743     6899999999999999999999999988885

lux regulon (activates the bioluminescence operon

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=97.65  E-value=0.00012  Score=57.70  Aligned_cols=46  Identities=24%  Similarity=0.335  Sum_probs=40.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|.+|+.+..     .|++.+|||+.+|||..+|+....++++||.
T Consensus         2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~   47 (58)
T PF00196_consen    2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLG   47 (58)
T ss_dssp             GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred             CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence            479999999999887     6999999999999999999999999999985

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.62  E-value=0.00015  Score=55.44  Aligned_cols=45  Identities=29%  Similarity=0.487  Sum_probs=40.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      |+++|++|+.+.+     .++|.+|||+.+|+|+.+|++..++++++|+.
T Consensus         1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~   45 (57)
T cd06170           1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGV   45 (57)
T ss_pred             CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            6899999998854     58999999999999999999999999888764

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=97.60  E-value=0.00033  Score=61.63  Aligned_cols=55  Identities=22%  Similarity=0.439  Sum_probs=49.6

Q ss_pred             HHHHHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          486 MRQHVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       486 ~~e~L~~aL~~L~-erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                      .+..+..+++.|+ +.+|.||.++|.    .+++..+|++.||+|+.++-.+.++|++.|
T Consensus        44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi----~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L   99 (100)
T PF07374_consen   44 EKLEIRRAINKLEDPDERLILRMRYI----NKLTWEQIAEELNISRRTYYRIHKKALKEL   99 (100)
T ss_pred             HHHHHHHHHHHccChhHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            3456788888886 899999999998    789999999999999999999999999876

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.59  E-value=0.00016  Score=60.21  Aligned_cols=47  Identities=19%  Similarity=0.213  Sum_probs=41.7

Q ss_pred             HHHHHHhcCCHHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          489 HVRNLLTLLNPKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       489 ~L~~aL~~L~erER~VL~LR-yGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .+.+-|+.||++.+.++.|. |.    +++|++|||+.||||..+|+.++++
T Consensus         8 ~~~~~l~~l~~~~r~af~L~R~~----eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879         8 KLAERLTWVDSLAEAAAALAREE----AGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             hHHHHHhcCCHHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            46677899999999999995 55    7999999999999999999998775

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.

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

Probab=97.54  E-value=0.0003  Score=55.02  Aligned_cols=48  Identities=27%  Similarity=0.428  Sum_probs=42.0

Q ss_pred             CCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       497 L~erER~VL~LRyGL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                      |+++|++||..-|-.+  + ...-|+.|||+.||||+.+|..++.+|.+||
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl   51 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL   51 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            7899999999866533  3 4678999999999999999999999999987

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

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.48  E-value=0.00017  Score=62.70  Aligned_cols=49  Identities=22%  Similarity=0.244  Sum_probs=42.7

Q ss_pred             HHHHHHH-hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHH
Q 008556          488 QHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQL  536 (561)
Q Consensus       488 e~L~~aL-~~L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqi  536 (561)
                      +.+..+| ..|+|+|+.+|.+||++.+   ..++|++|||+.+|||+.+|.+.
T Consensus        23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~   75 (94)
T TIGR01321        23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG   75 (94)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence            3566677 5599999999999999987   67899999999999999999764

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=97.31  E-value=0.00049  Score=66.34  Aligned_cols=47  Identities=23%  Similarity=0.352  Sum_probs=43.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ..|+++|++||.+.-     +|+|.+|||+.||+|..||+....++++||.-
T Consensus       132 ~~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV  178 (198)
T PRK15201        132 RHFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV  178 (198)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            469999999999986     79999999999999999999999999999954

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.28  E-value=0.00045  Score=68.10  Aligned_cols=46  Identities=11%  Similarity=0.237  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .|++||++||.+.-     +|+|.+|||+.||||..||+....+.++||.-
T Consensus       137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v  182 (207)
T PRK15411        137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT  182 (207)
T ss_pred             cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            49999999999986     79999999999999999999999999999963

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.23  E-value=0.00055  Score=66.76  Aligned_cols=46  Identities=22%  Similarity=0.291  Sum_probs=43.0

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|++||++|+.+.-     +|+|.+|||+.||||..||+.+..+.++||-
T Consensus       149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~  194 (216)
T PRK10840        149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG  194 (216)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            469999999999986     6999999999999999999999999999994

>PRK13870 transcriptional regulator TraR; Provisional

Probab=97.23  E-value=0.00054  Score=69.09  Aligned_cols=45  Identities=27%  Similarity=0.383  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .|++||++||.+-=     +|+|..|||.+||||..||...+++|++||-
T Consensus       173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg  217 (234)
T PRK13870        173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD  217 (234)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            59999999999976     7999999999999999999999999999994

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.23  E-value=0.00057  Score=69.61  Aligned_cols=48  Identities=21%  Similarity=0.261  Sum_probs=44.3

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +..|+++|++|+.+..     +|+|.+|||+.||||..||+...+++++||.-
T Consensus       188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v  235 (247)
T TIGR03020       188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV  235 (247)
T ss_pred             ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            4579999999999965     79999999999999999999999999999964

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.21  E-value=0.0006  Score=67.86  Aligned_cols=50  Identities=8%  Similarity=-0.050  Sum_probs=46.3

Q ss_pred             HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          491 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       491 ~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .++...|++||++||.+.-     +|+|.+|||+.|+||..||+....+.++||.
T Consensus       138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg  187 (217)
T PRK13719        138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFG  187 (217)
T ss_pred             hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            5667899999999999976     7999999999999999999999999999994

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.21  E-value=0.00058  Score=68.59  Aligned_cols=48  Identities=19%  Similarity=0.267  Sum_probs=44.3

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ...|+++|++||.+..     +|+|..|||++||||..+|+..+.++++||+.
T Consensus       169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~  216 (232)
T TIGR03541       169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGV  216 (232)
T ss_pred             hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            3579999999999964     79999999999999999999999999999974

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.20  E-value=0.00064  Score=67.29  Aligned_cols=46  Identities=20%  Similarity=0.342  Sum_probs=43.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|++||++||.+.-     +|+|.+|||+.|+||..||+....+.++||.
T Consensus       133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg  178 (207)
T PRK11475        133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLG  178 (207)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            469999999999986     6999999999999999999999999999994

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=97.16  E-value=0.00073  Score=68.34  Aligned_cols=45  Identities=16%  Similarity=0.258  Sum_probs=42.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .|++||++||.+-.     +|+|..|||++||||..||+..+.++++||-
T Consensus       179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~  223 (240)
T PRK10188        179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFN  223 (240)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            69999999999986     7999999999999999999999999999995

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=97.15  E-value=0.00076  Score=67.17  Aligned_cols=48  Identities=17%  Similarity=0.127  Sum_probs=44.2

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +..|++||++|+.+.+     +|+|.+|||+.|++|..+|+....++++||.-
T Consensus       153 ~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v  200 (216)
T PRK10100        153 SALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAV  200 (216)
T ss_pred             cCCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            3469999999999998     68999999999999999999999999999953

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=97.02  E-value=0.0017  Score=57.89  Aligned_cols=53  Identities=19%  Similarity=0.164  Sum_probs=48.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      .|+..|-+.|+|.+.    +++|++|-|+.||||+.|+-.++..|.+|+-..|....
T Consensus        41 ~L~~dElEAiRL~D~----egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk   93 (106)
T PF02001_consen   41 VLTVDELEAIRLVDY----EGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK   93 (106)
T ss_pred             EeeHHHHHHHHHHHH----cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence            478888999999998    89999999999999999999999999999999886543

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=97.02  E-value=0.0011  Score=65.73  Aligned_cols=46  Identities=30%  Similarity=0.371  Sum_probs=43.0

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|++||++|+++--     +|+|.+|||+.|++|..||+.+..+.++||.
T Consensus       147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~  192 (211)
T COG2197         147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLG  192 (211)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence            469999999999875     7999999999999999999999999999994

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=96.96  E-value=0.003  Score=61.62  Aligned_cols=59  Identities=17%  Similarity=0.260  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          485 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       485 e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      .....+...+.+|++|||+|+..--     .|+..++||..||||.-||..+-.+.++||+..-
T Consensus       131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~S  189 (202)
T COG4566         131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARS  189 (202)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhcc
Confidence            4456788999999999999999876     6899999999999999999999999999997643

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=96.96  E-value=0.0026  Score=50.11  Aligned_cols=47  Identities=34%  Similarity=0.441  Sum_probs=42.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ..|+++|++|+.+.-     .|++..|||..+|+|..+|+....++.+||.-
T Consensus         3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~   49 (65)
T COG2771           3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGV   49 (65)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            368999999998876     57999999999999999999999999999864

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=96.95  E-value=0.0011  Score=49.70  Aligned_cols=41  Identities=24%  Similarity=0.339  Sum_probs=24.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      ..|++.||..|...+-    +|+|..+||+.||+|+.||...++|
T Consensus         3 ~~Lt~~eR~~I~~l~~----~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALLE----QGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHHC----S---HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHHH----cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            4689999999988776    8899999999999999999988776

>PRK09483 response regulator; Provisional

Probab=96.86  E-value=0.0019  Score=61.73  Aligned_cols=46  Identities=22%  Similarity=0.300  Sum_probs=42.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|++||++||.+..     +|+|.+|||+.|++|..||+.+..+.++||-
T Consensus       147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~  192 (217)
T PRK09483        147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN  192 (217)
T ss_pred             cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            469999999998764     7899999999999999999999999999983

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.75  E-value=0.003  Score=58.97  Aligned_cols=46  Identities=22%  Similarity=0.382  Sum_probs=42.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|++||.+ +.    ++++.+|||+.+++|..||+....++++||.
T Consensus       148 ~~lt~~e~~vl~l-~~----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~  193 (211)
T PRK15369        148 PLLTPRERQILKL-IT----EGYTNRDIAEQLSISIKTVETHRLNMMRKLD  193 (211)
T ss_pred             cCCCHHHHHHHHH-HH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            4599999999998 44    7899999999999999999999999999995

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.74  E-value=0.0096  Score=54.55  Aligned_cols=63  Identities=21%  Similarity=0.231  Sum_probs=53.7

Q ss_pred             HHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          485 LMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       485 e~~e~L~~aL-~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      .....+..++ ..|++.+|+||..+|. . .++++..+|+..+|+|+.+...+.++|+.++-..+.
T Consensus        67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~  130 (132)
T TIGR01637        67 QEARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG  130 (132)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence            3345677777 9999999999999997 2 137899999999999999999999999999987654

This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.67  E-value=0.004  Score=61.84  Aligned_cols=53  Identities=23%  Similarity=0.350  Sum_probs=45.9

Q ss_pred             cCCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          496 LLNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      .|+++|++||+.-|-+|  | ....+++|||+.||||+.++.+++.+|.+||=..+
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~  210 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY  210 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            69999999999876543  3 36789999999999999999999999999996643

>PRK01381 Trp operon repressor; Provisional

Probab=96.50  E-value=0.003  Score=55.50  Aligned_cols=48  Identities=27%  Similarity=0.320  Sum_probs=40.4

Q ss_pred             HHHHHHHhc-CCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHH
Q 008556          488 QHVRNLLTL-LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQ  535 (561)
Q Consensus       488 e~L~~aL~~-L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRq  535 (561)
                      +.+..+|.. |+|+|+.+|..||++..   ..++|++||++.+|||..+|.+
T Consensus        23 ~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR   74 (99)
T PRK01381         23 DLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR   74 (99)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence            456666655 99999999999999875   4579999999999999988853

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.47  E-value=0.0052  Score=58.12  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=42.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|++|+.+..     ++++.++||+.+++|..||+....++++||.
T Consensus       154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~  199 (216)
T PRK10651        154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMK  199 (216)
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence            459999999999865     6899999999999999999999999999995

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=96.41  E-value=0.0026  Score=57.89  Aligned_cols=48  Identities=25%  Similarity=0.359  Sum_probs=44.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      -|+++|-.||.||-     +|+|++|||++||-|+..|+-++++|+.++.+.-
T Consensus         8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar   55 (143)
T COG1356           8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR   55 (143)
T ss_pred             eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence            48899999999997     7999999999999999999999999999997753

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.39  E-value=0.0094  Score=55.32  Aligned_cols=53  Identities=13%  Similarity=0.190  Sum_probs=46.7

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       489 ~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .+...+..|+++|++||.+.+     .+++.++||+.+|+|..+|+....++++||+.
T Consensus       134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~  186 (202)
T PRK09390        134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQA  186 (202)
T ss_pred             HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence            455667889999999999744     57899999999999999999999999999964

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.34  E-value=0.015  Score=51.12  Aligned_cols=48  Identities=25%  Similarity=0.328  Sum_probs=43.7

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .-|+.+|+..+.++|.    .++|+.|||+.++||+..|...++|.-+.|-.
T Consensus        16 sLLT~KQ~~Y~~lyy~----dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~   63 (105)
T COG2739          16 SLLTKKQKNYLELYYL----DDLSLSEIAEEFNVSRQAIYDNIKRTEKILED   63 (105)
T ss_pred             HHHhHHHHHHHHHHHH----hhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence            4589999999999998    89999999999999999999999998777644

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=96.07  E-value=0.017  Score=50.31  Aligned_cols=52  Identities=19%  Similarity=0.148  Sum_probs=46.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  551 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  551 (561)
                      .|+..|-+.|+|...    ++++++|-|..||||+.|+-..++.|++|+-.++...
T Consensus        33 ~lt~eElEAlRLvD~----~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG   84 (99)
T COG1342          33 ILTIEELEALRLVDY----EGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG   84 (99)
T ss_pred             eecHHHHHHHHHHhH----hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence            367778889999988    8999999999999999999999999999999887654

>PRK15320 transcriptional activator SprB; Provisional

Probab=95.93  E-value=0.014  Score=57.34  Aligned_cols=47  Identities=19%  Similarity=0.280  Sum_probs=43.1

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      --.|+++|.+|+.+--     +|+|.+|||+.|++|..+|+....+.+.||.
T Consensus       162 ~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLg  208 (251)
T PRK15320        162 PPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLG  208 (251)
T ss_pred             CCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence            3679999999999876     7999999999999999999999999999985

>PRK10403 transcriptional regulator NarP; Provisional

Probab=95.86  E-value=0.016  Score=54.57  Aligned_cols=46  Identities=15%  Similarity=0.230  Sum_probs=42.0

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|.+|+.+..     +++|.++||+.+|+|..+|+....+.++||.
T Consensus       152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~  197 (215)
T PRK10403        152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLN  197 (215)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence            459999999998765     6899999999999999999999999999984

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

Probab=95.53  E-value=0.32  Score=51.65  Aligned_cols=159  Identities=18%  Similarity=0.137  Sum_probs=96.6

Q ss_pred             HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556          323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  402 (561)
Q Consensus       323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~  402 (561)
                      +..+..-.+-++.---+|.++=.-.||.+||.|+.-.+.-.+=-|-++  -..|.+..-|+.-.+.++++.+.-..|.+ 
T Consensus         8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~--PaAWL~~v~R~~aiD~~Rr~~~~~~~~~e-   84 (415)
T COG4941           8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRN--PAAWLIAVGRNRAIDRVRRRARRDAAPPE-   84 (415)
T ss_pred             HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCC--hHHHHHHHHhhhHHHHHHHHHHhccCChh-
Confidence            334444444444444556666556799999999865555444333332  56788877888888888776533222211 


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHHH
Q 008556          403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  482 (561)
Q Consensus       403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le  482 (561)
                                                +                    .++      . ++.+..+.      +.+++...
T Consensus        85 --------------------------l--------------------~~~------~-e~~e~~~a------~~~~d~~i  105 (415)
T COG4941          85 --------------------------L--------------------LLS------D-EDEEMEEA------EALDDEHI  105 (415)
T ss_pred             --------------------------h--------------------ccc------c-cchhhhcc------cccccccc
Confidence                                      1                    000      0 00000000      00111111


Q ss_pred             HHHHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          483 KQLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       483 ~~e~~e~L~~aL-~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      .++....|--|. -.|++.+|-.|.||..    -|+|..|||..|=|+..++-|.+.||.++++..
T Consensus       106 ~Dd~LRLiFvccHPal~~~~riALtLR~v----~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a  167 (415)
T COG4941         106 RDDRLRLIFVCCHPALPPEQRIALTLRLV----GGLSTAEIARAFLVPEAAMAQRIVRAKARIREA  167 (415)
T ss_pred             chhhHHhhhhhcCCCCChhhHHHHHHHHH----cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence            111112222222 5699999999999988    789999999999999999999999999999874

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.44  E-value=0.031  Score=52.76  Aligned_cols=45  Identities=24%  Similarity=0.242  Sum_probs=40.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .|+++|.+|+.+..     +++|.+|||+.+++|..+|+....++++||.
T Consensus       149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~  193 (210)
T PRK09935        149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLG  193 (210)
T ss_pred             cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            48899999887644     5799999999999999999999999999984

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=95.42  E-value=0.031  Score=52.80  Aligned_cols=47  Identities=21%  Similarity=0.320  Sum_probs=42.5

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      +..|+++|++|+.+..     .+.+.+|||+.+++|..+|+....+.++||.
T Consensus       141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~  187 (204)
T PRK09958        141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE  187 (204)
T ss_pred             cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            3569999999998876     5789999999999999999999999999983

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.30  E-value=0.027  Score=52.94  Aligned_cols=46  Identities=20%  Similarity=0.255  Sum_probs=42.1

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|++|+.+..     ++++.++||+.+++|..+|+.+..+.++||.
T Consensus       136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~  181 (196)
T PRK10360        136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLG  181 (196)
T ss_pred             cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            469999999999865     5799999999999999999999999999985

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.30  E-value=0.033  Score=63.71  Aligned_cols=55  Identities=13%  Similarity=0.070  Sum_probs=45.7

Q ss_pred             HhcCCHHHHHHHHHHhccc---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          494 LTLLNPKERCIVRLRFGIE---DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~---d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      ...|+++|+++|..-|..+   -..+-|.+|||+.||||+.++.+++.+|.+||=..+
T Consensus       605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~~  662 (665)
T PRK13558        605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGAF  662 (665)
T ss_pred             hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            4679999999999988721   113349999999999999999999999999986543

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.21  E-value=0.031  Score=65.95  Aligned_cols=46  Identities=11%  Similarity=0.172  Sum_probs=43.0

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|++|+.+..     +|+|.+|||+.|+||..||+..+++.++||.
T Consensus       837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~  882 (903)
T PRK04841        837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLG  882 (903)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            449999999999976     7999999999999999999999999999995

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=94.97  E-value=0.032  Score=39.25  Aligned_cols=27  Identities=30%  Similarity=0.643  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          516 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       516 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ++|.+|||+.+|+|+|+|.    |++++|++
T Consensus         2 ~mtr~diA~~lG~t~ETVS----R~l~~l~~   28 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVS----RILKKLER   28 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence            4789999999999999996    56666664

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>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=94.87  E-value=0.11  Score=42.25  Aligned_cols=56  Identities=18%  Similarity=0.286  Sum_probs=45.1

Q ss_pred             HHHHHhhcHHHHHHHHHHHHHHHHHHHHhh----hC--CCCCHHHHHHHHHHHHHHhhhhcC
Q 008556          311 LKSELHSGNSSREKLINANLRLVVHVAKQY----QG--RGISLHDLLQEGSMGLMKSVEKFK  366 (561)
Q Consensus       311 L~~~l~~G~~Are~LI~~nlrLV~sIArrY----~~--~g~~~eDLIQEG~IGLirAiekFD  366 (561)
                      +.++.+|+..|.++++..|.+++.+.+.+-    .+  ++.-=+|+-|+-...|++++-+|+
T Consensus         4 I~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen    4 IKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            445556677999999999999999998772    22  133349999999999999999996

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

>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=94.53  E-value=0.057  Score=44.00  Aligned_cols=45  Identities=18%  Similarity=0.417  Sum_probs=29.4

Q ss_pred             HhcCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 008556          494 LTLLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLS-KERVRQLES  538 (561)
Q Consensus       494 L~~L~erER~VL~L--RyGL~d~e~~Tl~EIAe~LGIS-rerVRqie~  538 (561)
                      +..|+++|++||..  .|.-..|-+-|.+|||+.||++ ..+|.+.+.
T Consensus         1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen    1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            35799999999886  3333456788999999999997 999987654

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.

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=94.52  E-value=0.079  Score=45.82  Aligned_cols=37  Identities=14%  Similarity=0.220  Sum_probs=30.8

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  537 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie  537 (561)
                      ..|++| ..|+.+.-     .++|..+||+.+|||+.||..+.
T Consensus        35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~   71 (88)
T TIGR02531        35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK   71 (88)
T ss_pred             HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence            458888 77877754     57999999999999999998833

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>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=94.51  E-value=0.11  Score=39.10  Aligned_cols=40  Identities=18%  Similarity=0.271  Sum_probs=28.9

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      |++.++.||..-+-   +.+.|..|||+.+|+|..+|++++++
T Consensus         1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~   40 (48)
T PF13412_consen    1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKK   40 (48)
T ss_dssp             --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            56778888866543   35699999999999999999876554

...

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=94.44  E-value=0.1  Score=40.50  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      +|+..++-++.+.|.   ..+.++++||..+|||+.+|.++.+..+.-|...+
T Consensus         2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l   51 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL   51 (53)
T ss_pred             CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence            578888888888665   26789999999999999999999999888776543

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=94.27  E-value=0.039  Score=41.69  Aligned_cols=32  Identities=28%  Similarity=0.361  Sum_probs=22.6

Q ss_pred             HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      ||.+..     +++|..+||+.||||+.+|+++.++-
T Consensus        10 ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~   41 (50)
T PF13384_consen   10 IIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY   41 (50)
T ss_dssp             HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred             HHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence            555554     58999999999999999999887653

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=94.13  E-value=0.29  Score=44.84  Aligned_cols=55  Identities=18%  Similarity=0.123  Sum_probs=49.1

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      |..-.+.+-+||.++|.    .++|...||..+++|...||+.+.+|-..+..++.-.+
T Consensus        60 L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~~  114 (125)
T PF06530_consen   60 LKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSMLT  114 (125)
T ss_pred             HHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHhh
Confidence            45578999999999999    89999999999999999999999999999988865443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=94.10  E-value=0.07  Score=56.41  Aligned_cols=36  Identities=22%  Similarity=0.344  Sum_probs=32.7

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                      .|-.|||.    +++|+.|||++|||||.+|.+++.+|++
T Consensus        20 ~vA~lYY~----~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~   55 (318)
T PRK15418         20 RIAWFYYH----DGLTQSEIGERLGLTRLKVSRLLEKGRQ   55 (318)
T ss_pred             HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            46678888    8999999999999999999999999975

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=93.96  E-value=0.21  Score=46.26  Aligned_cols=53  Identities=17%  Similarity=0.356  Sum_probs=44.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      ..+.|...++.|.+.++.||.+||+  ...++|..+||..|+||..+++.....-
T Consensus        71 ~k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~f  123 (130)
T PF05263_consen   71 QKEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRF  123 (130)
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHH
Confidence            3456788889999999999999998  3346999999999999999998765443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>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=93.74  E-value=0.13  Score=42.41  Aligned_cols=38  Identities=32%  Similarity=0.613  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHH
Q 008556          278 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL  315 (561)
Q Consensus       278 ~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l  315 (561)
                      .++.+++.+|+..+||+||.+|.|+.+|++.+.+...+
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            35677889999999999999999999999988876443

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 ....

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=93.48  E-value=0.17  Score=33.67  Aligned_cols=36  Identities=19%  Similarity=0.335  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL  536 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqi  536 (561)
                      +++.++..+...|.    .+.+..+||+.+|+|+.+|..+
T Consensus         6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence            45555665555554    5679999999999999999865

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

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

Probab=93.47  E-value=0.97  Score=45.38  Aligned_cols=35  Identities=31%  Similarity=0.574  Sum_probs=29.1

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      ++.++...|...+|++||.+|.|+.+|++.+.+..
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~  122 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE  122 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34456777888899999999999999999887753

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.

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=93.40  E-value=0.1  Score=39.08  Aligned_cols=32  Identities=25%  Similarity=0.296  Sum_probs=23.4

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556          501 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  537 (561)
Q Consensus       501 ER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie  537 (561)
                      ..+|+.|+-     +|+|..+||+.+|||+.+|.+++
T Consensus        11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l   42 (45)
T PF02796_consen   11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYL   42 (45)
T ss_dssp             HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHH
T ss_pred             HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence            345666664     67999999999999999998765

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=93.32  E-value=1.1  Score=48.23  Aligned_cols=129  Identities=19%  Similarity=0.273  Sum_probs=71.8

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHH-HHHH
Q 008556          280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG-SMGL  358 (561)
Q Consensus       280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG-~IGL  358 (561)
                      +.++..+|...+|++||..|.|+.+|++.+.+...+...                   ..    .+++++.+.++ -..|
T Consensus       218 ~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~l  274 (367)
T PRK09210        218 LIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSHL  274 (367)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcchh
Confidence            455677888889999999999999999988775432211                   11    11111111110 1111


Q ss_pred             HHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHH
Q 008556          359 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE  438 (561)
Q Consensus       359 irAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e  438 (561)
                      ...+.  |+.............++..+.+++.      .+|..-...+..      .+.-..|.+.|.+|||+.+|+|.+
T Consensus       275 ~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~l------rygl~~~~~~tl~EIa~~lgvs~e  340 (367)
T PRK09210        275 GDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLRL------RFGLDDGRTRTLEEVGKVFGVTRE  340 (367)
T ss_pred             hhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHHH------HhccCCCCCccHHHHHHHHCCCHH
Confidence            11111  2111223444455566666666663      233322111111      111123467899999999999999


Q ss_pred             HHHHHHH
Q 008556          439 KLERLIF  445 (561)
Q Consensus       439 ~v~~ll~  445 (561)
                      +|+.+..
T Consensus       341 rVrQi~~  347 (367)
T PRK09210        341 RIRQIEA  347 (367)
T ss_pred             HHHHHHH
Confidence            9998854

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=93.19  E-value=1.5  Score=46.66  Aligned_cols=35  Identities=31%  Similarity=0.452  Sum_probs=29.5

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      ++.+++.+|...+|++||..|.|..+|++.+.+..
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~  208 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD  208 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            45567778888899999999999999999887753

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=93.15  E-value=1.2  Score=50.13  Aligned_cols=130  Identities=18%  Similarity=0.320  Sum_probs=70.6

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHH-HHHH
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG  357 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQE-G~IG  357 (561)
                      ++.+++.+|...+|++||.+|.|+.+|++.+.+....+                       +....+++++.+.+ +...
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-----------------------~~~~~~SLD~~i~~d~~~~  415 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK-----------------------YNREPISLDKTIGKEGDSQ  415 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-----------------------hcCCCcccccccccCCccc
Confidence            45567788888999999999999999999887754321                       11112222322211 1111


Q ss_pred             HHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCH
Q 008556          358 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV  437 (561)
Q Consensus       358 LirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~  437 (561)
                      |...+.  |+........+..+..+..+..++..      ||..-...+..    +  +.-..+.+.|..|||..+||+.
T Consensus       416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~~------L~eREr~VI~l----R--yGL~~~e~~TL~EIa~~lGVSr  481 (509)
T PRK05901        416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLET------LSEREAGVIRM----R--FGLTDGQPKTLDEIGQVYGVTR  481 (509)
T ss_pred             HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHhh------CCHHHHHHHHH----H--hhccCCCCCCHHHHHHHHCCCH
Confidence            222221  11111223334444455555555532      33222111111    1  1111246789999999999999


Q ss_pred             HHHHHHHH
Q 008556          438 EKLERLIF  445 (561)
Q Consensus       438 e~v~~ll~  445 (561)
                      ++|+++..
T Consensus       482 ERVRQIe~  489 (509)
T PRK05901        482 ERIRQIES  489 (509)
T ss_pred             HHHHHHHH
Confidence            99998844

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=92.09  E-value=0.29  Score=48.53  Aligned_cols=47  Identities=15%  Similarity=0.087  Sum_probs=36.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                      .|+++|.+++.....=..++|+|.+|||+.||+|..||+....++..
T Consensus       158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~  204 (239)
T PRK10430        158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN  204 (239)
T ss_pred             CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence            48899987764433111237899999999999999999999887754

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

Probab=92.04  E-value=4.4  Score=41.55  Aligned_cols=147  Identities=20%  Similarity=0.201  Sum_probs=81.8

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 008556          248 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  327 (561)
Q Consensus       248 ~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~G~~Are~LI~  327 (561)
                      .+-.||++-.  +.--+.--.+++.+      +..+..+|+..+|++||..|.|+..|++.+++...+..+.        
T Consensus        88 ei~d~LR~~~--~v~vpR~~~~~~~~------i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~--------  151 (247)
T COG1191          88 EILDYLRKND--SVKVPRSLRELGRR------IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAIN--------  151 (247)
T ss_pred             HHHHHHHhCC--CccCcHHHHHHHHH------HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhc--------
Confidence            4556888877  22223334444444      4457788899999999999999999999888765433322        


Q ss_pred             HHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHH
Q 008556          328 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  407 (561)
Q Consensus       328 ~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~  407 (561)
                        .....++--.....+.+  +            +   +...+..+..+-.|-..+.+.+++..      +|..-.    
T Consensus       152 --~~~~~sld~~~~~~~d~--~------------~---~~~~~~~~~~~~~~~~~~~l~~ai~~------L~EREk----  202 (247)
T COG1191         152 --GSQLLSLDEDVLKDDDD--D------------V---DDQIENPDDGVEKEELLEILKEAIEP------LPEREK----  202 (247)
T ss_pred             --cccccchhhhhcccccc--c------------h---hhccccchhHHHHHHHHHHHHHHHHc------cCHHHH----
Confidence              11111111111111110  0            1   11122344455566666666666541      222110    


Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          408 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF  445 (561)
Q Consensus       408 ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~  445 (561)
                      .|      +.-...-+-|..|||+.||||..+|..+..
T Consensus       203 ~V------l~l~y~eelt~kEI~~~LgISes~VSql~k  234 (247)
T COG1191         203 LV------LVLRYKEELTQKEIAEVLGISESRVSRLHK  234 (247)
T ss_pred             HH------HHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence            00      011112256889999999999999988754

>PF13730 HTH_36: Helix-turn-helix domain

Probab=91.76  E-value=0.59  Score=35.90  Aligned_cols=47  Identities=17%  Similarity=0.270  Sum_probs=33.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCC---CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKP---KSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~---~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .|++.++.|+..-..+.++.+   .|.+.||+.+|+|+.+|++    +++.|.+
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~----~i~~L~~   51 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQR----AIKELEE   51 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            588888888766444432222   2899999999999999964    5666654

>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=91.74  E-value=0.49  Score=35.20  Aligned_cols=40  Identities=35%  Similarity=0.460  Sum_probs=26.9

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      |++-.+.||..--.  | ...++.+||+.+|+|..+|.+.+.+
T Consensus         1 lD~~D~~Il~~Lq~--d-~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    1 LDELDRKILRLLQE--D-GRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--c-CCccHHHHHHHHCcCHHHHHHHHHH
Confidence            34556667765443  2 4689999999999999999887654

...

>PHA00675 hypothetical protein

Probab=91.54  E-value=0.35  Score=40.64  Aligned_cols=40  Identities=18%  Similarity=0.089  Sum_probs=30.6

Q ss_pred             hcCCHHHHHHHHHHh-cccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRF-GIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       495 ~~L~erER~VL~LRy-GL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ..|++.+-+.|+.++ -    .+.|+.+||+.||||+.+|.+|..
T Consensus        21 AKLt~~qV~~IR~l~~r----~G~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         21 AKLTDAEVERIRELHEV----EGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             cccCHHHHHHHHHHHHh----cCccHHHHHHHhCCCHHHHHHHHc
Confidence            346666655555555 4    678999999999999999998864

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=91.34  E-value=4.5  Score=44.48  Aligned_cols=37  Identities=22%  Similarity=0.399  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556          408 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI  444 (561)
Q Consensus       408 ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll  444 (561)
                      .+.+.+..+..++|++||.+|.|..+|+++..++..+
T Consensus       112 ~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l  148 (415)
T PRK07598        112 RLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL  148 (415)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence            3455667888899999999999988887766666554

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=91.02  E-value=0.3  Score=51.84  Aligned_cols=35  Identities=23%  Similarity=0.290  Sum_probs=31.2

Q ss_pred             HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                      +-.+||.    +++|..|||++||||+.+|+.++.+|.+
T Consensus        18 ~A~lYY~----~gltQ~eIA~~LgiSR~~v~rlL~~Ar~   52 (321)
T COG2390          18 AAWLYYV----EGLTQSEIAERLGISRATVSRLLAKARE   52 (321)
T ss_pred             HHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            5567887    8999999999999999999999988865

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=90.84  E-value=0.65  Score=42.03  Aligned_cols=50  Identities=20%  Similarity=0.300  Sum_probs=41.7

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       493 aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .+..|++.+..-|....- .   .=+++|+++.||||-.|||..+.+.+++|.-
T Consensus        30 ~~~~L~~E~~~Fi~~Fi~-~---rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   30 WFARLSPEQLEFIKLFIK-N---RGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hhhcCCHHHHHHHHHHHH-h---cCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            367899888887766543 3   3399999999999999999999999999975

>PF13518 HTH_28: Helix-turn-helix domain

Probab=90.82  E-value=0.43  Score=35.92  Aligned_cols=27  Identities=26%  Similarity=0.382  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                      ++.|+.+||..+|||+.+|+++..+-.
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~~y~   37 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIKRYR   37 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            456999999999999999988876543

>smart00351 PAX Paired Box domain

Probab=90.59  E-value=0.66  Score=42.40  Aligned_cols=41  Identities=15%  Similarity=0.074  Sum_probs=32.1

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                      |+..+|.=|...|-    ++.+..+||+.||||+.+|..++++..
T Consensus        18 ~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~   58 (125)
T smart00351       18 LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYY   58 (125)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45555554555554    678999999999999999999988864

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=90.07  E-value=0.38  Score=37.50  Aligned_cols=40  Identities=20%  Similarity=0.305  Sum_probs=27.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|+..|+.=|.-+|-    .|.+..+||..|||++.+|+.+...
T Consensus         6 ~LTl~eK~~iI~~~e----~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    6 SLTLEEKLEIIKRLE----EGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             S--HHHHHHHHHHHH----CTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            466666664445554    6679999999999999999998765

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=89.95  E-value=0.56  Score=36.03  Aligned_cols=38  Identities=21%  Similarity=0.438  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          500 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       500 rER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      |++.||.+-+  ..+.+.|.+|||+.||||+.+|++.++.
T Consensus         1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~   38 (55)
T PF08279_consen    1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKE   38 (55)
T ss_dssp             HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred             CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence            4556666542  2335699999999999999999865443

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>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=89.82  E-value=0.59  Score=37.64  Aligned_cols=35  Identities=17%  Similarity=0.294  Sum_probs=26.5

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      ..+.++..  .+..+++.+||+.||||..+||....+
T Consensus        11 kA~e~y~~--~~g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   11 KAFEIYKE--SNGKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             HHHHHHHH--hCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence            34555432  235899999999999999999987554

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 [].

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=89.79  E-value=0.66  Score=36.99  Aligned_cols=26  Identities=19%  Similarity=0.331  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      +|++..|||+.||+++.+|.....+-
T Consensus        12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   12 QGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            79999999999999999999887663

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=89.75  E-value=0.38  Score=56.40  Aligned_cols=45  Identities=18%  Similarity=0.100  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      -|+.||++|+.+-|     .|+|.+|||+.+.||-.||+....+...||.
T Consensus       831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLg  875 (894)
T COG2909         831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLG  875 (894)
T ss_pred             CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            38999999999999     6999999999999999999999999999984

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=89.49  E-value=17  Score=38.25  Aligned_cols=178  Identities=12%  Similarity=0.143  Sum_probs=92.9

Q ss_pred             HHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhH
Q 008556          323 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  402 (561)
Q Consensus       323 e~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~  402 (561)
                      ++-+...+..+..++.+.   ++  -+-+.|....+++.+..-..-+|.....++.-.|.-+++.               
T Consensus       119 er~l~~a~~~I~~~~~~L---~L--p~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~---------------  178 (310)
T PRK00423        119 ERNLAFALSELDRIASQL---GL--PRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRR---------------  178 (310)
T ss_pred             hHHHHHHHHHHHHHHHHc---CC--CHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHH---------------
Confidence            334444556666666655   23  3667777777888777667778877666665555544332               


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh-hhcccCCCCChhHHH
Q 008556          403 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ-EITADTGVEIPDISV  481 (561)
Q Consensus       403 ~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~-d~l~d~~~~~pee~l  481 (561)
                                       .+-+-|..||+..++++..++..........+.++.+..  .-..+. .+...-..  +....
T Consensus       179 -----------------~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~--~p~~~i~r~~~~L~L--~~~v~  237 (310)
T PRK00423        179 -----------------CKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT--DPIDYVPRFASELGL--SGEVQ  237 (310)
T ss_pred             -----------------cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC--CHHHHHHHHHHHcCC--CHHHH
Confidence                             223557888899999988888765443322222222211  111111 11111111  11111


Q ss_pred             HHHHHHHHHHHHHh-cC----CHHH--HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          482 QKQLMRQHVRNLLT-LL----NPKE--RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       482 e~~e~~e~L~~aL~-~L----~erE--R~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                      .  .....+..+.+ .|    +|.-  --+|.+-.-+. |.+.|++|||...|||..+|++..+.-.+.|
T Consensus       238 ~--~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l  304 (310)
T PRK00423        238 K--KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKL  304 (310)
T ss_pred             H--HHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence            1  11122222221 11    1111  11122211112 3789999999999999999998766655544

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=89.49  E-value=16  Score=40.41  Aligned_cols=46  Identities=24%  Similarity=0.453  Sum_probs=31.8

Q ss_pred             HHhcCCHHHHHHHHH---------HhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          493 LLTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       493 aL~~L~erER~VL~L---------RyGL~d~---e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ++..|.-|.+.+++.         -|+..|.   .++|+++||+.+|++.+||++..+
T Consensus       283 li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~  340 (429)
T TIGR02395       283 LIKALEQREETLLKVAEAIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN  340 (429)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
Confidence            345666666655432         2222232   799999999999999999987654

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 sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations

>PRK05932 RNA polymerase factor sigma-54; Reviewed

Probab=89.38  E-value=11  Score=41.90  Aligned_cols=46  Identities=15%  Similarity=0.394  Sum_probs=32.2

Q ss_pred             HHhcCCHHHHHHHHH---------HhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          493 LLTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       493 aL~~L~erER~VL~L---------RyGL~d~---e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ++..|..|.+.+++.         -|+..|.   .++|+++||+.+|+..+||++..+
T Consensus       308 li~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~  365 (455)
T PRK05932        308 LIKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATT  365 (455)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhc
Confidence            445666676665542         2322232   799999999999999999987653

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=89.29  E-value=1.4  Score=42.59  Aligned_cols=64  Identities=13%  Similarity=0.137  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHhhhCCCCC--H-HHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHH
Q 008556          327 NANLRLVVHVAKQYQGRGIS--L-HDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  390 (561)
Q Consensus       327 ~~nlrLV~sIArrY~~~g~~--~-eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir  390 (561)
                      .+-+..+..+.++|.-+|..  + +|.|.+|.-.+++.+..|||++...+-.|.+..+-++..+.|.
T Consensus        44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~  110 (179)
T PHA02547         44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIK  110 (179)
T ss_pred             HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHH
Confidence            34455555666666545555  4 8999999999999999999999887877777666655554443

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=89.26  E-value=0.79  Score=39.43  Aligned_cols=44  Identities=30%  Similarity=0.363  Sum_probs=33.5

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF--GLSKERVRQLESRA  540 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L--GISrerVRqie~RA  540 (561)
                      ++.||+..+++..+|.-   ....|+.|+|+.|  .||++.|..+..+.
T Consensus        35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl   80 (85)
T PF02650_consen   35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL   80 (85)
T ss_dssp             GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence            57899999999999875   3789999999999  99999998765543

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=89.19  E-value=2.8  Score=42.82  Aligned_cols=34  Identities=26%  Similarity=0.423  Sum_probs=27.3

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      +......|...+|++|+.+|.|+.+|++.+.+..
T Consensus       112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~  145 (257)
T PRK05911        112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSG  145 (257)
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence            3345556777889999999999999999887743

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=89.17  E-value=5.8  Score=43.04  Aligned_cols=34  Identities=32%  Similarity=0.584  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHH
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  312 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~  312 (561)
                      ++.+....|...+|++||.+|.|+.+|++.+.+.
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            4556677888889999999999999999987774

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=89.08  E-value=0.83  Score=35.62  Aligned_cols=43  Identities=23%  Similarity=0.287  Sum_probs=31.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|++.|..||..-+.-+ +.+.|..|||+.+|+++.+|.+++++
T Consensus         2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v~~   44 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIVKR   44 (62)
T ss_dssp             TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            47788888887666522 23489999999999999999765544

...

>PHA02591 hypothetical protein; Provisional

Probab=88.98  E-value=0.78  Score=38.73  Aligned_cols=24  Identities=21%  Similarity=0.436  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .|+|.++||+.||||.++||+.++
T Consensus        58 qGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         58 KGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHh
Confidence            689999999999999999999865

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=88.86  E-value=1.5  Score=40.55  Aligned_cols=53  Identities=21%  Similarity=0.289  Sum_probs=41.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ..+..++-.|++.+-+|+..-.  ..+.++|..|||+.+|+++.+|    .||+++|=.
T Consensus        16 ~dvl~c~~GLs~~Dv~v~~~LL--~~~~~~tvdelae~lnr~rStv----~rsl~~L~~   68 (126)
T COG3355          16 EDVLKCVYGLSELDVEVYKALL--EENGPLTVDELAEILNRSRSTV----YRSLQNLLE   68 (126)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHH--hhcCCcCHHHHHHHHCccHHHH----HHHHHHHHH
Confidence            3566788899999999887654  1236899999999999999999    467777744

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=88.54  E-value=0.66  Score=44.26  Aligned_cols=50  Identities=14%  Similarity=0.050  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS-----KERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGIS-----rerVRqie~RALkKLR~  546 (561)
                      .|+++|++|+.+-.. +.|.++|.+||++.++.+     ..+|+.+..+.++||..
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (228)
T PRK11083        154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA  208 (228)
T ss_pred             ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence            599999999988764 445679999999999986     78999999999999964

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=88.30  E-value=9  Score=39.16  Aligned_cols=35  Identities=29%  Similarity=0.532  Sum_probs=28.9

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      .+.+....|+..+|++||.++.|...|++.+.+..
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~  153 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS  153 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence            45556677888899999999999999999877653

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=88.29  E-value=1.3  Score=45.05  Aligned_cols=34  Identities=29%  Similarity=0.497  Sum_probs=28.9

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      +.++...|...+|++||.+|.|+.+|++.+++..
T Consensus       115 ~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~  148 (256)
T PRK07408        115 AKKVRQELRQELGRQPTDQEIAQALDISLEEWQE  148 (256)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence            4556778888999999999999999999887743

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=88.00  E-value=7.7  Score=39.82  Aligned_cols=34  Identities=26%  Similarity=0.524  Sum_probs=28.4

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      +.+...+|...+|++||.+|.|+.+|++.+++..
T Consensus       129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~  162 (264)
T PRK07122        129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE  162 (264)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            4456677888899999999999999999887754

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=87.82  E-value=0.8  Score=36.60  Aligned_cols=46  Identities=22%  Similarity=0.416  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       497 L~erER~VL~LRyGL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      |++....-|..-|.|. ++...+..+||+.||||+.+|..    +++||.+
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~----ml~~L~~   48 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTE----MLKRLAE   48 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHH----HHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHH----HHHHHHH
Confidence            4445555555555544 45788999999999999999975    5556654

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=87.58  E-value=1.4  Score=33.09  Aligned_cols=36  Identities=28%  Similarity=0.376  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      |.-..|+.+-..    .+++..||++.+|+|+.+|++.+.
T Consensus         2 ~~R~~Il~~L~~----~~~~~~el~~~l~~s~~~vs~hL~   37 (47)
T PF01022_consen    2 PTRLRILKLLSE----GPLTVSELAEELGLSQSTVSHHLK   37 (47)
T ss_dssp             HHHHHHHHHHTT----SSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHh----CCCchhhHHHhccccchHHHHHHH
Confidence            334455554443    689999999999999999987654

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=87.47  E-value=0.84  Score=44.09  Aligned_cols=50  Identities=18%  Similarity=0.120  Sum_probs=44.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  546 (561)
                      .|+++|++|+.+... +.|++.|.++|++.+.     ++..+|+....+.++||..
T Consensus       160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~  214 (240)
T PRK10710        160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES  214 (240)
T ss_pred             ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence            599999999998764 5567899999999998     9999999999999999963

>PRK05949 RNA polymerase sigma factor; Validated

Probab=87.24  E-value=8.3  Score=41.02  Aligned_cols=35  Identities=26%  Similarity=0.461  Sum_probs=28.3

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      ++.+.+..+...+|++|+..|.|+.+|++.+.+..
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            34456667778889999999999999999877754

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=87.07  E-value=1.4  Score=37.43  Aligned_cols=42  Identities=24%  Similarity=0.400  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLSKERVRQLE  537 (561)
Q Consensus       496 ~L~erER~VL~LRyG--L~d~e~~Tl~EIAe~LGISrerVRqie  537 (561)
                      .|++|+++||..-.-  ...|++-.-++||+.+|+|..+||+..
T Consensus         1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M   44 (78)
T PF03444_consen    1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEM   44 (78)
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHH
Confidence            388999998876322  346789999999999999999999754

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>cd00131 PAX Paired Box domain

Probab=87.07  E-value=1.6  Score=40.14  Aligned_cols=41  Identities=12%  Similarity=0.017  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                      |+...|.-|...|.    ++++..+||+.||||+.+|..+.++-.
T Consensus        18 lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~   58 (128)
T cd00131          18 LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYY   58 (128)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            44444443344454    689999999999999999999887754

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=87.04  E-value=1.3  Score=38.36  Aligned_cols=46  Identities=26%  Similarity=0.372  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                      -++|.|+.-|..|+-+-.   .+++|+.||++.+|+|..+|.+. +|+|+
T Consensus        26 L~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRv-sr~Lk   74 (87)
T PF01371_consen   26 LCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITRV-SRCLK   74 (87)
T ss_dssp             HSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHH-HHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHH-HHHHH
Confidence            467777776666654332   15899999999999999999642 44444

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=87.03  E-value=9  Score=38.73  Aligned_cols=35  Identities=23%  Similarity=0.363  Sum_probs=28.2

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHH
Q 008556          280 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  314 (561)
Q Consensus       280 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~  314 (561)
                      +.++...+...+|++|+..++|+..|++.+.+...
T Consensus       111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~  145 (251)
T PRK07670        111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT  145 (251)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence            34455667778899999999999999998877543

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=86.58  E-value=2.6  Score=41.88  Aligned_cols=32  Identities=38%  Similarity=0.579  Sum_probs=26.3

Q ss_pred             HHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          282 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       282 ~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      +....|...+|+.||..+.|+.+|++.+.+..
T Consensus       101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~  132 (231)
T TIGR02885       101 YMKEELSKELGREPTINELAEALGVSPEEIVM  132 (231)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence            44566777889999999999999999877643

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.

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=86.49  E-value=2.3  Score=33.52  Aligned_cols=35  Identities=29%  Similarity=0.384  Sum_probs=26.7

Q ss_pred             HHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556          499 PKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLE  537 (561)
Q Consensus       499 erER~VL~LR-yGL~d~e~~Tl~EIAe~LGISrerVRqie  537 (561)
                      |.-+.||.+- -.    .++|..|||+.+|++..+|+..+
T Consensus        10 p~R~~Il~~L~~~----~~~t~~ela~~l~~~~~t~s~hL   45 (61)
T PF12840_consen   10 PTRLRILRLLASN----GPMTVSELAEELGISQSTVSYHL   45 (61)
T ss_dssp             HHHHHHHHHHHHC----STBEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHhcC----CCCCHHHHHHHHCCCHHHHHHHH
Confidence            5556666655 33    79999999999999999998654

...

>PRK12423 LexA repressor; Provisional

Probab=86.42  E-value=1.3  Score=43.69  Aligned_cols=47  Identities=30%  Similarity=0.478  Sum_probs=35.3

Q ss_pred             cCCHHHHHHHHHHh--cccCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRF--GIEDGKPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRy--GL~d~e~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~  546 (561)
                      .|++++++|+..--  ...+|-+.|..|||+.|| +|+.+|+.    +|++|++
T Consensus         3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~   52 (202)
T PRK12423          3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE   52 (202)
T ss_pred             cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence            48999999987632  222344679999999999 59999984    6666665

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=86.06  E-value=1.2  Score=42.13  Aligned_cols=49  Identities=18%  Similarity=0.233  Sum_probs=41.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR  545 (561)
                      .|+++|.+|+.+... +.|...|.++|++.+.     +|..+|+....+.++||.
T Consensus       148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~  201 (221)
T PRK15479        148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ  201 (221)
T ss_pred             ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence            599999999987643 3346679999999986     999999999999999985

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=86.04  E-value=1.1  Score=42.44  Aligned_cols=49  Identities=16%  Similarity=0.180  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR  545 (561)
                      .|+++|.+|+.+..- +.|..+|.++|++.+.     ++..+|+....+.++||.
T Consensus       149 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~  202 (219)
T PRK10336        149 TLKPKEFALLELLMR-NAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG  202 (219)
T ss_pred             ecCHHHHHHHHHHHh-CCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence            499999999987652 3446699999999996     999999999999999985

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=86.01  E-value=9  Score=38.84  Aligned_cols=34  Identities=26%  Similarity=0.317  Sum_probs=28.0

Q ss_pred             HHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHH
Q 008556          281 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  314 (561)
Q Consensus       281 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~  314 (561)
                      .++..++...+|++||.+|.|+.+|++.+.+...
T Consensus       123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~  156 (254)
T TIGR02850       123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA  156 (254)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            3456677788899999999999999998877544

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.

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

Probab=85.91  E-value=12  Score=38.89  Aligned_cols=35  Identities=26%  Similarity=0.496  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      ++.+.+..+...+|++||..+.|..+|++.+.+..
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~  196 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE  196 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34455667777899999999999999999887753

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).

>PRK12469 RNA polymerase factor sigma-54; Provisional

Probab=85.86  E-value=38  Score=38.10  Aligned_cols=46  Identities=22%  Similarity=0.284  Sum_probs=33.0

Q ss_pred             HHhcCCHHHHHHHHH---------HhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          493 LLTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       493 aL~~L~erER~VL~L---------RyGL~d~---e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ++..|..|.+.+++.         -|+..|.   .++|+++||+.+|+..+||++..+
T Consensus       334 li~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~  391 (481)
T PRK12469        334 LIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG  391 (481)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence            456677777766542         2322222   799999999999999999987654

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=85.32  E-value=16  Score=37.94  Aligned_cols=25  Identities=20%  Similarity=0.337  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008556          422 HSPDKEDLARRVGITVEKLERLIFI  446 (561)
Q Consensus       422 r~Pt~eEIA~~lgis~e~v~~ll~~  446 (561)
                      ..-|.+|||+.+|++.++|..++..
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~  268 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEAR  268 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4678999999999999999988654

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=85.29  E-value=1.5  Score=34.67  Aligned_cols=41  Identities=20%  Similarity=0.332  Sum_probs=25.6

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      |+..|..||..-.  ..+.+++..+|++.+|+++.+|...+++
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~   41 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKK   41 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4566666665544  2447899999999999999999754443

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=85.18  E-value=2  Score=37.37  Aligned_cols=41  Identities=29%  Similarity=0.289  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      |++.++.||.....  + ...|..+||+.+|+|+.+|++.+.+-
T Consensus         1 ld~~D~~il~~L~~--~-~~~~~~~la~~l~~s~~tv~~~l~~L   41 (108)
T smart00344        1 LDEIDRKILEELQK--D-ARISLAELAKKVGLSPSTVHNRVKRL   41 (108)
T ss_pred             CCHHHHHHHHHHHH--h-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            46677888866543  2 46899999999999999998765443

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=84.99  E-value=1.9  Score=35.10  Aligned_cols=23  Identities=17%  Similarity=0.299  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q 008556          516 PKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       516 ~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      +.|..|||+.+||++.+|++++.
T Consensus        22 ~~ta~eLa~~lgl~~~~v~r~L~   44 (68)
T smart00550       22 TSTALQLAKNLGLPKKEVNRVLY   44 (68)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHH
Confidence            59999999999999999976543

Helix-turn-helix-containing domain. Also known as Zab.

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=84.95  E-value=0.69  Score=43.92  Aligned_cols=49  Identities=16%  Similarity=0.117  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEV-----GNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EI-----Ae~LGISrerVRqie~RALkKLR  545 (561)
                      .|+++|++|+.+-.. +.|.++|.++|     |..++++..+|+....+.++||.
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~  207 (226)
T TIGR02154       154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALN  207 (226)
T ss_pred             EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhc
Confidence            599999999988764 34467888888     77899999999999999999996

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=84.67  E-value=13  Score=39.35  Aligned_cols=34  Identities=26%  Similarity=0.522  Sum_probs=28.2

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHH
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  312 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~  312 (561)
                      ++.+.+..+...+|+.||..+.|+++|++.+.+.
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~  202 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR  202 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            4556677788889999999999999999877664

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=84.62  E-value=2.3  Score=32.16  Aligned_cols=33  Identities=27%  Similarity=0.405  Sum_probs=26.2

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      .|+.+..     +..|.++||+.+|||-.+|+.+..+.
T Consensus        19 ~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   19 YILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            4555544     34699999999999999999988764

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=84.35  E-value=1.3  Score=33.86  Aligned_cols=34  Identities=35%  Similarity=0.443  Sum_probs=24.5

Q ss_pred             HHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          505 VRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       505 L~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      -.+.+.-..+.++|+.|||+.+|+++.+|..++.
T Consensus         7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~   40 (52)
T PF09339_consen    7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQ   40 (52)
T ss_dssp             HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3344444455778999999999999999976543

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=84.26  E-value=1.1  Score=44.06  Aligned_cols=39  Identities=18%  Similarity=0.232  Sum_probs=28.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .|+++  +|+.+--  .+..++|.+|||+.||||+.||+....
T Consensus       161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~  199 (225)
T PRK10046        161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE  199 (225)
T ss_pred             HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence            35554  5665442  222479999999999999999998764

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=84.25  E-value=2  Score=36.06  Aligned_cols=38  Identities=26%  Similarity=0.347  Sum_probs=26.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH-----HHHHHHHHHhhcCc
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLES-----RALYRLKQSLGGKA  552 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~-----RALkKLR~~l~~~~  552 (561)
                      .++|..|+|+.+|||+.+|.++++     -.+.+|...+..-+
T Consensus        30 ~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG   72 (80)
T PF13744_consen   30 RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG   72 (80)
T ss_dssp             CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence            789999999999999999999985     23566666555443

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=84.20  E-value=10  Score=34.18  Aligned_cols=28  Identities=32%  Similarity=0.432  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .+.|+.|||+.||||..+|.    ++|++|.-
T Consensus        70 pd~tl~Ela~~l~Vs~~ti~----~~Lkrlg~   97 (119)
T PF01710_consen   70 PDATLRELAERLGVSPSTIW----RALKRLGI   97 (119)
T ss_pred             CCcCHHHHHHHcCCCHHHHH----HHHHHcCc
Confidence            78999999999999999986    45666543

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=84.09  E-value=23  Score=36.77  Aligned_cols=87  Identities=22%  Similarity=0.237  Sum_probs=46.9

Q ss_pred             CCCHHHHHHHhC--CCHHHHHHHHHhcCCCccCCCCCCCCCCchhh-hhcccCCCCChh-HHHHHHHHHHHHHHHHhcCC
Q 008556          423 SPDKEDLARRVG--ITVEKLERLIFITRMPLSMQQPVWADQDTTFQ-EITADTGVEIPD-ISVQKQLMRQHVRNLLTLLN  498 (561)
Q Consensus       423 ~Pt~eEIA~~lg--is~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~-d~l~d~~~~~pe-e~le~~e~~e~L~~aL~~L~  498 (561)
                      .+++++||+.++  |+.++|++.+..-...--+. ..+ ++.-... ..+.......+. -.-.+.++.+.-.++|+..|
T Consensus       137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glik-k~~-~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~~~p  214 (271)
T TIGR02147       137 ADDPEELAKRCFPKISAEQVKESLDLLERLGLIK-KNE-DGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALDALP  214 (271)
T ss_pred             CCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCee-ECC-CCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHHHhCC
Confidence            567889999999  99999999876432111110 000 1100000 111111111121 11123344455677889999


Q ss_pred             HHHHHHHHHHhcc
Q 008556          499 PKERCIVRLRFGI  511 (561)
Q Consensus       499 erER~VL~LRyGL  511 (561)
                      +.+|.+=-+-+|+
T Consensus       215 ~~eR~~S~lT~~i  227 (271)
T TIGR02147       215 PSERDVSTVTFGI  227 (271)
T ss_pred             ccccccceeeEec
Confidence            9999977776664

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

>PF12728 HTH_17: Helix-turn-helix domain

Probab=83.50  E-value=1.2  Score=33.64  Aligned_cols=24  Identities=17%  Similarity=0.376  Sum_probs=21.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          517 KSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       517 ~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      +|.+|+|+.||||+.+|+++..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g   25 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQG   25 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            689999999999999999987653

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=83.50  E-value=4.6  Score=35.07  Aligned_cols=49  Identities=18%  Similarity=0.244  Sum_probs=36.2

Q ss_pred             HhcCCHHHHHHHHHH----hccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLR----FGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       494 L~~L~erER~VL~LR----yGL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ...|++++..||..-    ||.. ...+.|..|||+.+|+++++|.    |++++|.+
T Consensus        20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~   73 (95)
T TIGR01610        20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR   73 (95)
T ss_pred             hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            467899999877642    3322 2368999999999999999996    46666654

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=83.26  E-value=2  Score=32.74  Aligned_cols=30  Identities=37%  Similarity=0.508  Sum_probs=23.8

Q ss_pred             CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          513 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       513 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .|..+ |..|||+.+|+|+.+|++    ++++|.+
T Consensus        16 ~~~~l~s~~~la~~~~vs~~tv~~----~l~~L~~   46 (60)
T smart00345       16 PGDKLPSERELAAQLGVSRTTVRE----ALSRLEA   46 (60)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence            34556 899999999999999975    5666654

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=83.26  E-value=1.2  Score=33.85  Aligned_cols=22  Identities=18%  Similarity=0.356  Sum_probs=19.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q 008556          518 SLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       518 Tl~EIAe~LGISrerVRqie~R  539 (561)
                      |++|||+..|||..+|+..++.
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~   22 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNG   22 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTT
T ss_pred             CHHHHHHHHCcCHHHHHHHHhC
Confidence            7899999999999999988764

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>TIGR00498 lexA SOS regulatory protein LexA

Probab=82.99  E-value=2  Score=41.91  Aligned_cols=43  Identities=19%  Similarity=0.285  Sum_probs=33.6

Q ss_pred             hcCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCC-HHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLS-KERVRQLE  537 (561)
Q Consensus       495 ~~L~erER~VL~LRyG--L~d~e~~Tl~EIAe~LGIS-rerVRqie  537 (561)
                      ..|+++|++||..-.-  ..++.+.|.+|||+.+|++ +.+|+.++
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l   47 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHL   47 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHH
Confidence            3589999999887542  2245678999999999998 99997543

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>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=82.88  E-value=3.7  Score=33.44  Aligned_cols=40  Identities=28%  Similarity=0.472  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHhCCC-HHHHHHHHHh
Q 008556          407 SKVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI  446 (561)
Q Consensus       407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis-~e~v~~ll~~  446 (561)
                      .+|-.....+..+.|..||..|||+.+|++ ...|...+..
T Consensus         9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~   49 (65)
T PF01726_consen    9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA   49 (65)
T ss_dssp             HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            344455566677889999999999999997 8888877653

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.

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=82.47  E-value=3.2  Score=32.27  Aligned_cols=39  Identities=21%  Similarity=0.242  Sum_probs=25.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .|++-||--|....-    .++++.|||..+|-|+..|+..++
T Consensus         4 ~Lt~~Eqaqid~m~q----lG~s~~~isr~i~RSr~~Ir~yl~   42 (50)
T PF11427_consen    4 TLTDAEQAQIDVMHQ----LGMSLREISRRIGRSRTCIRRYLK   42 (50)
T ss_dssp             ---HHHHHHHHHHHH----TT--HHHHHHHHT--HHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH----hchhHHHHHHHhCccHHHHHHHhc
Confidence            467777766666555    589999999999999999987653

>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]

Probab=82.26  E-value=35  Score=37.97  Aligned_cols=48  Identities=21%  Similarity=0.439  Sum_probs=33.3

Q ss_pred             HHHHhcCCHHHHHHHH-------HHhcc-cCC----CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          491 RNLLTLLNPKERCIVR-------LRFGI-EDG----KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       491 ~~aL~~L~erER~VL~-------LRyGL-~d~----e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      +.++..|..|++.++.       .-+++ .+|    .++++++||+.+|+..+||++...
T Consensus       293 ~wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~  352 (444)
T COG1508         293 KWLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT  352 (444)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence            3345777777776654       22222 222    579999999999999999987654

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=82.01  E-value=1.4  Score=35.44  Aligned_cols=44  Identities=23%  Similarity=0.344  Sum_probs=32.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .|++.|..|+..-.  .. .+.|..|||+.+|+++.+|+.    ++++|.+
T Consensus         5 gLs~~E~~vy~~Ll--~~-~~~t~~eIa~~l~i~~~~v~~----~L~~L~~   48 (68)
T PF01978_consen    5 GLSENEAKVYLALL--KN-GPATAEEIAEELGISRSTVYR----ALKSLEE   48 (68)
T ss_dssp             CHHHHHHHHHHHHH--HH-CHEEHHHHHHHHTSSHHHHHH----HHHHHHH
T ss_pred             CcCHHHHHHHHHHH--Hc-CCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            46777777775432  11 589999999999999999975    5555543

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=81.87  E-value=2  Score=41.20  Aligned_cols=49  Identities=14%  Similarity=0.090  Sum_probs=41.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEV--GNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EI--Ae~LGISrerVRqie~RALkKLR  545 (561)
                      .|+++|.+||.+-.- +.|..+|.++|  +..++++..+|+.+..+.++||.
T Consensus       156 ~Lt~~E~~il~~l~~-~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~  206 (227)
T TIGR03787       156 DLTVTEFWMVHALAK-HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQ  206 (227)
T ss_pred             cCCHHHHHHHHHHHh-CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhc
Confidence            499999999988652 22355699999  88899999999999999999996

This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=81.86  E-value=2.6  Score=39.45  Aligned_cols=27  Identities=26%  Similarity=0.208  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                      +|+|.+|||++||||..+|....++-.
T Consensus        20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415          20 EGLSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence            699999999999999999998887754

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

Probab=81.66  E-value=19  Score=35.51  Aligned_cols=35  Identities=31%  Similarity=0.635  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHH
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  313 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~  313 (561)
                      ++.++..+|...+|++|+.+|.|+.+|++.+.+..
T Consensus        84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~  118 (224)
T TIGR02479        84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQ  118 (224)
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHH
Confidence            35556677888899999999999999998877653

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.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=81.56  E-value=3.1  Score=39.01  Aligned_cols=41  Identities=15%  Similarity=0.276  Sum_probs=32.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|++.++.||..--.  | ...|+.|||+.+|+|+.+|+.+.++
T Consensus         6 ~lD~~D~~Il~~Lq~--d-~R~s~~eiA~~lglS~~tV~~Ri~r   46 (153)
T PRK11179          6 QIDNLDRGILEALME--N-ARTPYAELAKQFGVSPGTIHVRVEK   46 (153)
T ss_pred             ccCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            377888888876543  2 4689999999999999999865543

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=81.43  E-value=25  Score=27.92  Aligned_cols=23  Identities=35%  Similarity=0.496  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q 008556          423 SPDKEDLARRVGITVEKLERLIF  445 (561)
Q Consensus       423 ~Pt~eEIA~~lgis~e~v~~ll~  445 (561)
                      +++.++||+.+|++...+..++.
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f~   23 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFK   23 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Confidence            36889999999999999988765

>TIGR01764 excise DNA binding domain, excisionase family

Probab=81.33  E-value=1.8  Score=31.66  Aligned_cols=24  Identities=25%  Similarity=0.407  Sum_probs=21.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          517 KSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       517 ~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      +|.+|+|+.||||+.+|+++.+..
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            589999999999999999988654

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>PRK00215 LexA repressor; Validated

Probab=81.21  E-value=2.8  Score=41.03  Aligned_cols=43  Identities=26%  Similarity=0.306  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHHHh--cccCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRF--GIEDGKPKSLSEVGNIFGL-SKERVRQLESR  539 (561)
Q Consensus       497 L~erER~VL~LRy--GL~d~e~~Tl~EIAe~LGI-SrerVRqie~R  539 (561)
                      |+++|++||.+-.  ....+.+.|+.|||+.+|+ ++.+|..++.+
T Consensus         2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~   47 (205)
T PRK00215          2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA   47 (205)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            7889999986543  2334578899999999999 99999766544

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=80.89  E-value=3.1  Score=32.12  Aligned_cols=41  Identities=24%  Similarity=0.416  Sum_probs=28.6

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      |+..|-.||..-+-   ..+.|..+||+.+|+++.+|.++.++-
T Consensus         1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L   41 (59)
T PF01047_consen    1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRL   41 (59)
T ss_dssp             STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence            45555566655443   256999999999999999997665543

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>CHL00148 orf27 Ycf27; Reviewed

Probab=80.76  E-value=2.2  Score=41.08  Aligned_cols=50  Identities=18%  Similarity=0.115  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-------GLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L-------GISrerVRqie~RALkKLR~  546 (561)
                      .|+++|.+|+.+... +.|.++|.+||++.+       +++..+|+.+..+.++||..
T Consensus       161 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~  217 (240)
T CHL00148        161 RLTGMEFSLLELLIS-KSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED  217 (240)
T ss_pred             EcCHHHHHHHHHHHH-CCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence            499999999987653 345789999999999       48999999999999999964

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=80.56  E-value=2.9  Score=40.89  Aligned_cols=34  Identities=26%  Similarity=0.293  Sum_probs=27.3

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          501 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       501 ER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      ++.|..++-     .++|+.+||+.||||+.+|.++.+.
T Consensus       162 ~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        162 EEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             HHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            345666643     5799999999999999999988763

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=80.41  E-value=2  Score=31.11  Aligned_cols=25  Identities=16%  Similarity=0.300  Sum_probs=22.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          517 KSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       517 ~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                      +|..|+|+.+|||+.+|++......
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~   25 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGK   25 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence            5889999999999999999988754

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=80.25  E-value=7  Score=36.76  Aligned_cols=64  Identities=19%  Similarity=0.326  Sum_probs=36.4

Q ss_pred             HHHHHhcCCHHHHHHHHHH----hcccCCCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHHHhhcCch
Q 008556          490 VRNLLTLLNPKERCIVRLR----FGIEDGKPKSLSEVGNIFGLSKERVRQLES--RALYRLKQSLGGKAS  553 (561)
Q Consensus       490 L~~aL~~L~erER~VL~LR----yGL~d~e~~Tl~EIAe~LGISrerVRqie~--RALkKLR~~l~~~~l  553 (561)
                      +..+=..|++.|+....+-    |...+|+.+|+.|||+.+||++.+.-++.+  ++.....+.+....+
T Consensus         4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~   73 (142)
T PF13022_consen    4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFL   73 (142)
T ss_dssp             HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            4455578999998843332    222234789999999999999999998874  334444444443333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	561
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		4e-45
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		4e-45
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		5e-45
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		6e-44
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		5e-43
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		5e-43
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		7e-43
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		2e-26
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		3e-26
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		1e-20
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		1e-17
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		3e-14
1tty_A	87	Solution Structure Of Sigma A Region 4 From Thermot		2e-11
4g6d_A	73	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		7e-11
4g94_A	62	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		9e-11
1rp3_A	239	Cocrystal Structure Of The Flagellar SigmaANTI-Sigm		6e-07
1rio_H	73	Structure Of Bacteriophage Lambda Ci-Ntd In Complex		9e-07
1ku3_A	73	Crystal Structure Of Thermus Aquaticus Rna Polymera		1e-06
1tlh_B	81	T4 Asia Bound To Sigma70 Region 4 Length = 81		2e-06
3t72_q	99	Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna		3e-06
3n97_A	72	Rna Polymerase Alpha C-Terminal Domain (E. Coli) An		3e-06
2p7v_B	68	Crystal Structure Of The Escherichia Coli Regulator		1e-05

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score =  179 bits (454), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 106/320 (33%), Positives = 188/320 (58%), Gaps = 23/320 (7%)
Query: 246 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 302
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 303 AIGLS------------CRDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISL 347
            +G +             ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S 
Sbjct: 59  ILGTARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSF 118
Query: 348 HDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 407
            DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +RTIR+P ++   ++
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETIN 178
Query: 408 KVLEAKRLYIQEGNHSPDKEDLARRV--GITVEKLERLIFITRMPLSMQQPVWADQDTTF 465
           K+    R   QE    P  E++A  +  G   +++E  + I + P+S++ P+  ++D+ +
Sbjct: 179 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFY 238
Query: 466 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 525
            +   D  +  P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  
Sbjct: 239 GDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAY 298
Query: 526 FGLSKERVRQLESRALYRLK 545
           FG+++ER+RQ+E++AL +LK
Sbjct: 299 FGVTRERIRQIENKALRKLK 318

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score =  179 bits (453), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 84/242 (34%), Positives = 155/242 (64%), Gaps = 4/242 (1%)
Query: 308 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 363
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 364 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 423
           KF+ + G +F++YA WW+RQ I ++I   +RTIR+P ++   ++K+    R  +QE    
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 424 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 483
           P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+D+   +   DT +E+P  S   
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT 537
Query: 484 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 543
           + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +
Sbjct: 538 ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 597
Query: 544 LK 545
           L+
Sbjct: 598 LR 599

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

Iteration: 1
 Score =  179 bits (453), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 84/242 (34%), Positives = 155/242 (64%), Gaps = 4/242 (1%)
Query: 308 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 363
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 364 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 423
           KF+ + G +F++YA WW+RQ I ++I   +RTIR+P ++   ++K+    R  +QE    
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 424 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 483
           P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+D+   +   DT +E+P  S   
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT 537
Query: 484 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 543
           + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +
Sbjct: 538 ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRK 597
Query: 544 LK 545
           L+
Sbjct: 598 LR 599

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score =  175 bits (444), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 106/335 (31%), Positives = 188/335 (56%), Gaps = 38/335 (11%)
Query: 246 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 302
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 93  SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 149
Query: 303 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 332
            +G +                            ++LK  LH    G ++R+ LI ANLRL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 333 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 392
           VV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 393 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI--TVEKLERLIFITRMP 450
           +RTIR+P ++   ++K+    R   QE    P  E++A  +G     +++E  + I + P
Sbjct: 270 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 329
Query: 451 LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFG 510
           +S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+ L+ +E  +++LR G
Sbjct: 330 VSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKG 389
Query: 511 IEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           + DG+  +L EVG  FG+++ER+RQ+E++AL +LK
Sbjct: 390 LIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 424

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

Iteration: 1
 Score =  172 bits (435), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 377
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 378 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 435
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 436 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 495
             +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
            L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409

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

Iteration: 1
 Score =  172 bits (435), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 377
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 378 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 435
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 436 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 495
             +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
            L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409

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

Iteration: 1
 Score =  171 bits (434), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 377
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 378 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 435
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 436 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 495
             +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 379
Query: 496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
            L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK
Sbjct: 380 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 429

>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 =  117 bits (292), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 60/150 (40%), Positives = 97/150 (64%), Gaps = 5/150 (3%)
Query: 309 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 365
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 92  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 151
Query: 366 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 425
           + +   +F++YA WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P 
Sbjct: 152 EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPS 211
Query: 426 KEDLARRV--GITVEKLERLIFITRMPLSM 453
            E++A  +  G   +++E  + I + P+S+
Sbjct: 212 YEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241

>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2 Complexed With -10 Promoter Element Ssdna Oligo (Tacaat) Length = 245

Iteration: 1
 Score =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 130/243 (53%), Gaps = 38/243 (15%)
Query: 246 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 302
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 6   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 62
Query: 303 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 332
            +G +                            ++LK  LH    G ++R+ LI ANLRL
Sbjct: 63  ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 122
Query: 333 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 392
           VV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   
Sbjct: 123 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 182
Query: 393 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRV--GITVEKLERLIFITRMP 450
           +RTIR+P ++   ++K+    R   QE    P  E++A  +  G   +++E  + I + P
Sbjct: 183 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 242
Query: 451 LSM 453
           +S+
Sbjct: 243 VSL 245

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 45/89 (50%), Positives = 65/89 (73%), Gaps = 3/89 (3%)
Query: 309 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 365
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 91  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 366 KPQAGCRFASYAYWWVRQTIRKAIFQHSR 394
           + + 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 = 87.8 bits (216), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 34/74 (45%), Positives = 58/74 (78%)
Query: 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380
           ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 381 VRQTIRKAIFQHSR 394
           +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 = 77.0 bits (188), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 117/229 (51%), Gaps = 18/229 (7%)
Query: 321 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 380
           +R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF      +F++YA   
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 381 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 440
           +   I++   +   T+++  ++  + +K+ +AK    +    +P   ++A  +GI+ E +
Sbjct: 89  IIGEIQR-FLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 441 ERLIFITRMPLSMQQPVW---ADQDTTFQEIT-ADTGVEIPDISVQKQLMRQHVRNLLTL 496
                  R+P S+ + V+    D  T   +I  AD       I+++K +           
Sbjct: 148 VLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASWFDKIALKKAIEE--------- 198
Query: 497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           L+ +ER IV LR+     K ++ SEV +  G+S+ ++ +LE + L  +K
Sbjct: 199 LDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK 243

>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga Maritima Length = 87

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 48/64 (75%)
Query: 483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542
           + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +AL 
Sbjct: 5   RMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALR 64
Query: 543 RLKQ 546
           +L+ 
Sbjct: 65  KLRH 68

>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 73

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 48/61 (78%)
Query: 486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           M++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 546 Q 546
Sbjct: 61  H 61

>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 62

Iteration: 1
 Score = 65.5 bits (158), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 48/61 (78%)
Query: 486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           M++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 546 Q 546
Sbjct: 61  H 61

>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma Complex, Sigma-28FLGM Length = 239

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/248 (26%), Positives = 123/248 (49%), Gaps = 31/248 (12%)
Query: 316 HSGNSSREKLINANLRLVVHVA---KQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 372
           +S    RE+LI   L LV  +A   K++    + + DL+  G +GL+K+V+    +   R
Sbjct: 8   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67
Query: 373 FASYAYWWVRQTIRKAIFQH-------SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 425
               A  +++  I+ AI+ +       SR +R  E     + +V+E  +   ++    P 
Sbjct: 68  ----AEAYIKLRIKGAIYDYLRSLDFGSRQVREKER---RIKEVVEKLK---EKLGREPT 117
Query: 426 KEDLARRVGITVEKLERLIFITRMP--LSMQQPVWADQDTTFQE-ITADTGVEIPDISVQ 482
            E++A+ +GI+ E+L + +        LS+++ V+ D    + E I + T VE     V 
Sbjct: 118 DEEVAKELGISTEELFKTLDKINFSYILSLEE-VFRDFARDYSELIPSSTNVE---EEVI 173
Query: 483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 542
           K+ + + V+  ++ L  +E+ +++L F  E+   K   EV  I   S  RV QL+++AL 
Sbjct: 174 KRELTEKVKEAVSKLPEREKLVIQLIF-YEELPAK---EVAKILETSVSRVSQLKAKALE 229
Query: 543 RLKQSLGG 550
           RL++ L  
Sbjct: 230 RLREMLSN 237

>pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With Sigma-Region4 Of Thermus Aquaticus Bound To Dna Length = 73

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 40/52 (76%)
Query: 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK
Sbjct: 8   LSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59

>pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase Sigma Subunit Fragment, Region 4 Length = 73

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 40/52 (76%)
Query: 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           L+ L+ +E  ++++R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK
Sbjct: 8   LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59

>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4 Length = 81

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 2   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 61
Query: 540 ALYRLKQ 546
           AL +L+ 
Sbjct: 62  ALRKLRH 68

>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna Transcription Activation Sub-Complex Length = 99

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 3   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62
Query: 540 ALYRLKQ 546
           AL +L+ 
Sbjct: 63  ALRKLRH 69

>pdb|3N97|A Chain A, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna Length = 72

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 40/53 (75%)
Query: 494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
           L+ L+ +E  ++++R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +L+ 
Sbjct: 8   LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRH 60

>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of Sigma 70, Rsd, In Complex With Sigma 70 Domain 4 Length = 68

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 38/55 (69%)
Query: 492 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
           ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +L+ 
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH 55

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	561
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	2e-65
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	3e-64
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	2e-63
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	3e-57
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	6e-46
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	1e-38
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	1e-22
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	5e-17
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	2e-16
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	1e-14
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	3e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-13
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	3e-09

>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 =  218 bits (556), Expect = 2e-65
 Identities = 101/339 (29%), Positives = 180/339 (53%), Gaps = 32/339 (9%)

Query: 240 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQ---------------------DLI 278
                 +DP+R +L       LLT +EE EL  +++                     +++
Sbjct: 72  IPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVV 131

Query: 279 RLEKEKSKL--QSQFGREPTLIEWAKAIGLSCRDLKSEL-------HSGNSSREKLINAN 329
           R +   S         +E    +  + I    + L  E          G ++R+ LI AN
Sbjct: 132 RAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEAN 191

Query: 330 LRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 389
           LRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI
Sbjct: 192 LRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAI 251

Query: 390 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR--VGITVEKLERLIFIT 447
              +RTIR+P ++   ++K+    R   QE    P  E++A     G   +++E  + I 
Sbjct: 252 ADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIA 311

Query: 448 RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRL 507
           + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+ L+ +E  +++L
Sbjct: 312 QEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKL 371

Query: 508 RFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
           R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 372 RKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKY 410

>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 =  215 bits (549), Expect = 3e-64
 Identities = 92/294 (31%), Positives = 163/294 (55%), Gaps = 6/294 (2%)

Query: 255 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 314
           G +   +        L       I   KEK   ++    +  L    K +    +     
Sbjct: 136 GLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKEL----KRYLHI 191

Query: 315 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 374
              G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F+
Sbjct: 192 AREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 251

Query: 375 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR-- 432
           +YA WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A    
Sbjct: 252 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMG 311

Query: 433 VGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRN 492
            G   +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +  
Sbjct: 312 PGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEK 371

Query: 493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
            L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 372 ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 425

>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 =  217 bits (555), Expect = 2e-63
 Identities = 115/504 (22%), Positives = 226/504 (44%), Gaps = 37/504 (7%)

Query: 66  PLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM 125
            LL    E   ++   D  N    +     +    L +    +E +     DL       
Sbjct: 109 ELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDP 168

Query: 126 KRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTD 185
              ED + + T        E+  D E  D      +           + +P+L   +F +
Sbjct: 169 NAEEDLAPTATHVGSELSQEDLDDDEDED-----EEDGDDDSADDDNSIDPELAREKFAE 223

Query: 186 ISLTSSLGYPLEEVKQFSQPRFLERRSK----------KRKVSKPQVTNHETYNSRKASV 235
           +     +     + K  S     E   K            K     V +      R  + 
Sbjct: 224 LRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQ 283

Query: 236 KKKLSE------GFDRNDPLRLFL-------WGPETRKLLTADEEFELIAQIQDLIRLEK 282
           ++ + +         + + + LF        W      +     E  L    +++ R  +
Sbjct: 284 ERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEK-LHDVSEEVHRALQ 342

Query: 283 EKSKLQSQFGREPT-LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQ 341
           +  +++ + G     + +  + + +     +        ++++++ ANLRLV+ +AK+Y 
Sbjct: 343 KLQQIEEETGLTIEQVKDINRRMSIGEAKARR-------AKKEMVEANLRLVISIAKKYT 395

Query: 342 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 401
            RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I   +RTIR+P +
Sbjct: 396 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 455

Query: 402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 461
           +   ++K+    R  +QE    P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+
Sbjct: 456 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDE 515

Query: 462 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSE 521
           D+   +   DT +E+P  S   + +R    ++L  L  +E  ++R+RFGI+     +L E
Sbjct: 516 DSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEE 575

Query: 522 VGNIFGLSKERVRQLESRALYRLK 545
           VG  F +++ER+RQ+E++AL +L+
Sbjct: 576 VGKQFDVTRERIRQIEAKALRKLR 599

>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 =  190 bits (486), Expect = 3e-57
 Identities = 59/238 (24%), Positives = 117/238 (49%), Gaps = 11/238 (4%)

Query: 309 RDLKSELHSGNSS-REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 367
           ++L      G+   R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF  
Sbjct: 16  KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDL 75

Query: 368 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 427
               +F++YA   +   I++ +     T+++  ++  + +K+ +AK    +    +P   
Sbjct: 76  SYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVT 134

Query: 428 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 487
           ++A  +GI+ E +       R+P S+ + V+ +          D    I D        +
Sbjct: 135 EIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPIT--LLDQ---IADADEASWFDK 189

Query: 488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
             ++  +  L+ +ER IV LR+     K ++ SEV +  G+S+ ++ +LE + L  +K
Sbjct: 190 IALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK 243

>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 =  160 bits (408), Expect = 6e-46
 Identities = 53/238 (22%), Positives = 108/238 (45%), Gaps = 15/238 (6%)

Query: 316 HSGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 372
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 8   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67

Query: 373 FASYAYWWVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLAR 431
             +Y    ++     AI+ + R++      +     ++ E      ++    P  E++A+
Sbjct: 68  AEAYIKLRIKG----AIYDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAK 123

Query: 432 RVGITVEKLERLIFITRMPLSMQ-QPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHV 490
            +GI+ E+L + +        +  + V+ D    + E+   +     +  V K+ + + V
Sbjct: 124 ELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSS--TNVEEEVIKRELTEKV 181

Query: 491 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 548
           +  ++ L  +E+ +++L F  E        EV  I   S  RV QL+++AL RL++ L
Sbjct: 182 KEAVSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLREML 235

>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 =  141 bits (356), Expect = 1e-38
 Identities = 71/242 (29%), Positives = 122/242 (50%), Gaps = 36/242 (14%)

Query: 246 NDPLRLFLWGPETRK--LLTADEEFELIAQI------------------QDLIRLEKEKS 285
           +DP+R +L   E  +  LLT +EE +L  ++                  + +  + + K 
Sbjct: 6   SDPVRQYLH--EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKI 63

Query: 286 KLQSQFGREPTLIEWAKAIGLS------------CRDLKSELHSGNSSREKLINANLRLV 333
              ++  + P L E      +              +        G ++R+ LI ANLRLV
Sbjct: 64  LGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLV 123

Query: 334 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 393
           V +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +
Sbjct: 124 VSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQA 183

Query: 394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR--VGITVEKLERLIFITRMPL 451
           RTIR+P ++   ++K+    R   QE    P  E++A     G   +++E  + I + P+
Sbjct: 184 RTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV 243

Query: 452 SM 453
           S+
Sbjct: 244 SL 245

>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 = 98.4 bits (245), Expect = 1e-22
 Identities = 40/123 (32%), Positives = 69/123 (56%), Gaps = 10/123 (8%)

Query: 279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK-------LINANLR 331
           +L     ++     +   L +  +  GL+   +K      +    K       ++ ANLR
Sbjct: 220 KLHDVSEEVHRALQK---LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLR 276

Query: 332 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 391
           LV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I  
Sbjct: 277 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 336

Query: 392 HSR 394
            +R
Sbjct: 337 QAR 339

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Length = 87

 Score = 75.1 bits (185), Expect = 5e-17
 Identities = 28/66 (42%), Positives = 48/66 (72%)

Query: 480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539
              + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +
Sbjct: 2   EAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVK 61

Query: 540 ALYRLK 545
           AL +L+
Sbjct: 62  ALRKLR 67

>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 Length = 99

 Score = 74.0 bits (182), Expect = 2e-16
 Identities = 23/66 (34%), Positives = 42/66 (63%)

Query: 480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 539
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 3   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62

Query: 540 ALYRLK 545
           AL +L+
Sbjct: 63  ALRKLR 68

>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 Length = 68

 Score = 67.7 bits (166), Expect = 1e-14
 Identities = 21/54 (38%), Positives = 38/54 (70%)

Query: 492 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +L+
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 54

>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* Length = 73

 Score = 67.0 bits (164), Expect = 3e-14
 Identities = 22/59 (37%), Positives = 42/59 (71%)

Query: 488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
           + +   L+ L+ +E  ++++R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 60

>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 = 73.0 bits (178), Expect = 1e-13
 Identities = 94/556 (16%), Positives = 171/556 (30%), Gaps = 147/556 (26%)

Query: 39  VASVPTSSVARHFPTSVL---LQEQRDEYRPLLH-MFKEDKTSQATSDSRNIETEAFF-- 92
                  +V+R  P   L   L E R     L+  +    KT  A     + + +     
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182

Query: 93  ------VEEKNSGD--LDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVS----LTMQSL 140
                 ++  NS +  L+ L Q L +Q    P+  + S      +    S    L     
Sbjct: 183 KIFWLNLKNCNSPETVLEML-QKLLYQID--PNWTSRSDHSSNIKLRIHSIQAELRRLLK 239

Query: 141 SNDTEES------V-DAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLT-SSL 192
           S   E        V +A+ ++A  L+ K L  ++    + +   L+ A  T ISL   S+
Sbjct: 240 SKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK-QVTD--FLSAATTTHISLDHHSM 296

Query: 193 GYPLEEVKQ-FSQPRFLERRSKK--RKVSK--PQVTNHETYNSRKASVKKKLSEGFDRND 247
               +EVK      ++L+ R +   R+V    P+           + + + + +G    D
Sbjct: 297 TLTPDEVKSLLL--KYLDCRPQDLPREVLTTNPRRL---------SIIAESIRDGLATWD 345

Query: 248 PLRLFLWGPETRKL---LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTL-IEWAKA 303
             +       T  +   L   E  E       L       + + +       L + W   
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS-AHIPTI-----LLSLIWFDV 399

Query: 304 IGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKS-- 361
           I      + ++LH     +  L+           KQ +   IS+  +  E  + L     
Sbjct: 400 IKSDVMVVVNKLH-----KYSLVE----------KQPKESTISIPSIYLELKVKLENEYA 444

Query: 362 -----VEKFK-PQAGCRFA-------SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSK 408
                V+ +  P+              Y Y          I  H + I  PE   TL   
Sbjct: 445 LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH--------IGHHLKNIEHPER-MTLFRM 495

Query: 409 V------LEAK-RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 461
           V      LE K R      N S    +        ++  +   +I             D 
Sbjct: 496 VFLDFRFLEQKIRHDSTAWNASGSILNTL----QQLKFYKP--YIC------------DN 537

Query: 462 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSE 521
           D  ++ +       +  I      + +   NL+     K   ++R+    ED        
Sbjct: 538 DPKYERL-------VNAI---LDFLPKIEENLI---CSKYTDLLRIALMAEDE------- 577

Query: 522 VGNIFGLSKERVRQLE 537
                 + +E  +Q++
Sbjct: 578 -----AIFEEAHKQVQ 588

>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 = 55.2 bits (133), Expect = 3e-09
 Identities = 27/205 (13%), Positives = 69/205 (33%), Gaps = 49/205 (23%)

Query: 344 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 403
           G    DL+QEG +GL+K+++ +       F+S+A+  +R+ +  AI + +    +  N  
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDET-KSSFSSFAFLCIRREMISAIRKANTQKHMVLNEA 59

Query: 404 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 463
              + +LE    +  EG++  + +                                    
Sbjct: 60  LKTNAILEDSAYFDDEGHNINNYK------------------------------------ 83

Query: 464 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVG 523
                   +     +  + K+ + +  +      +  E+ ++        G   S  E+ 
Sbjct: 84  -------SSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLI---RG--YSYREIA 131

Query: 524 NIFGLSKERVRQLESRALYRLKQSL 548
            I   + + +     R   + ++ +
Sbjct: 132 TILSKNLKSIDNTIQRIRKKSEEWI 156

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	561
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	100.0
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.98
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.97
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.89
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.88
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.86
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.71
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.64
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.55
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.54
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.33
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.3
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.29
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.27
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	98.99
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	98.93
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.84
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.83
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.7
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.69
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.51
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.49
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.48
3c57_A	95	Two component transcriptional regulatory protein;	98.47
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.36
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.19
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	97.98
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.92
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.86
2q0o_A	236	Probable transcriptional activator protein TRAR; h	97.46
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	97.44
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	97.27
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	97.17
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.91
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.5
1yio_A	208	Response regulatory protein; transcription regulat	96.43
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.29
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.11
3c3w_A	225	Two component transcriptional regulatory protein;	95.8
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	95.06
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	94.8
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	94.25
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	93.37
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	93.28
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	93.24
2oqr_A	230	Sensory transduction protein REGX3; response regul	92.94
2gwr_A	238	DNA-binding response regulator MTRA; two-component	92.88
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	92.77
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	91.71
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	91.49
1ys7_A	233	Transcriptional regulatory protein PRRA; response	91.29
1u78_A	141	TC3 transposase, transposable element TC3 transpos	90.97
3r0j_A	250	Possible two component system response transcript	90.58
3q9s_A	249	DNA-binding response regulator; DNA binding protei	90.57
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	90.51
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	90.49
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	90.44
2hqr_A	223	Putative transcriptional regulator; phosporylation	89.53
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	89.0
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	88.65
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	88.44
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	88.27
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	88.15
3r0a_A	123	Putative transcriptional regulator; structural gen	87.5
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	87.27
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	86.92
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	85.98
3nqo_A	189	MARR-family transcriptional regulator; structural	85.87
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	85.77
1y0u_A	96	Arsenical resistance operon repressor, putative; s	85.77
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	85.48
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	84.5
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	84.25
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	84.22
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	84.17
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	84.16
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	84.12
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	84.0
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	83.95
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	83.9
2w25_A	150	Probable transcriptional regulatory protein; trans	83.78
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	83.6
2gxg_A	146	146AA long hypothetical transcriptional regulator;	83.15
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	83.07
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	82.95
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	82.89
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	82.81
3sqn_A	485	Conserved domain protein; structural genomics, PSI	82.6
2k27_A	159	Paired box protein PAX-8; paired domain, solution	82.48
1sfx_A	109	Conserved hypothetical protein AF2008; structural	82.45
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	82.16
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	82.09
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	81.82
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	81.57
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	81.42
3frw_A	107	Putative Trp repressor protein; structural genomic	81.33
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	81.27
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	81.22
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	81.15
3jth_A	98	Transcription activator HLYU; transcription factor	81.12
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	80.98
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	80.64
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	80.63
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	80.63
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	80.54
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	80.44
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	80.1
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	80.07

>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=6.5e-55  Score=468.70  Aligned_cols=315  Identities=31%  Similarity=0.569  Sum_probs=284.3

Q ss_pred             CCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHhhhhCCCCcHHHHHH---
Q 008556          244 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAK---  302 (561)
Q Consensus       244 ~~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~------------------~l~~~~g~~pt~~ewA~---  302 (561)
                      ...|+++.||++|+++|+||++||++|+++|+.++.++....                  ......|+.|+..+|+.   
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            356899999999999999999999999999998754432211                  11223567788888743   


Q ss_pred             ---------HccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCch
Q 008556          303 ---------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF  373 (561)
Q Consensus       303 ---------a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rF  373 (561)
                               +++++..+|...+++|..|+++||.+|+++|++||++|.++|.+++|||||||||||+|+++|||.+|++|
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                     23567788999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCCc
Q 008556          374 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPL  451 (561)
Q Consensus       374 STYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~~~  451 (561)
                      +|||+||||+.|.++|++++|++|+|.|+...+++++++.+.+.+.+||.|+.++||+.+|  +++++|..++......+
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  99999999998888899


Q ss_pred             cCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHH
Q 008556          452 SMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE  531 (561)
Q Consensus       452 SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISre  531 (561)
                      |+|.+++++++..+.+++.+....+|++.+....+...|..+|..||++||.||.+||||+||+++|++|||+.||||++
T Consensus       331 SLd~~~~~d~d~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~ereR~VI~LRygL~~~e~~TleEIAe~LgIS~e  410 (438)
T 1l9z_H          331 SLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRE  410 (438)
T ss_pred             ccccccccccchhhhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCCCCHHHHHHHHCcCHH
Confidence            99999887766677888877665678888888888899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH-HHhhcCchhhhhh
Q 008556          532 RVRQLESRALYRLK-QSLGGKASYGYAD  558 (561)
Q Consensus       532 rVRqie~RALkKLR-~~l~~~~l~~yld  558 (561)
                      ||||+++||++||| ..+....+++|++
T Consensus       411 rVRqi~~RAlkKLR~~~~~~~~l~~yl~  438 (438)
T 1l9z_H          411 RIRQIENKALRKLKYHESRTRKLRDFLE  438 (438)
T ss_pred             HHHHHHHHHHHHHHHhHhhHHHHHHhhC
Confidence            99999999999999 7888888999874

>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=4.8e-55  Score=469.47  Aligned_cols=311  Identities=33%  Similarity=0.585  Sum_probs=276.3

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhh---------------------hCCCCcHHH----
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQ---------------------FGREPTLIE----  299 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~~~---------------------~g~~pt~~e----  299 (561)
                      ..|+++.||++|+++|+||++||++|+++|+.+..+..   .|...                     .++.|+..+    
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            56899999999999999999999999999998654332   22222                     234555443    


Q ss_pred             -----HHH---HccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCC
Q 008556          300 -----WAK---AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGC  371 (561)
Q Consensus       300 -----wA~---a~g~~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~  371 (561)
                           |+.   ++++++.+|...+++|..|+++||.+|+++|++||++|.++|.+++|||||||||||+|+++|||.+|+
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   356778889999998999999999999999999999999999999999999999999999999999999


Q ss_pred             chhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC--CCHHHHHHHHHhcCC
Q 008556          372 RFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRM  449 (561)
Q Consensus       372 rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~  449 (561)
                      +|+|||+||||+.|.++|++++|+||+|.|+...+++++++.+.+.+.+||.|+.++||+.+|  +++++|..++.....
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  999999999998889


Q ss_pred             CccCCCCCCCCCCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC
Q 008556          450 PLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS  529 (561)
Q Consensus       450 ~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGIS  529 (561)
                      ++|+|.+++++++..+.+++.+....+|++.+....+...|..+|..||++||.||.+||||+||+++|++|||+.||||
T Consensus       314 ~~Sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~L~~aL~~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS  393 (423)
T 2a6h_F          314 PVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVT  393 (423)
T ss_dssp             CEESSCBCSSSSSCBGGGSSCCSSSCCHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTCC-----CHHHHSSSSC
T ss_pred             CcccccccCCCCccchhhhhccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcC
Confidence            99999999877777788888877666888888888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH-HHhhcCchhhhhh
Q 008556          530 KERVRQLESRALYRLK-QSLGGKASYGYAD  558 (561)
Q Consensus       530 rerVRqie~RALkKLR-~~l~~~~l~~yld  558 (561)
                      ++||||++.+|++||| ..+....+++|++
T Consensus       394 ~erVrqi~~rAl~kLR~~~~~~~~l~~~l~  423 (423)
T 2a6h_F          394 RERIRQIENKALRKLKYHESRTRKLRDFLD  423 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSSSSCCC
T ss_pred             HHHHHHHHHHHHHHHHhhhhhhHHHHHhhC
Confidence            9999999999999999 8888888999874

>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=100.00  E-value=6.6e-42  Score=382.91  Aligned_cols=252  Identities=34%  Similarity=0.668  Sum_probs=237.0

Q ss_pred             CHHHHHHHHhhcH-HH---HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHH
Q 008556          307 SCRDLKSELHSGN-SS---REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  382 (561)
Q Consensus       307 ~~~eL~~~l~~G~-~A---re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR  382 (561)
                      +...|+.+++.|+ .|   ++.||..|+++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+||++||||
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            3456777777666 66   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCC
Q 008556          383 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD  462 (561)
Q Consensus       383 qaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~  462 (561)
                      |.|.++++++.+++|+|.|+...+++++++...+.+++||.||.+|||+.+|+++++++.++.....++|++.+++++++
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            99999999999999999999999999999999999999999999999999999999999999999999999999988777


Q ss_pred             chhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          463 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       463 ~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                      ..+.+++.+....+|++.+...++...|..+|..||+++|.||.||||+++++++|++|||+.||||++||+++++||++
T Consensus       517 ~~l~d~i~d~~~~~p~~~~~~~e~~~~l~~aL~~Lp~~er~Vl~Lr~~~~~~e~~s~~EIA~~lgis~~tVk~~~~rAl~  596 (613)
T 3iyd_F          517 SHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR  596 (613)
T ss_dssp             CCGGGSCCCSSSCCHHHHHHHHTTSSSHHHHTTSSCHHHHHHHHHHHTSSSCCCCSTTGGGTTTSSCSSHHHHHHHHHHT
T ss_pred             ccHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            78888888877778998888888888899999999999999999999999889999999999999999999999999999


Q ss_pred             HHHHHhhcCchhhhhh
Q 008556          543 RLKQSLGGKASYGYAD  558 (561)
Q Consensus       543 KLR~~l~~~~l~~yld  558 (561)
                      +||+++....++.|++
T Consensus       597 kLR~~~~~~~l~~~l~  612 (613)
T 3iyd_F          597 KLRHPSRSEVLRSFLD  612 (613)
T ss_dssp             TTTSCSSSCSSTTCC-
T ss_pred             HhhCcchhhHHHHHhc
Confidence            9999999999999986

>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=2.5e-36  Score=302.55  Aligned_cols=209  Identities=33%  Similarity=0.577  Sum_probs=132.2

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHHh--h-----------------------hhCCCCcHH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR-LEKEKSKLQ--S-----------------------QFGREPTLI  298 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~-le~~~~~l~--~-----------------------~~g~~pt~~  298 (561)
                      ..|+++.||++|+++||||++||++|+++|+.++. .+.+.....  .                       ..+.+|+..
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            57999999999999999999999999999999765 333322110  0                       024689999


Q ss_pred             HHHHHccCC----HHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchh
Q 008556          299 EWAKAIGLS----CRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA  374 (561)
Q Consensus       299 ewA~a~g~~----~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFS  374 (561)
                      +||.+.|++    ...|...+++|+.|+++||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+
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            999998885    3456777888999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCCcc
Q 008556          375 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLS  452 (561)
Q Consensus       375 TYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~~~S  452 (561)
                      ||++||||++|.++++++.+.+++|.++...++++.++.+.+...+++.||.+|||+.||  +++.+|...+...+..+|
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  999999999988887776


Q ss_pred             C
Q 008556          453 M  453 (561)
Q Consensus       453 L  453 (561)
                      |
T Consensus       245 l  245 (245)
T 3ugo_A          245 L  245 (245)
T ss_dssp             -
T ss_pred             C
Confidence            5

>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=99.98  E-value=9e-32  Score=261.56  Aligned_cols=222  Identities=22%  Similarity=0.304  Sum_probs=191.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccc
Q 008556          319 NSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       319 ~~Are~LI~~nlrLV~sIArrY~---~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~  395 (561)
                      ..|++.|+..|.++|+.+|++|.   +++.+++||+|||+++||+++++||+.+|.+|.||+++||++.|.++++++.  
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            46899999999999999999998   6789999999999999999999999999999999999999999999999876  


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCccCCCCCCCCCCchhhhhcccCC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTG  473 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~d~~~~l~d~l~d~~  473 (561)
                       +.|.+.....++++++...+....|+.|+.+++|..+|++++++..++....  ...|++.+..++++.. .+. .++ 
T Consensus        89 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~-~~~-~~~-  164 (239)
T 1rp3_A           89 -FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDY-SEL-IPS-  164 (239)
T ss_dssp             -TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTT-GGG-
T ss_pred             -ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccccCCCccc-ccc-cCC-
Confidence             5678888889999999999999999999999999999999999998876432  2345554332221112 233 222 


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008556          474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  550 (561)
Q Consensus       474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  550 (561)
                      ..+|++.+...+....|..+|..||+++|.||.++|+    +++|++|||+.||||.++|++++++|+++||+.+..
T Consensus       165 ~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l~~  237 (239)
T 1rp3_A          165 STNVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQLKAKALERLREMLSN  237 (239)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHT----SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            3467778888888889999999999999999999998    899999999999999999999999999999998754

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

Probab=99.97  E-value=1.3e-31  Score=260.22  Aligned_cols=217  Identities=26%  Similarity=0.439  Sum_probs=52.8

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++..|++.|+..|.++|+++|++|.++..+++||+|||+++||+++++||+.+|.+|.||+++|+++.+.++++++. .+
T Consensus        25 gd~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~~d~~r~~~-~~  103 (243)
T 1l0o_C           25 GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TV  103 (243)
T ss_dssp             ---------------------------------------------------------------------------CC-CC
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-Cc
Confidence            34589999999999999999999999999999999999999999999999999889999999999999999999887 78


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCC--chhhhhcccCCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQEITADTGV  474 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~--~~l~d~l~d~~~  474 (561)
                      ++|.++....++++++...+.+..++.|+.++++..+|++.+.+...+.......|++.++.++++  .++.+.+     
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~-----  178 (243)
T 1l0o_C          104 KVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQI-----  178 (243)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC---------------------------
T ss_pred             cCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCcccchhhcc-----
Confidence            999999999999999999999999999999999999999999998888776667888877543322  2223322     


Q ss_pred             CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          475 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       475 ~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                        |+..+...+....|..+|..||+++|+||.++|+    +++|++|||+.||||.++|++++++|+++||
T Consensus       179 --~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr  243 (243)
T 1l0o_C          179 --ADADEASWFDKIALKKAIEELDERERLIVYLRYY----KDQTQSEVASRLGISQVQMSRLEKKILQHIK  243 (243)
T ss_dssp             -----------------------------------------------------------------------
T ss_pred             --CcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence              2223344455677899999999999999999998    8999999999999999999999999999997

>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=99.89  E-value=1.3e-22  Score=191.79  Aligned_cols=180  Identities=16%  Similarity=0.180  Sum_probs=136.4

Q ss_pred             HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHH
Q 008556          308 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  386 (561)
Q Consensus       308 ~~eL~~~l~~G-~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~  386 (561)
                      +.+|+..++.| ..|++.|+..|.+.|+.+|++|.+ ..+++|++||+++++|+++++|++..  .|.+|++.++++.+.
T Consensus        10 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~   86 (194)
T 1or7_A           10 DQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAK   86 (194)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHH
Confidence            45566666555 599999999999999999999999 89999999999999999999999875  499999999999999


Q ss_pred             HHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh
Q 008556          387 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  466 (561)
Q Consensus       387 ~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~  466 (561)
                      ++++++.+..+.                            .++.           ....     ..++..      ..  
T Consensus        87 d~~R~~~~~~~~----------------------------~~~~-----------~~~~-----~~~~~~------~~--  114 (194)
T 1or7_A           87 NYLVAQGRRPPS----------------------------SDVD-----------AIEA-----ENFESG------GA--  114 (194)
T ss_dssp             HHHHHHTTCCTH----------------------------HHHH-----------HHHH-----HSCCSS------CC--
T ss_pred             HHHHHHhccCcc----------------------------cccc-----------cccc-----cccccc------cc--
Confidence            999876543211                            0000           0000     000000      00  


Q ss_pred             hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          467 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       467 d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                        +.+.  .+|++.+...+....|..+|..||+++|+||.|+|.    +++|++|||+.||||..+|++++.||+++||+
T Consensus       115 --~~~~--~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~  186 (194)
T 1or7_A          115 --LKEI--SNPENLMLSEELRQIVFRTIESLPEDLRMAITLREL----DGLSYEEIAAIMDCPVGTVRSRIFRAREAIDN  186 (194)
T ss_dssp             ------------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHT----TCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             --ccCC--CChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence              0010  123322333455667889999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhhc
Q 008556          547 SLGG  550 (561)
Q Consensus       547 ~l~~  550 (561)
                      .+..
T Consensus       187 ~l~~  190 (194)
T 1or7_A          187 KVQP  190 (194)
T ss_dssp             HHCC
T ss_pred             HHHH
Confidence            8753

>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=99.86  E-value=2.8e-21  Score=176.56  Aligned_cols=155  Identities=15%  Similarity=0.189  Sum_probs=108.0

Q ss_pred             CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCC
Q 008556          344 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS  423 (561)
Q Consensus       344 g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~  423 (561)
                      |.+++|++|||++++|+++.+||+.+ .+|.||+++++++.+.++++++.+..+.+..                      
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~----------------------   57 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLN----------------------   57 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhH----------------------
Confidence            57899999999999999999999987 6899999999999999999886533222210                      


Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhh----hhcccCCCCChhHHHHHHHHHHHHHHHHh-cCC
Q 008556          424 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ----EITADTGVEIPDISVQKQLMRQHVRNLLT-LLN  498 (561)
Q Consensus       424 Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~----d~l~d~~~~~pee~le~~e~~e~L~~aL~-~L~  498 (561)
                                               ..++.+.+..++....+.    +.+.+ ...+|++.+...+....|..+|. .||
T Consensus        58 -------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~~L~  111 (164)
T 3mzy_A           58 -------------------------EALKTNAILEDSAYFDDEGHNINNYKS-SESNPEEAYLLKEEIEEFKKFSENNFS  111 (164)
T ss_dssp             ----------------------------------------------------------CHHHHHHHHHHHHHHHHHHHSC
T ss_pred             -------------------------HHhhhhhhhccCCCCCcccchhhhhcc-cCCCHHHHHHHHHHHHHHHHHHHhhCC
Confidence                                     001111111111111111    11111 22367777888888889999999 999


Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      +++|.||. +|.    +|+|++|||+.||||..+|++++.||+++||+.+...+
T Consensus       112 ~~~r~v~~-~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~~  160 (164)
T 3mzy_A          112 KFEKEVLT-YLI----RGYSYREIATILSKNLKSIDNTIQRIRKKSEEWIKEEE  160 (164)
T ss_dssp             HHHHHHHH-HHT----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence            99999999 676    89999999999999999999999999999999987543

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

Probab=99.71  E-value=1e-19  Score=168.69  Aligned_cols=143  Identities=11%  Similarity=0.094  Sum_probs=119.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcccccccchh
Q 008556          322 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  401 (561)
Q Consensus       322 re~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~IRlP~~  401 (561)
                      ++.|+..|.+.|+.+|.++.++..+++|++||+++++|+++++|++..  .|.+|++.++++.+.+++++..        
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~--------   72 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGE--------   72 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTS--------
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccC--------
Confidence            567899999999999999999989999999999999999999999763  5999999999999998876421        


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCChhHHH
Q 008556          402 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  481 (561)
Q Consensus       402 ~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~pee~l  481 (561)
                                           ..                             +.+.  +           .         
T Consensus        73 ---------------------~~-----------------------------~~~~--e-----------~---------   80 (157)
T 2lfw_A           73 ---------------------AQ-----------------------------TSQS--D-----------A---------   80 (157)
T ss_dssp             ---------------------CC-----------------------------CCCC--S-----------C---------
T ss_pred             ---------------------cc-----------------------------cCCc--c-----------h---------
Confidence                                 00                             0000  0           0         


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          482 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       482 e~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                        .+....|..+|..||+++|+||.|+|.    +|+|++|||+.||||..+|++.+.||+++||+.+....
T Consensus        81 --~~~~~~l~~~l~~Lp~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~  145 (157)
T 2lfw_A           81 --EGTEAVARARLARMTPLSRQALLLTAM----EGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRALE  145 (157)
T ss_dssp             --SSSSSTTTTTTTTSCTTHHHHHTTTSS----SCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSCCC
T ss_pred             --HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence              001124667899999999999999998    89999999999999999999999999999999886543

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.64  E-value=2.4e-16  Score=163.96  Aligned_cols=85  Identities=41%  Similarity=0.902  Sum_probs=76.8

Q ss_pred             HHHHHHHhhc-H---HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          309 RDLKSELHSG-N---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       309 ~eL~~~l~~G-~---~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      ..|..+++.| .   .|++.||..|+++|+++|++|.+++.+++||+||||||||+++++|++.+|++|+||++|||+|.
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            3455555544 4   79999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcc
Q 008556          385 IRKAIFQHS  393 (561)
Q Consensus       385 I~~~Ir~~s  393 (561)
                      |.++++++.
T Consensus       330 ~~~~lr~~~  338 (339)
T 1sig_A          330 ITRSIADQA  338 (339)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHhc
Confidence            999998865

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

Probab=99.55  E-value=2.9e-15  Score=152.20  Aligned_cols=143  Identities=13%  Similarity=0.040  Sum_probs=118.5

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhccccc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  396 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~sr~I  396 (561)
                      ++..+++.|+..|.+.++.+|++|.++..+.+|++||.|+.+|+..++|++.  ..|.+|++.+++|.+.+++++..   
T Consensus        18 g~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~~---   92 (286)
T 3n0r_A           18 GSEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQLE---   92 (286)
T ss_dssp             --CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC------
T ss_pred             CCcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhccccc---
Confidence            3347999999999999999999999999999999999999999999999975  36999999999998877654210   


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCchhhhhcccCCCCC
Q 008556          397 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  476 (561)
Q Consensus       397 RlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~l~d~~~~~  476 (561)
                                                .                                +  ...         +.   .
T Consensus        93 --------------------------~--------------------------------~--~~~---------~~---~  100 (286)
T 3n0r_A           93 --------------------------V--------------------------------G--HDQ---------GL---H  100 (286)
T ss_dssp             -----------------------------------------------------------C--CCC---------CC---C
T ss_pred             --------------------------c--------------------------------C--CCc---------cc---c
Confidence                                      0                                0  000         00   0


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                               ....|..+|..||+++|+||.|+|.    +++|++|||+.+|+|..+|+....+|+++|+..+.
T Consensus       101 ---------~~~~l~~al~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tVks~l~rA~~~Lr~~l~  160 (286)
T 3n0r_A          101 ---------AGDDAAQRLMRIAPRSRQAFLLTAL----EGFTPTEAAQILDCDFGEVERLIGDAQAEIDAELA  160 (286)
T ss_dssp             ---------TTSHHHHHHHHHSCHHHHHHHHHHT----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCC
T ss_pred             ---------hHHHHHHHHHhCCHHHeeEEEEEee----CCCCHHHHHHHhCcCHHHHHHHHHHHHhhhhccCC
Confidence                     0124788999999999999999998    99999999999999999999999999999987654

>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=99.54  E-value=2.4e-14  Score=124.33  Aligned_cols=80  Identities=29%  Similarity=0.490  Sum_probs=74.6

Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhh
Q 008556          480 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADL  559 (561)
Q Consensus       480 ~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yldl  559 (561)
                      .+...++...|..+|+.||++||+||.+|||++|++++|++|||+.||||+++|++++.+|+++||..+....++.|+..
T Consensus         3 ~~~~~el~~~l~~aL~~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l~~~~~~   82 (99)
T 3t72_q            3 SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSGSSG   82 (99)
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45667788899999999999999999999999988999999999999999999999999999999999999999999763

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

Probab=99.33  E-value=1.5e-12  Score=109.50  Aligned_cols=72  Identities=38%  Similarity=0.713  Sum_probs=66.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhh
Q 008556          488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADL  559 (561)
Q Consensus       488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yldl  559 (561)
                      ..|..+|+.||+++|+||.++|+|++++++|++|||+.||||.++|++++.+|+++||..+....+..|+..
T Consensus        10 ~~l~~~l~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l~~~~~~~~~~~   81 (87)
T 1tty_A           10 EELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLSL   81 (87)
T ss_dssp             SHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            357889999999999999999999988999999999999999999999999999999999988888888754

>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=99.30  E-value=8.4e-13  Score=107.22  Aligned_cols=68  Identities=32%  Similarity=0.627  Sum_probs=55.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH-HHhhcCchhhhh
Q 008556          490 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK-QSLGGKASYGYA  557 (561)
Q Consensus       490 L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR-~~l~~~~l~~yl  557 (561)
                      |..+|+.||++||+||.++|+|+|++++|++|||+.||+|.++|++++.+|+++|| ..+....++.|+
T Consensus         4 l~~~l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   72 (73)
T 1ku3_A            4 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL   72 (73)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTC---------
T ss_pred             HHHHHHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHhhHHHHHHhh
Confidence            45678899999999999999998889999999999999999999999999999999 888888888775

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

Probab=99.29  E-value=1.4e-11  Score=104.33  Aligned_cols=75  Identities=16%  Similarity=0.211  Sum_probs=69.7

Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          474 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       474 ~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      ..+|++.++..+....|..+|..||+++|+||.|+|.    +++|++|||+.||||..+|++++.||+++||+.+...+
T Consensus        15 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~   89 (92)
T 3hug_A           15 EQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYY----RGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELG   89 (92)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHT----SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCchHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            3478888999999999999999999999999999998    89999999999999999999999999999999987654

>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=99.27  E-value=1.8e-12  Score=103.79  Aligned_cols=66  Identities=33%  Similarity=0.614  Sum_probs=61.0

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556          493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  558 (561)
Q Consensus       493 aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld  558 (561)
                      +|+.||++||+||.++|||++.+++|++|||+.||||.++|++++.+|++|||..+....+..|++
T Consensus         2 ~l~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   67 (68)
T 2p7v_B            2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD   67 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTTC
T ss_pred             HHHcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            467899999999999999887789999999999999999999999999999999998888887764

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

Probab=98.99  E-value=6.8e-10  Score=88.20  Aligned_cols=64  Identities=16%  Similarity=0.067  Sum_probs=53.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      ....|..+|..||++++.||.++|.    +++|++|||+.||+|..+|+++.++|+++||..+....+
T Consensus         5 ~~~~l~~~l~~L~~~~r~il~l~~~----~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l~~~~~   68 (70)
T 2o8x_A            5 DLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDALLADAEPDDL   68 (70)
T ss_dssp             HHHHHHTTTTSSCHHHHHHHHHHHT----SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcccC
Confidence            4457888999999999999999998    899999999999999999999999999999998876543

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

Probab=98.93  E-value=2.1e-09  Score=93.27  Aligned_cols=82  Identities=16%  Similarity=0.133  Sum_probs=69.2

Q ss_pred             HHHHHHh-hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHH
Q 008556          310 DLKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  388 (561)
Q Consensus       310 eL~~~l~-~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~  388 (561)
                      .|...+. ++..|++.|+..|.+.++.+|.++ ++..+.+|++||+++.+|+.+.+|++.  ..|.+|++..+++.+.++
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            3444444 455999999999999999999999 888899999999999999999999974  369999999999999999


Q ss_pred             HHhccc
Q 008556          389 IFQHSR  394 (561)
Q Consensus       389 Ir~~sr  394 (561)
                      ++++.+
T Consensus        90 ~R~~~~   95 (112)
T 2o7g_A           90 IRHVRS   95 (112)
T ss_dssp             TC----
T ss_pred             HHHhhc
Confidence            987654

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

Probab=98.84  E-value=4.1e-09  Score=87.33  Aligned_cols=75  Identities=15%  Similarity=0.135  Sum_probs=67.2

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556          317 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  393 (561)
Q Consensus       317 ~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s  393 (561)
                      ++..+++.|+..|.+.++.+|.++.++..+.+|++||+++.+|+.+++|++.  ..|.+|++.++++.+.++++++.
T Consensus         9 g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~   83 (87)
T 1h3l_A            9 ERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ   83 (87)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence            4559999999999999999999999998999999999999999999999975  36999999999999999987654

>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=98.83  E-value=1.3e-08  Score=89.84  Aligned_cols=69  Identities=22%  Similarity=0.202  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          481 VQKQLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       481 le~~e~~e~L~~aL-~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      ++..+....+..++ ..||+++|+||.++|.    +++|++|||+.||||..+|+.+++||+++||..+...++
T Consensus         9 ~e~~~~~~~l~~~l~~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   78 (113)
T 1xsv_A            9 LVKTLRMNYLFDFYQSLLTNKQRNYLELFYL----EDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   78 (113)
T ss_dssp             HHHHHHHHHHHHHHGGGSCHHHHHHHHHHHT----SCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            44455566788999 9999999999999998    899999999999999999999999999999998876544

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

Probab=98.70  E-value=1.4e-11  Score=123.11  Aligned_cols=153  Identities=10%  Similarity=0.044  Sum_probs=109.6

Q ss_pred             HHHHHHhhcH-HHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHH----HHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHH
Q 008556          310 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLL----QEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  384 (561)
Q Consensus       310 eL~~~l~~G~-~Are~LI~~nlrLV~sIArrY~~~g~~~eDLI----QEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  384 (561)
                      .|..+++.++ .+.+.+...+.+++..+.+..........|+.    ||.++.+|+.+..|++..  .|.+|++..+++.
T Consensus        86 ~ll~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~~--~~~~WL~~ia~n~  163 (258)
T 3clo_A           86 CIYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTP--AGNVWLIFCLYSL  163 (258)
T ss_dssp             HHHTTBCHHHHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECT--TSCEEEEEEEEEE
T ss_pred             HHHHhCChHHHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCCC--chHHHHHHHHHHH
Confidence            4556666665 78999999999999999888766667778886    999999999999998654  5888877655543


Q ss_pred             HHHHHHhcccccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCCCCCCch
Q 008556          385 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  464 (561)
Q Consensus       385 I~~~Ir~~sr~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  464 (561)
                      +.++.+...                                                           +...+.....  
T Consensus       164 ~~d~~r~~~-----------------------------------------------------------~~~~~~~~~~--  182 (258)
T 3clo_A          164 SADQRPEQG-----------------------------------------------------------IYATITQMER--  182 (258)
T ss_dssp             CSCCCCCSS-----------------------------------------------------------CCCEEEETTT--
T ss_pred             HcchhhhhH-----------------------------------------------------------HHHHHHhhcc--
Confidence            332211000                                                           0000000000  


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008556          465 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  544 (561)
Q Consensus       465 l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  544 (561)
                       .+...     ..           .+..++..||+++|+||.|++     +|+|.+|||+.||||..+|+.+..||++||
T Consensus       183 -~~~~~-----~~-----------~~~~~~~~L~~~erevl~L~~-----~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL  240 (258)
T 3clo_A          183 -GEVET-----LS-----------LSEEHRNILSEREKEILRCIR-----KGLSSKEIAATLYISVNTVNRHRQNILEKL  240 (258)
T ss_dssp             -TEEEE-----CC-----------CHHHHTTSSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             -ccccc-----ch-----------hhHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence             00000     00           145567899999999999984     799999999999999999999999999999


Q ss_pred             HHH
Q 008556          545 KQS  547 (561)
Q Consensus       545 R~~  547 (561)
                      |..
T Consensus       241 ~~~  243 (258)
T 3clo_A          241 SVG  243 (258)
T ss_dssp             TCS
T ss_pred             cCC
Confidence            864

>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=98.69  E-value=2.5e-08  Score=88.17  Aligned_cols=63  Identities=21%  Similarity=0.212  Sum_probs=57.3

Q ss_pred             HHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          487 RQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       487 ~e~L~~aL-~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      ...+..++ ..||+++++||.++|.    +|+|++|||+.+|||..+|+....+|+++||..+...++
T Consensus        12 ~~~l~~~l~~~L~~~~r~vl~l~y~----~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   75 (113)
T 1s7o_A           12 MNALFEFYAALLTDKQMNYIELYYA----DDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   75 (113)
T ss_dssp             HHHHHHHHGGGSCHHHHHHHHHHHH----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            44677888 8999999999999998    899999999999999999999999999999998876544

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

Probab=98.51  E-value=3.8e-08  Score=83.04  Aligned_cols=59  Identities=20%  Similarity=0.173  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          484 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       484 ~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      ......+..++..|+++|++||.++ .    +|+|.+|||+.||||..+|+.++.++++||+..
T Consensus        17 ~~~~~~l~~~l~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   75 (91)
T 2rnj_A           17 GSHMKKRAELYEMLTEREMEILLLI-A----KGYSNQEIASASHITIKTVKTHVSNILSKLEVQ   75 (91)
T ss_dssp             --------CTGGGCCSHHHHHHHHH-H----TTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            3345568889999999999999995 4    799999999999999999999999999999763

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

Probab=98.49  E-value=1.7e-07  Score=76.11  Aligned_cols=54  Identities=15%  Similarity=0.190  Sum_probs=49.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          488 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       488 e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ..+..++..|+++|++||.++ .    +++|.+|||+.||||..+|+++..++++||+.
T Consensus         8 ~~l~~~l~~L~~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~   61 (79)
T 1x3u_A            8 NDIRARLQTLSERERQVLSAV-V----AGLPNKSIAYDLDISPRTVEVHRANVMAKMKA   61 (79)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHH-T----TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            357788999999999999995 4    78999999999999999999999999999985

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=98.48  E-value=1.1e-07  Score=82.64  Aligned_cols=63  Identities=24%  Similarity=0.209  Sum_probs=54.3

Q ss_pred             HHHHHHHHH-hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          486 MRQHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       486 ~~e~L~~aL-~~L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      ..+.+..++ +.|+++|+.+|.+|||+.+   +.++|++|||+.+|||+.+|.++ +|+|++|...++
T Consensus        24 ~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k   90 (101)
T 1jhg_A           24 QNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELR   90 (101)
T ss_dssp             HTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHH
T ss_pred             CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHH
Confidence            344567777 6799999999999999975   45699999999999999999999 999999887653

>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=98.47  E-value=1.9e-07  Score=79.62  Aligned_cols=59  Identities=20%  Similarity=0.258  Sum_probs=45.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      ....|..++..|+++|++||.++ .    +++|.+|||+.||||..+|+.++.++++||+..-.
T Consensus        17 ~~~~l~~~l~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   75 (95)
T 3c57_A           17 RGSHMQDPLSGLTDQERTLLGLL-S----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERR   75 (95)
T ss_dssp             ----------CCCHHHHHHHHHH-H----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence            34567889999999999999997 4    79999999999999999999999999999986543

>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=98.36  E-value=2.9e-07  Score=76.31  Aligned_cols=55  Identities=16%  Similarity=0.231  Sum_probs=47.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          489 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       489 ~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      .+..++..|+++|++||.++ .    +++|.+|||+.||||..+|+..+.++++||+...
T Consensus        14 ~~~~~~~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~   68 (82)
T 1je8_A           14 TTERDVNQLTPRERDILKLI-A----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKS   68 (82)
T ss_dssp             ---CCGGGSCHHHHHHHHHH-T----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSS
T ss_pred             HHHHHHccCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCC
Confidence            35677899999999999995 4    7899999999999999999999999999997643

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

Probab=98.19  E-value=1.4e-06  Score=69.51  Aligned_cols=53  Identities=25%  Similarity=0.238  Sum_probs=45.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          490 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       490 L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      +...+..|+++|++||.+. .    +++|.+|||+.||+|..+|++...++++||+..
T Consensus         5 ~~~~~~~L~~~e~~il~~~-~----~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~   57 (74)
T 1fse_A            5 EFQSKPLLTKREREVFELL-V----QDKTTKEIASELFISEKTVRNHISNAMQKLGVK   57 (74)
T ss_dssp             ---CCCCCCHHHHHHHHHH-T----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             cCCCCCCCCHHHHHHHHHH-H----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            4456788999999999994 4    789999999999999999999999999999753

>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=97.98  E-value=9.7e-06  Score=68.57  Aligned_cols=49  Identities=20%  Similarity=0.225  Sum_probs=42.9

Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          492 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       492 ~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .....|+++|++||.+.+     +|+|.+|||+.||||..+|+....++++||.
T Consensus        25 ~~~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klg   73 (90)
T 3ulq_B           25 KEQDVLTPRECLILQEVE-----KGFTNQEIADALHLSKRSIEYSLTSIFNKLN   73 (90)
T ss_dssp             ----CCCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             ccccCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            346789999999999987     6899999999999999999999999999985

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

Probab=97.92  E-value=7.6e-06  Score=63.09  Aligned_cols=43  Identities=14%  Similarity=0.227  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ++|++|+.+ +.    +|+|.+|||+.||||..+|+....++++||+.
T Consensus         1 ~re~~vl~l-~~----~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   43 (61)
T 2jpc_A            1 LRERQVLKL-ID----EGYTNHGISEKLHISIKTVETHRMNMMRKLQV   43 (61)
T ss_dssp             CHHHHHHHH-HH----TSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHH-HH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCC
Confidence            479999999 55    79999999999999999999999999999975

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

Probab=97.86  E-value=1.9e-05  Score=68.09  Aligned_cols=47  Identities=21%  Similarity=0.275  Sum_probs=43.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ..|+++|++||.+.+     +++|.+|||+.||||..+|+....++++||.-
T Consensus        33 ~~Lt~re~~Vl~l~~-----~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv   79 (99)
T 1p4w_A           33 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV   79 (99)
T ss_dssp             SSCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            679999999999965     68999999999999999999999999999953

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=97.46  E-value=0.00017  Score=70.42  Aligned_cols=46  Identities=24%  Similarity=0.327  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .|+++|++||.+.+     +|+|.+|||++||||..||+....++++||.-
T Consensus       175 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (236)
T 2q0o_A          175 MLSPREMLCLVWAS-----KGKTASVTANLTGINARTVQHYLDKARAKLDA  220 (236)
T ss_dssp             SCCHHHHHHHHHHH-----TTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            59999999999964     79999999999999999999999999999953

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=97.44  E-value=0.00017  Score=70.30  Aligned_cols=45  Identities=27%  Similarity=0.383  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .|+++|++||.+.+     +|+|.+|||++||||..+|+..+.++++||.
T Consensus       173 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~  217 (234)
T 1l3l_A          173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD  217 (234)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence            59999999999964     7999999999999999999999999999994

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=97.27  E-value=0.0003  Score=69.01  Aligned_cols=46  Identities=20%  Similarity=0.307  Sum_probs=42.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|++|+.+..     +|+|.+|||+.||||..||+..+.++++||.
T Consensus       174 ~~Lt~re~~vl~~~~-----~G~s~~eIa~~l~is~~tV~~~~~~~~~kl~  219 (237)
T 3szt_A          174 VRLTARETEMLKWTA-----VGKTYGEIGLILSIDQRTVKFHIVNAMRKLN  219 (237)
T ss_dssp             CCCCHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence            469999999999974     7999999999999999999999999999984

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=97.17  E-value=0.00043  Score=69.27  Aligned_cols=46  Identities=20%  Similarity=0.239  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .|+++|++||.+..     +|+|.+|||++||||..||+..+.++++||.-
T Consensus       197 ~Lt~re~~vl~~~~-----~G~s~~eIA~~l~is~~TV~~~~~~~~~kl~~  242 (265)
T 3qp6_A          197 PLSQREYDIFHWMS-----RGKTNWEIATILNISERTVKFHVANVIRKLNA  242 (265)
T ss_dssp             CCCHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            69999999999985     79999999999999999999999999999853

>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=96.91  E-value=0.0013  Score=47.26  Aligned_cols=40  Identities=20%  Similarity=0.124  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|++.++..+...|.    +++|..|||+.||||+.+|+.++.+
T Consensus         5 ~l~~~~~~~i~~~~~----~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMKL----LNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            478888866656565    6899999999999999999987654

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.50  E-value=0.0055  Score=53.00  Aligned_cols=46  Identities=17%  Similarity=0.147  Sum_probs=42.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .+++.-..|-.++|.    +|+|..|||+.||||+.+|.+++.+|...+.
T Consensus        18 ~~~~~~~~~A~lyYv----~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~   63 (101)
T 2w7n_A           18 EVGQQTIEIARGVLV----DGKPQATFATSLGLTRGAVSQAVHRVWAAFE   63 (101)
T ss_dssp             CCCHHHHHHHHHHHT----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            678888899999998    8999999999999999999999999988764

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=96.43  E-value=0.0065  Score=56.53  Aligned_cols=51  Identities=14%  Similarity=0.316  Sum_probs=44.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          490 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       490 L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      +...+..|+++|++|+.+..     +++|.++||+.+|+|..+|+.+..++++||.
T Consensus       136 ~~~~~~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~  186 (208)
T 1yio_A          136 LEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLN  186 (208)
T ss_dssp             HHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhcCHHHHHHHHHHH-----cCCcHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence            34456689999999998864     6799999999999999999999999999985

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

Probab=96.29  E-value=0.0024  Score=47.94  Aligned_cols=39  Identities=15%  Similarity=0.204  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      +++..+.|+.+ |.    .++|..|||+.||||+.+|+.++.+|
T Consensus        17 ~~~~~~~i~~l-~~----~g~s~~eIA~~lgis~~TV~~~l~~a   55 (55)
T 2x48_A           17 EDDLVSVAHEL-AK----MGYTVQQIANALGVSERKVRRYLESC   55 (55)
T ss_dssp             HHHHHHHHHHH-HH----TTCCHHHHHHHHTSCHHHHHHHHTC-
T ss_pred             CHHHHHHHHHH-HH----cCCCHHHHHHHHCcCHHHHHHHHHhC
Confidence            34455666666 44    68999999999999999999887654

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=96.11  E-value=0.0095  Score=55.83  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=42.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|++|+.+-.     +++|.+|||+.+++|..+|+.+..+.++||.
T Consensus       153 ~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~hi~~i~~Kl~  198 (215)
T 1a04_A          153 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMK  198 (215)
T ss_dssp             GGSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            469999999998865     6889999999999999999999999999994

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=95.80  E-value=0.012  Score=55.89  Aligned_cols=46  Identities=22%  Similarity=0.260  Sum_probs=41.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..|+++|++||.+-.     +++|.+|||+.+++|..||+....+.++||.
T Consensus       148 ~~LT~rE~~vL~~l~-----~g~s~~eIa~~l~is~~TV~~hi~~l~~KL~  193 (225)
T 3c3w_A          148 SGLTDQERTLLGLLS-----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLG  193 (225)
T ss_dssp             TTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            469999999998865     6799999999999999999999999999984

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=95.06  E-value=0.02  Score=54.26  Aligned_cols=47  Identities=17%  Similarity=0.197  Sum_probs=42.0

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ...|+++|++|+.+-.     .++|.+|||+.+++|..+|+....+.++||.
T Consensus       157 ~~~Lt~rE~~vL~~l~-----~g~s~~~Ia~~l~~s~~Tv~~~i~~l~~KL~  203 (225)
T 3klo_A          157 YAKLTKREQQIIKLLG-----SGASNIEIADKLFVSENTVKTHLHNVFKKIN  203 (225)
T ss_dssp             HHTSCHHHHHHHHHHT-----TTCCHHHHHHHTTCCHHHHHHHHHHHTTTSC
T ss_pred             cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            3469999999998854     6899999999999999999999999998883

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=94.80  E-value=0.075  Score=50.86  Aligned_cols=55  Identities=22%  Similarity=0.306  Sum_probs=48.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ........+..|++++++|+.+..     .+++.++||..||+|..+|+....++++||.
T Consensus       188 ~~~~~~~~l~~L~~r~~~i~~~~~-----~g~~~~eia~~l~~s~~tv~~~l~~i~~kl~  242 (258)
T 3p7n_A          188 RRERAAEMLKTLSPRQLEVTTLVA-----SGLRNKEVAARLGLSEKTVKMHRGLVMEKLN  242 (258)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhhcCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            344667889999999999999865     5799999999999999999999999999884

>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=94.25  E-value=0.011  Score=65.91  Aligned_cols=33  Identities=30%  Similarity=0.547  Sum_probs=13.0

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHH
Q 008556          245 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDL  277 (561)
Q Consensus       245 ~~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~  277 (561)
                      .+||+++||++|++.||||+++|++|+++|..+
T Consensus        94 ~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g  126 (613)
T 3iyd_F           94 TTDPVRMYMREMGTVELLTREGEIDIAKRIEDG  126 (613)
T ss_dssp             -----------C--------CSSSTTTHHHHHH
T ss_pred             CCCcHHHHHHHhcccccCCchhHHHHHHHHHHh
Confidence            679999999999999999999999999999874

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=93.37  E-value=0.092  Score=42.76  Aligned_cols=44  Identities=20%  Similarity=0.466  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +.++.||.+-.-...|++.|..|||+.+|||+.+|+++    |.+|.+
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~----L~~L~~   57 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRV----LYSLAK   57 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHH----HHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            34566766555544456899999999999999998765    555544

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=93.28  E-value=0.098  Score=48.95  Aligned_cols=50  Identities=20%  Similarity=0.121  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG---LSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG---ISrerVRqie~RALkKLR~  546 (561)
                      .|+++|++||.+-.- +.|+.+|.+|||+.++   +|..+|+....+.++||..
T Consensus       145 ~Lt~rE~~vl~~l~~-~~~~~~s~~~Ia~~l~~~~~s~~tv~~~i~~l~~Kl~~  197 (220)
T 1p2f_A          145 HLPKKEFEILLFLAE-NAGKVVTREKLLETFWEDPVSPRVVDTVIKRIRKAIED  197 (220)
T ss_dssp             CCCHHHHHHHHHHHH-TTTSCEEHHHHHHHHCSSCCCTHHHHHHHHHHHHHHCS
T ss_pred             ecCHHHHHHHHHHHH-CCCceEcHHHHHHHHhCCCCCcchHHHHHHHHHHHHhc
Confidence            599999999987543 2345699999999999   9999999999999999963

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=93.24  E-value=0.043  Score=39.51  Aligned_cols=33  Identities=21%  Similarity=0.296  Sum_probs=25.5

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          502 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       502 R~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      +.|+.+ +.    .+.|..+||+.+|||+.+|..++.+
T Consensus        12 ~~i~~l-~~----~g~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C           12 EQISRL-LE----KGHPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             HHHHHH-HH----TTCCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             HHHHHH-HH----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            345555 43    5699999999999999999887543

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}

Probab=92.94  E-value=0.11  Score=48.94  Aligned_cols=50  Identities=10%  Similarity=0.034  Sum_probs=43.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  546 (561)
                      .|+++|.+||.+-.- +.|+.+|.+|||+.+     ++|..+|+.+..+.++||..
T Consensus       156 ~Lt~rE~~vL~~l~~-~~~~~~s~~~Ia~~lw~~~~~~s~~tv~~hi~~i~~Kl~~  210 (230)
T 2oqr_A          156 TLPLKEFDLLEYLMR-NSGRVLTRGQLIDRVWGADYVGDTKTLDVHVKRLRSKIEA  210 (230)
T ss_dssp             CCCHHHHHHHHHHHH-TTTSCEEHHHHHHHHTSSCCTTHHHHHHHHHHHHHHHHCS
T ss_pred             ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCcCHHHHHHHHHHHHhh
Confidence            599999999987653 334569999999999     99999999999999999853

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=92.88  E-value=0.15  Score=48.61  Aligned_cols=50  Identities=10%  Similarity=-0.049  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  546 (561)
                      .|+++|++||.+-.- +.|..+|.+|||+.+     ++|..+|+....+.++||..
T Consensus       153 ~LT~rE~~vL~~l~~-~~~~~~s~~eIa~~lw~~~~~~s~~tV~~hi~~lr~KL~~  207 (238)
T 2gwr_A          153 SLTPLEFDLLVALAR-KPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKVEK  207 (238)
T ss_dssp             CCCHHHHHHHHHHHH-STTCCBCHHHHHHHHTCCC--CCTHHHHHHHHHHHHHHCS
T ss_pred             ccCHHHHHHHHHHHH-CCCceecHHHHHHHHcCCCCCCCcccHHHHHHHHHHHhcc
Confidence            599999999987653 334569999999999     99999999999999999953

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=92.77  E-value=0.16  Score=41.85  Aligned_cols=43  Identities=21%  Similarity=0.469  Sum_probs=31.4

Q ss_pred             HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          500 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       500 rER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .++.||.+-.....|+..|..|||+.||||+.+|++    +|.+|.+
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~----~L~~Le~   53 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINR----VLYSLAK   53 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHH----HHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            355666555444445789999999999999988865    5666654

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=91.71  E-value=0.13  Score=48.03  Aligned_cols=50  Identities=12%  Similarity=0.056  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  546 (561)
                      .|+++|++||.+-.- +.|..+|.+|||+.++     +|..+|+....+.++||..
T Consensus       151 ~Lt~rE~~vL~~l~~-~~~~~~s~~eIa~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  205 (225)
T 1kgs_A          151 DLTKKEYQILEYLVM-NKNRVVTKEELQEHLWSFDDEVFSDVLRSHIKNLRKKVDK  205 (225)
T ss_dssp             CCCHHHHHHHHHHHH-TTTSCEEHHHHHHHCC-----CHHHHHHHHHHHHHHHHHT
T ss_pred             ecCHHHHHHHHHHHh-CCCcccCHHHHHHHhcCCCCCCCcchHHHHHHHHHHHhhC
Confidence            599999999987542 2235599999999998     9999999999999999964

>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=91.49  E-value=0.035  Score=54.95  Aligned_cols=51  Identities=18%  Similarity=0.266  Sum_probs=0.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHHHH
Q 008556          490 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG--LSKERVRQLESRALYRLK  545 (561)
Q Consensus       490 L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG--ISrerVRqie~RALkKLR  545 (561)
                      +...+..|++.++. |...||    .+.|.+|||+.||  ||.++|+.++.+|++.|.
T Consensus       192 l~e~i~~l~~~~~~-L~~~~~----~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~ls  244 (245)
T 3ugo_A          192 MVETINKLSRTARQ-LQQELG----REPSYEEIAEAMGPGWDAKRVEETLKIAQEPVS  244 (245)
T ss_dssp             ----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHH-HHHHhC----CCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccC
Confidence            45566777777777 445666    7899999999999  999999999999988763

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=91.29  E-value=0.13  Score=48.43  Aligned_cols=50  Identities=10%  Similarity=-0.023  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  546 (561)
                      .|+++|.+||.+-.- +.|..+|.+|||+.++     +|..+|+.+..+.++||..
T Consensus       159 ~Lt~rE~~vL~~l~~-g~~~~~s~~~Ia~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  213 (233)
T 1ys7_A          159 DLTKREFDLLAVLAE-HKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLEA  213 (233)
T ss_dssp             CCCHHHHHHHHHHHH-TTTCCBCHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHC
T ss_pred             ccCHHHHHHHHHHHh-CCCCeEcHHHHHHHhcCcccCCCccCHHHHHHHHHHHhcc
Confidence            599999999987653 2334599999999998     9999999999999999974

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=90.97  E-value=0.27  Score=42.91  Aligned_cols=40  Identities=20%  Similarity=0.124  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|++.++..|...+.    .|+|..+||+.||||+.+|+.+..+
T Consensus         6 ~~s~~~r~~i~~~~~----~G~s~~~ia~~lgis~~Tv~r~~~~   45 (141)
T 1u78_A            6 ALSDTERAQLDVMKL----LNVSLHEMSRKISRSRHCIRVYLKD   45 (141)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHc
Confidence            467777766665555    6799999999999999999988765

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=90.58  E-value=0.38  Score=46.12  Aligned_cols=50  Identities=18%  Similarity=0.130  Sum_probs=43.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  546 (561)
                      .|+++|.+||.+... +.|+..|.++|++.+     +++..+|+.+..+.++||..
T Consensus       176 ~LT~rE~~iL~~l~~-~~~~~~s~~~i~~~lw~~~~~~~~~tv~~~i~~lr~KL~~  230 (250)
T 3r0j_A          176 SLSPTEFTLLRYFVI-NAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDT  230 (250)
T ss_dssp             CCCHHHHHHHHHHHH-TTTCCBCHHHHHHHHTTTSCCSCTHHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHHH-CCCceEcHHHHHHHHcCCCCCCCccCHHHHHHHHHHhhcC
Confidence            599999999988653 446889999999999     78999999999999999964

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=90.57  E-value=0.22  Score=48.25  Aligned_cols=50  Identities=24%  Similarity=0.246  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe-----~LGISrerVRqie~RALkKLR~  546 (561)
                      .|+++|++||.+-.- +.|..+|.+|||+     .++++..+|+....+.++||..
T Consensus       182 ~LT~rE~evL~ll~~-g~~~~~s~~eIa~~l~~~~l~~s~~TV~~hi~~lr~KL~~  236 (249)
T 3q9s_A          182 RLSPKEFDILALLIR-QPGRVYSRQEIGQEIWQGRLPEGSNVVDVHMANLRAKLRD  236 (249)
T ss_dssp             CCCHHHHHHHHHHHH-STTCCCCHHHHHHHHHTTCSCTTCSHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHHH-CCCceEcHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhhc
Confidence            599999999998763 3356799999999     5888999999999999999863

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=90.51  E-value=0.24  Score=43.95  Aligned_cols=35  Identities=9%  Similarity=0.130  Sum_probs=27.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQ  535 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRq  535 (561)
                      ..|..| .+|+.+-.     +++|+.|||+.+|+|..||.+
T Consensus        60 ~aLs~R-~eV~klL~-----~G~syreIA~~~g~S~aTIsR   94 (119)
T 3kor_A           60 QSLSQR-LQVAKMIK-----QGYTYATIEQESGASTATISR   94 (119)
T ss_dssp             HHHHHH-HHHHHHHH-----HTCCHHHHHHHHCCCHHHHHH
T ss_pred             HHHHHH-HHHHHHHH-----cCCCHHHHHHHHCCCHHHHHH
Confidence            345666 67777754     579999999999999999965

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=90.49  E-value=0.42  Score=40.55  Aligned_cols=41  Identities=12%  Similarity=-0.006  Sum_probs=31.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      .++..+|.-+...+.    .++|..+||+.||||+.+|+.++.+.
T Consensus        17 ~~s~~~r~~i~~~~~----~g~s~~~ia~~lgis~~Tv~~w~~~~   57 (128)
T 1pdn_C           17 PLPNNIRLKIVEMAA----DGIRPCVISRQLRVSHGCVSKILNRY   57 (128)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            355555554444444    67999999999999999999988764

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=90.44  E-value=0.24  Score=47.48  Aligned_cols=35  Identities=20%  Similarity=0.196  Sum_probs=29.2

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          502 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       502 R~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                      ..+..+ |.    .|+|..|||+.||||+.+|.+++..|.
T Consensus        15 ~ria~~-y~----~g~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           15 LRLMRM-KN----DGMSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HHHHHH-HH----TTCCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HHHHHH-HH----cCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            345555 65    789999999999999999999988764

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=89.53  E-value=0.11  Score=48.65  Aligned_cols=50  Identities=4%  Similarity=-0.050  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  546 (561)
                      .|+++|++||.+-.- +.|..+|.+|||+.++     +|..+|+....+.++||..
T Consensus       143 ~Lt~rE~~vL~~l~~-~~~~~~s~~~Ia~~l~~~~~~~s~~tv~~~i~~lr~KL~~  197 (223)
T 2hqr_A          143 EVKGKPFEVLTHLAR-HRDQIVSKEQLLDAIWEEPEMVTPNVIEVAINQIRQKMDK  197 (223)
T ss_dssp             CCCSTTTHHHHHHHH-TCSEEEEHHHHHHHHCCSSCSCGGGTHHHHHHHHHHHHHT
T ss_pred             ecCHHHHHHHHHHHh-CCCCcCCHHHHHHHhcCCccCCCCcCHHHHHHHHHHHHhc
Confidence            599999999987652 1224499999999999     9999999999999999974

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=89.00  E-value=0.77  Score=37.78  Aligned_cols=42  Identities=21%  Similarity=0.216  Sum_probs=32.4

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  537 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie  537 (561)
                      ...|++.+..+|...+.  .+.+.|..|||+.+|+|+.+|++++
T Consensus        16 ~~~l~~~~~~~l~~l~~--~~~~~t~~ela~~l~is~~tv~~~l   57 (109)
T 2d1h_A           16 CYKITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVENSL   57 (109)
T ss_dssp             HHTCCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            45789888887755432  1267999999999999999997644

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=88.65  E-value=0.65  Score=41.31  Aligned_cols=42  Identities=12%  Similarity=-0.002  Sum_probs=31.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                      .++..+|.-|...+.    .++|..+||+.||||+.+|+.++.+..
T Consensus        32 ~~s~e~r~~iv~~~~----~G~s~~~iA~~lgis~~TV~rw~~~~~   73 (149)
T 1k78_A           32 PLPDVVRQRIVELAH----QGVRPCDISRQLRVSHGCVSKILGRYY   73 (149)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            355555554444444    579999999999999999999887653

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=88.44  E-value=0.48  Score=44.67  Aligned_cols=42  Identities=17%  Similarity=0.235  Sum_probs=32.9

Q ss_pred             cCCHHHHHHHHHHhcc--cCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGI--EDGKPKSLSEVGNIFGLSKERVRQLE  537 (561)
Q Consensus       496 ~L~erER~VL~LRyGL--~d~e~~Tl~EIAe~LGISrerVRqie  537 (561)
                      .|+++|++|+..-..+  ..|.+.|.+|||+.||+|..+|++++
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l   45 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHL   45 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHH
Confidence            5899999999875322  23468999999999999988876543

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=88.27  E-value=0.52  Score=36.98  Aligned_cols=43  Identities=28%  Similarity=0.439  Sum_probs=29.6

Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       498 ~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ++..+.||.+--.  ++.++|..|||+.+|+|+.+|.+    .++.|++
T Consensus         9 ~~~~~~IL~~L~~--~~~~~s~~eLA~~lglsr~tv~~----~l~~L~~   51 (67)
T 2heo_A            9 DNLEQKILQVLSD--DGGPVAIFQLVKKCQVPKKTLNQ----VLYRLKK   51 (67)
T ss_dssp             CHHHHHHHHHHHH--HCSCEEHHHHHHHHCSCHHHHHH----HHHHHHH
T ss_pred             cHHHHHHHHHHHH--cCCCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            4445556654321  23679999999999999888865    5566665

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=88.15  E-value=0.37  Score=39.95  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=21.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          516 PKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       516 ~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      +.|..|||+.||||+.+|++++.+
T Consensus        30 g~sa~eLAk~LgiSk~aVr~~L~~   53 (82)
T 1oyi_A           30 GATAAQLTRQLNMEKREVNKALYD   53 (82)
T ss_dssp             TEEHHHHHHHSSSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            499999999999999999887654

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=87.50  E-value=1.1  Score=39.04  Aligned_cols=49  Identities=8%  Similarity=0.137  Sum_probs=37.3

Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          492 NLLTLLNPKERCIVRLRFGIEDGKP-KSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       492 ~aL~~L~erER~VL~LRyGL~d~e~-~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ...-.|++.+..|+..-..  .+.+ +|..|||+.+|+|+.+|.+    ++++|.+
T Consensus        19 ~~~~gLt~~e~~il~~L~~--~~~~~~t~~eLa~~l~~s~sTV~r----~L~~L~~   68 (123)
T 3r0a_A           19 KCALNLTKADLNVMKSFLN--EPDRWIDTDALSKSLKLDVSTVQR----SVKKLHE   68 (123)
T ss_dssp             HHHHTCCHHHHHHHHHHHH--STTCCEEHHHHHHHHTSCHHHHHH----HHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHH--CCCCCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            4456799999999876553  2234 8999999999999999964    5566654

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=87.27  E-value=0.58  Score=47.41  Aligned_cols=36  Identities=14%  Similarity=0.284  Sum_probs=30.4

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008556          503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  542 (561)
Q Consensus       503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  542 (561)
                      .|..++|.    +++|.+|||+.||||+.+||+.+..+.+
T Consensus        12 ~ia~l~~~----~~~~~~ela~~l~vS~~tIrRdL~~l~~   47 (315)
T 2w48_A           12 KIAQLYYE----QDMTQAQIARELGIYRTTISRLLKRGRE   47 (315)
T ss_dssp             HHHHHHHT----SCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            46677776    7899999999999999999988776644

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=86.92  E-value=1.1  Score=36.76  Aligned_cols=27  Identities=15%  Similarity=0.139  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESRAL  541 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~RAL  541 (561)
                      .+.|..+||+.||||+.+|+++..+..
T Consensus        37 ~g~s~~~iA~~~gIs~sTl~rW~k~~~   63 (87)
T 2elh_A           37 DGESKASVARDIGVPESTLRGWCKNED   63 (87)
T ss_dssp             HTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            358999999999999999999876543

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=85.98  E-value=1.4  Score=39.28  Aligned_cols=41  Identities=12%  Similarity=0.229  Sum_probs=31.8

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ..|++.++.||.+-..   +...|..|||+.+|+|+.+|+++++
T Consensus         5 ~~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~   45 (151)
T 2dbb_A            5 RKLDRVDMQLVKILSE---NSRLTYRELADILNTTRQRIARRID   45 (151)
T ss_dssp             -CCCHHHHHHHHHHHH---CTTCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3588999988875432   2579999999999999999976543

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=85.87  E-value=1.8  Score=40.06  Aligned_cols=53  Identities=11%  Similarity=0.256  Sum_probs=40.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      +...+...+..|++.|..||..-+... +.+.|..+||+.+|+++.+|.+++.+
T Consensus        28 ~~~~~~~~~~~lt~~q~~vL~~L~~~~-~~~~t~~eLa~~l~is~~tvs~~l~~   80 (189)
T 3nqo_A           28 IQIEGDKYFGILTSRQYMTILSILHLP-EEETTLNNIARKMGTSKQNINRLVAN   80 (189)
T ss_dssp             HHHHHHHHHCSSCHHHHHHHHHHHHSC-GGGCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHhcc-CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            344556667779999999988766321 25799999999999999999765443

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=85.77  E-value=2  Score=37.02  Aligned_cols=49  Identities=16%  Similarity=0.247  Sum_probs=38.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          488 QHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       488 e~L~~aL~~L~erER~VL~LRyGL~d~---e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ..|......|++.|+.|..+-..  ..   ..+|..|||+..|+|..+|-+..+
T Consensus        10 ~~i~~~~~~ls~~e~~ia~yil~--~~~~~~~~si~elA~~~~vS~aTv~Rf~k   61 (111)
T 2o3f_A           10 AIIQSMXHXLPPSERKLADYILA--HPHXAIESTVNEISALANSSDAAVIRLCX   61 (111)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHH--CHHHHHTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHhccCCHHHHHHHHHHHH--ChHHHHhcCHHHHHHHHCCCHHHHHHHHH
Confidence            45677788999999998775442  21   369999999999999999987654

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=85.77  E-value=3.7  Score=33.71  Aligned_cols=35  Identities=31%  Similarity=0.382  Sum_probs=27.2

Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008556          498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  537 (561)
Q Consensus       498 ~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie  537 (561)
                      ++....||.+- .    .++|..|||+.+|+|+.+|++.+
T Consensus        30 ~~~r~~Il~~L-~----~~~~~~eLa~~l~is~~tv~~~L   64 (96)
T 1y0u_A           30 NPVRRKILRML-D----KGRSEEEIMQTLSLSKKQLDYHL   64 (96)
T ss_dssp             CHHHHHHHHHH-H----TTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHHH-c----CCCCHHHHHHHHCcCHHHHHHHH
Confidence            45566666654 2    57999999999999999997654

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=85.48  E-value=1.4  Score=39.17  Aligned_cols=40  Identities=23%  Similarity=0.175  Sum_probs=31.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .|++.++.||.+-..  + ...|..|||+.+|+|+.+|+.+++
T Consensus         2 ~ld~~d~~il~~L~~--~-~~~s~~ela~~lg~s~~tv~~~l~   41 (144)
T 2cfx_A            2 KLDQIDLNIIEELKK--D-SRLSMRELGRKIKLSPPSVTERVR   41 (144)
T ss_dssp             CCCHHHHHHHHHHHH--C-SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            378888888875432  2 569999999999999999976543

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=84.50  E-value=1.9  Score=38.50  Aligned_cols=40  Identities=20%  Similarity=0.350  Sum_probs=31.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .|++.++.||.+-..  + ...|..|||+.+|+|+.+|+++++
T Consensus         4 ~ld~~~~~il~~L~~--~-~~~s~~ela~~lg~s~~tv~~~l~   43 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN--D-GKAPLREISKITGLAESTIHERIR   43 (151)
T ss_dssp             CCCHHHHHHHHHHHH--C-TTCCHHHHHHHHCSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            478888888875432  2 479999999999999999976543

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=84.25  E-value=3.1  Score=34.88  Aligned_cols=46  Identities=17%  Similarity=0.187  Sum_probs=32.1

Q ss_pred             HHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          489 HVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       489 ~L~~aL~~L~-erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .+..++..|. +....||.+-..    .++|..|||+.+|+|+.+|+++++
T Consensus        15 ~~~~~~~~l~~~~r~~IL~~L~~----~~~~~~ela~~l~is~stvs~~L~   61 (106)
T 1r1u_A           15 RVTEIFKALGDYNRIRIMELLSV----SEASVGHISHQLNLSQSNVSHQLK   61 (106)
T ss_dssp             HHHHHHHHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445555555 445566665432    568999999999999999976543

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=84.22  E-value=1.8  Score=32.61  Aligned_cols=32  Identities=6%  Similarity=0.182  Sum_probs=26.0

Q ss_pred             CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008556          516 PKS----LSEVGNIFGLSKERVRQLESRALYRLKQSL  548 (561)
Q Consensus       516 ~~T----l~EIAe~LGISrerVRqie~RALkKLR~~l  548 (561)
                      +.|    ..+||..+||++.+|++.... ...++..+
T Consensus        21 g~s~~~~~~~vA~~~gIs~~tl~~W~~~-~~~~~~~~   56 (59)
T 2glo_A           21 DNDCKGNQRATARKYNIHRRQIQKWLQC-ESNLRSSV   56 (59)
T ss_dssp             CTTTTTCHHHHHHHTTSCHHHHHHHHTT-HHHHHHHH
T ss_pred             CCCcchHHHHHHHHHCcCHHHHHHHHHH-HHHHHHHH
Confidence            467    999999999999999999764 46666554

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=84.17  E-value=1.6  Score=35.62  Aligned_cols=32  Identities=16%  Similarity=0.436  Sum_probs=23.6

Q ss_pred             ccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          511 IEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       511 L~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      |..|+..|..+||+.||+++..|.    |+|.+|.+
T Consensus        24 L~~~~~~Ta~~IAkkLg~sK~~vN----r~LY~L~k   55 (75)
T 1sfu_A           24 LNTNDYTTAISLSNRLKINKKKIN----QQLYKLQK   55 (75)
T ss_dssp             SCTTCEECHHHHHHHTTCCHHHHH----HHHHHHHH
T ss_pred             CCCCcchHHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            444466899999999999987775    45555543

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=84.16  E-value=1.6  Score=38.18  Aligned_cols=39  Identities=15%  Similarity=0.358  Sum_probs=29.7

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      |++.++.||..-..   +...|..|||+.+|+|+.+|++.++
T Consensus         2 ld~~~~~il~~L~~---~~~~~~~ela~~lg~s~~tv~~~l~   40 (141)
T 1i1g_A            2 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRKRVK   40 (141)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            66777888774321   2568999999999999999976443

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=84.12  E-value=2  Score=38.39  Aligned_cols=41  Identities=22%  Similarity=0.408  Sum_probs=31.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|++.++.||.+-..   +...|+.|||+.+|+|+.+|++++++
T Consensus         5 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   45 (152)
T 2cg4_A            5 LIDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVEK   45 (152)
T ss_dssp             CCCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888875432   25789999999999999999865443

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=84.00  E-value=1.8  Score=37.55  Aligned_cols=40  Identities=18%  Similarity=0.130  Sum_probs=30.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|++.+..||..-+.   +. .|..|||+.+|+|+.+|++++.+
T Consensus        35 ~lt~~~~~iL~~l~~---~~-~t~~eLa~~l~~s~~tvs~~l~~   74 (146)
T 3tgn_A           35 ALTNTQEHILMLLSE---ES-LTNSELARRLNVSQAAVTKAIKS   74 (146)
T ss_dssp             CCCHHHHHHHHHHTT---CC-CCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CC-CCHHHHHHHHCCCHHHHHHHHHH
Confidence            467777777765543   23 99999999999999999865443

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=83.95  E-value=3.9  Score=35.04  Aligned_cols=52  Identities=12%  Similarity=0.051  Sum_probs=37.9

Q ss_pred             HHHHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          487 RQHVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       487 ~e~L~~aL--~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      ...+...+  ..|++.|..||..-+.- ++.+.|..|||+.+|+++.+|.+++.+
T Consensus        20 ~~~~~~~~~~~~lt~~~~~iL~~l~~~-~~~~~~~~ela~~l~~~~~tvs~~l~~   73 (141)
T 3bro_A           20 STRFDIFAKKYDLTGTQMTIIDYLSRN-KNKEVLQRDLESEFSIKSSTATVLLQR   73 (141)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHT-TTSCCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCCCcchHHHHHHH
Confidence            34455555  35899999888776642 223799999999999999999765443

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=83.90  E-value=1.6  Score=38.10  Aligned_cols=45  Identities=11%  Similarity=0.105  Sum_probs=33.0

Q ss_pred             hcCCHHHHHHHHHHhcc-cCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL-~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      ..|++.+..+|..-+.+ ..+.+.|..+||+.+|+|+.+|++++++
T Consensus         9 ~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~   54 (139)
T 2x4h_A            9 SNLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSH   54 (139)
T ss_dssp             --CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHH
Confidence            46888888777665433 2346899999999999999999765443

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=83.78  E-value=1.7  Score=38.75  Aligned_cols=40  Identities=30%  Similarity=0.300  Sum_probs=31.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .|++.++.||.+-..  + ...|..|||+.+|+|+.+|+++++
T Consensus         4 ~ld~~~~~iL~~L~~--~-~~~s~~ela~~lg~s~~tv~~~l~   43 (150)
T 2w25_A            4 ALDDIDRILVRELAA--D-GRATLSELATRAGLSVSAVQSRVR   43 (150)
T ss_dssp             CCCHHHHHHHHHHHH--C-TTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            488888888875432  2 479999999999999999976543

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=83.60  E-value=1.8  Score=39.18  Aligned_cols=41  Identities=12%  Similarity=0.057  Sum_probs=32.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|++.++.||.+-..  + ...|..|||+.+|+|+.+|++++.+
T Consensus         7 ~ld~~~~~il~~L~~--~-~~~s~~ela~~lg~s~~tv~~~l~~   47 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE--N-GRLTNVELSERVALSPSPCLRRLKQ   47 (162)
T ss_dssp             CCCHHHHHHHHHHHH--C-TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888876432  2 4689999999999999999876443

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=83.15  E-value=3.5  Score=35.60  Aligned_cols=47  Identities=13%  Similarity=0.185  Sum_probs=36.0

Q ss_pred             HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          489 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       489 ~L~~aL--~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .+...+  ..|++.+..||..-+    +.+.|..|||+.+|+|+.+|..++.+
T Consensus        25 ~~~~~~~~~~l~~~~~~iL~~l~----~~~~~~~ela~~l~~s~~tvs~~l~~   73 (146)
T 2gxg_A           25 ELNRRLGELNLSYLDFLVLRATS----DGPKTMAYLANRYFVTQSAITASVDK   73 (146)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHT----TSCBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHh----cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence            344444  358999998887655    26899999999999999999765443

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=83.07  E-value=1.8  Score=39.33  Aligned_cols=39  Identities=15%  Similarity=0.236  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      |++.++.||.+--.   +...|+.|||+.+|+|+.+|+..++
T Consensus         1 lD~~d~~il~~L~~---~~~~s~~~la~~lg~s~~tv~~rl~   39 (162)
T 3i4p_A            1 MDRLDRKILRILQE---DSTLAVADLAKKVGLSTTPCWRRIQ   39 (162)
T ss_dssp             CCHHHHHHHHHHTT---CSCSCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            56777888776432   2578999999999999999986543

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=82.95  E-value=1.9  Score=38.29  Aligned_cols=39  Identities=13%  Similarity=0.126  Sum_probs=29.5

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      |++.++.||.+-.   .+...|..|||+.+|+|+.+|+++++
T Consensus         1 ld~~~~~il~~L~---~~~~~~~~ela~~lg~s~~tv~~~l~   39 (150)
T 2pn6_A            1 MDEIDLRILKILQ---YNAKYSLDEIAREIRIPKATLSYRIK   39 (150)
T ss_dssp             CCHHHHHHHHHHT---TCTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CChHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4667777776532   22479999999999999999976543

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=82.89  E-value=2.7  Score=36.45  Aligned_cols=51  Identities=16%  Similarity=0.251  Sum_probs=36.0

Q ss_pred             HHHHHHHHHhc----CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          486 MRQHVRNLLTL----LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       486 ~~e~L~~aL~~----L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      +...+...+..    |++.|-.||..-+.   ..+.|..|||+.+|+++.+|.+++.+
T Consensus        20 ~~~~~~~~l~~~~~~lt~~~~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~   74 (142)
T 3ech_A           20 VRTRIQSELDCQRLDLTPPDVHVLKLIDE---QRGLNLQDLGRQMCRDKALITRKIRE   74 (142)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHH---TTTCCHHHHHHHHC---CHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCCHHHHHHHHHHHh---CCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence            34456666654    89999988887654   24799999999999999999865544

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=82.81  E-value=2.1  Score=35.30  Aligned_cols=41  Identities=15%  Similarity=0.189  Sum_probs=29.0

Q ss_pred             CCHHHHH-HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          497 LNPKERC-IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       497 L~erER~-VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      .++..+. |+.+...  + .+.|..+||..+|||+.+|+++..+.
T Consensus         6 ys~e~k~~~v~~~~~--~-~g~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            6 YSEEFKRDAVALYEN--S-DGASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCHHHHHHHHHHHTT--G-GGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH--c-CCChHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555554 4444432  1 26899999999999999999987653

>3sqn_A Conserved domain protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MGA family; 2.31A {Enterococcus faecalis}

Probab=82.60  E-value=1.5  Score=47.45  Aligned_cols=106  Identities=15%  Similarity=0.109  Sum_probs=60.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHhcCCCccCCCCCC-CCCCchhhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHH
Q 008556          423 SPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW-ADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKE  501 (561)
Q Consensus       423 ~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~-~d~~~~l~d~l~d~~~~~pee~le~~e~~e~L~~aL~~L~erE  501 (561)
                      ..|..+||+.+|+|...|+.-+..-+..+.-...+. .+.+..    +.........             .....+.+.+
T Consensus        32 ~it~~eLA~~L~VS~RTIr~dI~~In~~L~~~~~I~~~~~Gy~----L~~~~~~~~~-------------~~~~~~~~~e   94 (485)
T 3sqn_A           32 QLTAKRLAAQIQTTERTVFSDLQYIRSQLPADWSIETDSSGIR----LRNQGNAQTN-------------ELWSLFLPQS   94 (485)
T ss_dssp             SCBCGGGHHHHTSCHHHHHHHHHHHHTTCCTTEEEEEETTEEE----EEEC---CTH-------------HHHHHHGGGS
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHhcccCcEEEEcCCEEE----EecCcHHHHH-------------HHHHhcCHHH
Confidence            578999999999999999987765443321000110 011111    1111000110             0112234555


Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          502 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       502 R~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      |....+.+.|.. ++.|+.++|+.+.||+.||.+-+++..+.|++
T Consensus        95 R~~~Il~~LL~~-~~isi~~Lae~l~VS~sTi~~DLk~i~~~L~~  138 (485)
T 3sqn_A           95 ISIQLLKELLFT-KELVTTSFLSTSGVSYETLKRHIKKMNQALRD  138 (485)
T ss_dssp             HHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHHHGG
T ss_pred             HHHHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            655555554443 58999999999999999998776665555543

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=82.48  E-value=0.72  Score=41.61  Aligned_cols=39  Identities=13%  Similarity=0.027  Sum_probs=29.3

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      ++..+|.-|...+-    .++|..+||+.||||+.+|++++.+
T Consensus        26 ~s~e~r~~ii~l~~----~G~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           26 LPEVVRQRIVDLAH----QGVRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             SCHHHHHHHHHHHH----HTCCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            55555544444443    5789999999999999999998765

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=82.45  E-value=1.8  Score=35.33  Aligned_cols=40  Identities=23%  Similarity=0.213  Sum_probs=31.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .|++.+..||..-..   +.+.|..|||+.+|+|+.+|++++.
T Consensus        17 ~l~~~~~~il~~l~~---~~~~s~~ela~~l~is~~tv~~~l~   56 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLK   56 (109)
T ss_dssp             CCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            578888888876432   2579999999999999999976543

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=82.16  E-value=1.2  Score=37.49  Aligned_cols=45  Identities=22%  Similarity=0.341  Sum_probs=33.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .+.+....||...+-  .|+.+|..|||+.+|||+.+|++    ++++|..
T Consensus        15 ~~~~~~l~Il~~l~~--~g~~~s~~eLa~~lgvs~~tV~~----~L~~L~~   59 (110)
T 1q1h_A           15 LLGDDVIDVLRILLD--KGTEMTDEEIANQLNIKVNDVRK----KLNLLEE   59 (110)
T ss_dssp             TSCSTTHHHHHHHHH--HCSCBCHHHHHHTTTSCHHHHHH----HHHHHHH
T ss_pred             HcChHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            345666677765432  34679999999999999999975    6666765

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=82.09  E-value=1.3  Score=37.38  Aligned_cols=38  Identities=18%  Similarity=0.209  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      +|...|+.+...    .+.|..+||+.+|||..||+..++.-
T Consensus         7 ~R~~~I~~~l~~----~~~ti~dlA~~~gVS~~TVsR~L~~~   44 (93)
T 2l0k_A            7 ERTIKIGKYIVE----TKKTVRVIAKEFGVSKSTVHKDLTER   44 (93)
T ss_dssp             HHHHHHHHHHHH----HCCCHHHHHHHHTSCHHHHHHHHTTH
T ss_pred             HHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence            345555555443    34899999999999999999988753

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=81.82  E-value=1.9  Score=34.98  Aligned_cols=45  Identities=27%  Similarity=0.290  Sum_probs=31.0

Q ss_pred             HHHHhcC-CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          491 RNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       491 ~~aL~~L-~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ..++..| ++.+..||.+-   ..+.+.|..|||+.+|+|+.+|++.+.
T Consensus        15 ~~~~~~l~~~~~~~il~~l---~~~~~~s~~ela~~l~is~~tvs~~l~   60 (99)
T 3cuo_A           15 AALLKAMSHPKRLLILCML---SGSPGTSAGELTRITGLSASATSQHLA   60 (99)
T ss_dssp             HHHHHHHCSHHHHHHHHHH---TTCCSEEHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHhCChHHHHHHHHH---HhCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3344444 35566666543   234589999999999999999976543

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

Probab=81.57  E-value=1.7  Score=35.40  Aligned_cols=24  Identities=25%  Similarity=0.320  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .+.|.+|||+.||||..+||..+.
T Consensus        23 ~~psv~EIa~~lgvS~~TVrr~L~   46 (77)
T 2jt1_A           23 APVKTRDIADAAGLSIYQVRLYLE   46 (77)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            578999999999999999986554

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=81.42  E-value=4.1  Score=33.68  Aligned_cols=50  Identities=24%  Similarity=0.269  Sum_probs=32.9

Q ss_pred             HHHHHHhcCCH-HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          489 HVRNLLTLLNP-KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       489 ~L~~aL~~L~e-rER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .+..++..|.. .-..||.+-.   + .++|..||++.+|+|+.+|+++    |++|++
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L~---~-~~~~~~ela~~l~is~~tvs~~----L~~L~~   62 (102)
T 3pqk_A           12 EVANLLKTLSHPVRLMLVCTLV---E-GEFSVGELEQQIGIGQPTLSQQ----LGVLRE   62 (102)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHHH---T-CCBCHHHHHHHHTCCTTHHHHH----HHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH---h-CCCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            34455555554 4444544432   2 4699999999999999999764    455544

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=81.33  E-value=2.3  Score=36.91  Aligned_cols=40  Identities=13%  Similarity=0.228  Sum_probs=29.0

Q ss_pred             cCCHHHHHHHHHHhcccC--CCCCCHHHHHHHhCCCHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIED--GKPKSLSEVGNIFGLSKERVRQ  535 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d--~e~~Tl~EIAe~LGISrerVRq  535 (561)
                      -+++.|+.-|..|+.+-.  .+|+|+.||++.+|+|..+|.+
T Consensus        36 L~T~~E~~alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsR   77 (107)
T 3frw_A           36 VCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISR   77 (107)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHH
Confidence            367777666655544221  1569999999999999999965

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=81.22  E-value=4.7  Score=34.60  Aligned_cols=53  Identities=9%  Similarity=0.131  Sum_probs=39.3

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          486 MRQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       486 ~~e~L~~aL~--~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      +...+...+.  .|++.|..||..-+.- ++++.|..|||+.+|+++.+|.+++.+
T Consensus        16 ~~~~~~~~~~~~~lt~~~~~vL~~l~~~-~~~~~t~~ela~~l~~~~~tvs~~l~~   70 (139)
T 3eco_A           16 MKQKADQKLEQFDITNEQGHTLGYLYAH-QQDGLTQNDIAKALQRTGPTVSNLLRN   70 (139)
T ss_dssp             HHHHHHHHHGGGTCCHHHHHHHHHHHHS-TTTCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHhc-CCCCcCHHHHHHHhCCCcccHHHHHHH
Confidence            3445555553  5899999998876642 225899999999999999999765544

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=81.15  E-value=4.6  Score=34.44  Aligned_cols=50  Identities=14%  Similarity=0.101  Sum_probs=37.2

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          487 RQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       487 ~e~L~~aL~--~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      ...+...+.  .|++.+..||..-+.   +.+.|..|||+.+|+|+.+|.+++.+
T Consensus        15 ~~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~~~~ela~~l~~s~~tvs~~l~~   66 (138)
T 3bpv_A           15 RVFIGRELGHLNLTDAQVACLLRIHR---EPGIKQDELATFFHVDKGTIARTLRR   66 (138)
T ss_dssp             HHHHHHHSGGGTCCHHHHHHHHHHHH---STTCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            334455553  589999888876553   26799999999999999999765443

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=81.12  E-value=4.6  Score=33.06  Aligned_cols=50  Identities=20%  Similarity=0.236  Sum_probs=33.0

Q ss_pred             HHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          489 HVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       489 ~L~~aL~~L~-erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .+..++..|. +....||.+-   .+ .++|..|||+.+|+|+.+|++    .+++|++
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L---~~-~~~~~~ela~~l~is~~tvs~----~L~~L~~   62 (98)
T 3jth_A           12 KAVVLLKAMANERRLQILCML---HN-QELSVGELCAKLQLSQSALSQ----HLAWLRR   62 (98)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHT---TT-SCEEHHHHHHHHTCCHHHHHH----HHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHH---hc-CCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            3445555554 4444555432   23 579999999999999999975    4555554

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=80.98  E-value=2.4  Score=35.35  Aligned_cols=37  Identities=24%  Similarity=0.242  Sum_probs=27.8

Q ss_pred             CHHHHHHHH-HHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          498 NPKERCIVR-LRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       498 ~erER~VL~-LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      +|....||. +.-.    .++|..|||+.+|+|+.+|+++++
T Consensus        26 ~~~Rl~IL~~l~~~----~~~~~~ela~~l~is~stvs~hL~   63 (99)
T 2zkz_A           26 HPMRLKIVNELYKH----KALNVTQIIQILKLPQSTVSQHLC   63 (99)
T ss_dssp             SHHHHHHHHHHHHH----SCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHC----CCcCHHHHHHHHCcCHHHHHHHHH
Confidence            466667773 3222    479999999999999999987654

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=80.64  E-value=5.7  Score=34.98  Aligned_cols=50  Identities=16%  Similarity=0.074  Sum_probs=37.9

Q ss_pred             HHHHHHH---hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          488 QHVRNLL---TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       488 e~L~~aL---~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      ..+...+   ..|++.|..||..-+.   +.+.|..|||+.+|+++.+|.+++.+-
T Consensus        35 ~~~~~~l~~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~L   87 (162)
T 2fa5_A           35 GNIAKVYGDRYGMAIPEWRVITILAL---YPGSSASEVSDRTAMDKVAVSRAVARL   87 (162)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHHH---STTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3444444   3699999998877654   257999999999999999998765443

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=80.63  E-value=3.4  Score=34.57  Aligned_cols=45  Identities=11%  Similarity=0.101  Sum_probs=31.1

Q ss_pred             HHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          490 VRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       490 L~~aL~~L~-erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      +..++..|. +....||.+-.   + .+.|..|||+.+|+|+.+|++++.
T Consensus        11 ~~~~~~~l~~~~r~~IL~~L~---~-~~~~~~ela~~l~is~~tv~~~l~   56 (114)
T 2oqg_A           11 LASVFAALSDETRWEILTELG---R-ADQSASSLATRLPVSRQAIAKHLN   56 (114)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHH---H-SCBCHHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHHH---c-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            444455554 55556665432   2 469999999999999999976544

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=80.63  E-value=3.9  Score=34.70  Aligned_cols=46  Identities=15%  Similarity=0.228  Sum_probs=32.7

Q ss_pred             HHHHHhc-CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          490 VRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       490 L~~aL~~-L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      +..++.. .++.+..||.+-..    .+.|+.|||+.+|+|+.+|.+.+++
T Consensus        22 ~~~~~~~l~~~~~~~il~~L~~----~~~s~~ela~~l~is~stvsr~l~~   68 (119)
T 2lkp_A           22 VASTLQALATPSRLMILTQLRN----GPLPVTDLAEAIGMEQSAVSHQLRV   68 (119)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHHH----CCCCHHHHHHHHSSCHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3344433 35667777766543    4799999999999999999765443

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=80.54  E-value=1.7  Score=35.74  Aligned_cols=44  Identities=11%  Similarity=0.079  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~-d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|+.++..||...+.-. +|.+.|..|||+.+|+++.+|.+++.+
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~   53 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKK   53 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            47888888887654322 234489999999999999999766543

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=80.44  E-value=4.5  Score=34.60  Aligned_cols=41  Identities=7%  Similarity=0.046  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .|++.+..||..-+.   +.+.|..|||+.+|+|+.+|.+++.+
T Consensus        28 ~l~~~~~~iL~~l~~---~~~~~~~ela~~l~is~~~vs~~l~~   68 (142)
T 3bdd_A           28 GISLTRYSILQTLLK---DAPLHQLALQERLQIDRAAVTRHLKL   68 (142)
T ss_dssp             SSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            799999988876543   24799999999999999999765443

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=80.10  E-value=2.6  Score=38.82  Aligned_cols=41  Identities=20%  Similarity=0.195  Sum_probs=31.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ..|++.++.||.+-..  + ...|..|||+.+|+|+.+|+++++
T Consensus        13 ~~ld~~d~~IL~~L~~--~-~~~s~~eLA~~lglS~~tv~~~l~   53 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKK--D-ARLTISELSEQLKKPESTIHFRIK   53 (171)
T ss_dssp             -CCCHHHHHHHHHHHH--C-TTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4578888888776432  2 468999999999999999986543

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=80.07  E-value=1  Score=42.20  Aligned_cols=44  Identities=9%  Similarity=0.098  Sum_probs=31.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCC--CHHHHHHHhCCC-HHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPK--SLSEVGNIFGLS-KERVRQLESR  539 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~--Tl~EIAe~LGIS-rerVRqie~R  539 (561)
                      .|+++|++++..--.+-...++  |.+|+|+.+|++ +.+|++++.+
T Consensus         3 ~lt~~q~~i~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~~   49 (202)
T 1jhf_A            3 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   49 (202)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHHH
Confidence            5888888776543221111356  999999999999 9999988763

---

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	561
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	1e-28
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	1e-27
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	4e-20
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	6e-20
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	4e-16
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	1e-15
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	4e-09
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	5e-07
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	6e-07
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	2e-06
d1or7a1	68	a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escheri	2e-04

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 180

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score =  110 bits (275), Expect = 1e-28
 Identities = 57/179 (31%), Positives = 92/179 (51%), Gaps = 30/179 (16%)

Query: 247 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIR------------------LEKEKSKLQ 288
           DP+R +L       LLT +EE +L  ++++ +                   + + K    
Sbjct: 2   DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGT 61

Query: 289 SQFGREPTLIEWAKAIGLSCRDLKSE------------LHSGNSSREKLINANLRLVVHV 336
           ++  + P L E      +   D K +               G ++R+ LI ANLRLVV +
Sbjct: 62  ARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSI 121

Query: 337 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 395
           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 (278), Expect = 1e-27
 Identities = 46/190 (24%), Positives = 84/190 (44%)

Query: 200 KQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETR 259
           + F Q R + ++      S   + +      R             + + + LF     + 
Sbjct: 142 EVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSD 201

Query: 260 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 319
               A          +     E+    LQ     E       + +    R +        
Sbjct: 202 TWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKAR 261

Query: 320 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 379
            ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA W
Sbjct: 262 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 321

Query: 380 WVRQTIRKAI 389
           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 = 82.6 bits (204), Expect = 4e-20
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 316 HSGNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCR 372
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 6   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 65

Query: 373 FASYAYWWVRQTIRKAI 389
             +Y    ++  I   +
Sbjct: 66  AEAYIKLRIKGAIYDYL 82

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]} Length = 87

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]

 Score = 82.1 bits (203), Expect = 6e-20
 Identities = 30/80 (37%), Positives = 51/80 (63%)

Query: 481 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 540
             + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +A
Sbjct: 3   AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62

Query: 541 LYRLKQSLGGKASYGYADLL 560
           L +L+     K       L+
Sbjct: 63  LRKLRHPSRSKYLKSLLSLM 82

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

 Score = 70.9 bits (174), Expect = 4e-16
 Identities = 22/67 (32%), Positives = 41/67 (61%)

Query: 492 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 551
           ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +L+     +
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 552 ASYGYAD 558
               + D
Sbjct: 61  VLRSFLD 67

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]} Length = 61

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]

 Score = 68.9 bits (169), Expect = 1e-15
 Identities = 22/57 (38%), Positives = 41/57 (71%)

Query: 490 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 546
           +   L+ L+ +E  ++++R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 2   LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 58

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 71

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]

 Score = 51.0 bits (122), Expect = 4e-09
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 536
            +  V K+ + + V+  ++ L  +E+ +++L F     +     EV  I   S  RV QL
Sbjct: 2   VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQL 57

Query: 537 ESRALYRLKQSL 548
           +++AL RL++ L
Sbjct: 58  KAKALERLREML 69

>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 = 45.1 bits (107), Expect = 5e-07
 Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 9/82 (10%)

Query: 393 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MP 450
           SR +R          ++ E      ++    P  E++A+ +GI+ E+L + +        
Sbjct: 2   SRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI 55

Query: 451 LSMQQPVWADQDTTFQEITADT 472
           LS+++  + D    + E+   +
Sbjct: 56  LSLEEV-FRDFARDYSELIPSS 76

>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 = 44.3 bits (105), Expect = 6e-07
 Identities = 10/56 (17%), Positives = 27/56 (48%)

Query: 394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM 449
            T+++  ++  + +K+ +AK    +    +P   ++A  +GI+ E +       R+
Sbjct: 2   GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRL 57

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score = 43.1 bits (102), Expect = 2e-06
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLSM 453
           IR+P ++   ++K+    R   QE    P  E++A  +G     +++E  + I + P+S+
Sbjct: 1   IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 60

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]} Length = 68

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]

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 14/63 (22%), Positives = 22/63 (34%), Gaps = 4/63 (6%)

Query: 486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 545
           +RQ V   +  L    R  + LR  ++     S  E+  I       VR    RA   + 
Sbjct: 8   LRQIVFRTIESLPEDLRMAITLRE-LDG---LSYEEIAAIMDCPVGTVRSRIFRAREAID 63

Query: 546 QSL 548
             +
Sbjct: 64  NKV 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	561
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
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.66
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.63
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.55
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.38
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.2
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.18
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	98.99
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.79
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.79
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.77
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.55
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.32
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.27
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	98.04
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.87
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.81
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.48
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	95.45
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	95.18
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.47
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	94.09
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	91.75
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	91.35
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	90.89
d1hlva1	66	DNA-binding domain of centromere binding protein B	90.68
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.62
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	89.93
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	89.09
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	87.64
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	86.64
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	86.44
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	86.4
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	86.08
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	85.63
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	85.49
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	85.46
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	85.46
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	85.36
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	85.3
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	84.63
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	84.37
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	84.14
d1zyba1	73	Probable transcription regulator BT4300, C-termina	84.07
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	83.1
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	83.1
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	83.04
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	82.87
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	82.54
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	81.86
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	81.44
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	81.43
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	81.35
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	80.95
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	80.54
d1y7ya1	69	Restriction-modification controller protein C.AhdI	80.54
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	80.26
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	80.11

>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=7.4e-34  Score=268.94  Aligned_cols=150  Identities=37%  Similarity=0.638  Sum_probs=122.8

Q ss_pred             ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh------------------hhhCCCCcHHHH-------
Q 008556          246 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ------------------SQFGREPTLIEW-------  300 (561)
Q Consensus       246 ~d~l~~Yl~~i~~~~lLT~eEE~eL~~~i~~~~~le~~~~~l~------------------~~~g~~pt~~ew-------  300 (561)
                      +||+++||++|+++||||+|||++|+++|+.++.+.....+..                  ...+..|...+|       
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            5899999999999999999999999999998765543322221                  112333333333       


Q ss_pred             --HHHccC---CHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhH
Q 008556          301 --AKAIGL---SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAS  375 (561)
Q Consensus       301 --A~a~g~---~~~eL~~~l~~G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFST  375 (561)
                        ......   ..+.+....+.|+.|+++||.+|++||++||++|.+.|++++||||||+||||+|+++|||++|++|+|
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              222222   234566677888999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcccc
Q 008556          376 YAYWWVRQTIRKAIFQHSRT  395 (561)
Q Consensus       376 YA~~wIRqaI~~~Ir~~sr~  395 (561)
                      ||+|||+++|.++|++++|+
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=2.6e-21  Score=197.46  Aligned_cols=75  Identities=44%  Similarity=0.939  Sum_probs=72.2

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhc
Q 008556          318 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  392 (561)
Q Consensus       318 G~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~  392 (561)
                      ...|+++||+.|++||++||++|.++|++++||||+|++||++|+++|||.+|++|+|||+||||++|.++|+++
T Consensus       260 ~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         260 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHHHHHHhCC
Confidence            347999999999999999999999999999999999999999999999999999999999999999999999875

>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=3.9e-19  Score=148.98  Aligned_cols=75  Identities=24%  Similarity=0.377  Sum_probs=69.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhCC---CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHhcc
Q 008556          319 NSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  393 (561)
Q Consensus       319 ~~Are~LI~~nlrLV~sIArrY~~~---g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~s  393 (561)
                      ...+++||..|++||.++|++|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|.+++|+..
T Consensus         9 ~~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~d   86 (87)
T d1rp3a3           9 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD   86 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            3568999999999999999998654   78999999999999999999999999999999999999999999998753

>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=99.66  E-value=2.4e-17  Score=137.77  Aligned_cols=75  Identities=39%  Similarity=0.737  Sum_probs=71.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 008556          486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL  560 (561)
Q Consensus       486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yldll  560 (561)
                      +++.|..+|+.|+++|+.||.+||||++++++|+.|||+.||||+++|||++.+|++|||.......++.|++++
T Consensus         8 l~~~l~~~l~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~kLr~~~~~~~L~~~l~~~   82 (87)
T d1ttya_           8 MREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLSLM   82 (87)
T ss_dssp             CCSHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHHHHT
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHHHhh
Confidence            445788999999999999999999999999999999999999999999999999999999998899999999975

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=99.63  E-value=4.1e-17  Score=130.31  Aligned_cols=66  Identities=33%  Similarity=0.614  Sum_probs=63.2

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008556          493 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  558 (561)
Q Consensus       493 aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l~~yld  558 (561)
                      +|+.|+++|+.||.+||||++++++|++|||+.||||+++|||++.+|++|||+......++.|++
T Consensus         2 ~L~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr~~~~~~~L~~yl~   67 (68)
T d2p7vb1           2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD   67 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTTC
T ss_pred             hhhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHhc
Confidence            468899999999999999999999999999999999999999999999999999999999999986

>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=99.55  E-value=1.1e-15  Score=119.41  Aligned_cols=58  Identities=38%  Similarity=0.726  Sum_probs=54.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          490 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       490 L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      |..+|+.|+++||.||.+||||++++++|++|||+.||||+++|||++.+|++|||+.
T Consensus         2 l~~~L~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR~~   59 (61)
T d1ku3a_           2 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH   59 (61)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcC
Confidence            3457899999999999999999999999999999999999999999999999999974

>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=99.38  E-value=7.7e-13  Score=105.04  Aligned_cols=69  Identities=29%  Similarity=0.418  Sum_probs=65.5

Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          477 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       477 pee~le~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      +++.+...+..+.|..+|+.||+++|+||.++|+    +++|++|||+.||+|.++|++++.||+++||+.+.
T Consensus         2 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~L~   70 (71)
T d1rp3a2           2 VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQLKAKALERLREMLS   70 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHT----SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHh----HhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHcc
Confidence            6777888889999999999999999999999998    89999999999999999999999999999999875

>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=99.18  E-value=3.8e-11  Score=94.72  Aligned_cols=63  Identities=22%  Similarity=0.153  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008556          483 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  549 (561)
Q Consensus       483 ~~e~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  549 (561)
                      .++....|..+|+.||+++|+||.++|.    +++|++|||+.||||.++|++...||+++||..++
T Consensus         5 ~~e~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~   67 (68)
T d1or7a1           5 SEELRQIVFRTIESLPEDLRMAITLREL----DGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQ   67 (68)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHHHHHHHHT----TCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcC
Confidence            3456778999999999999999999999    99999999999999999999999999999999874

>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=98.99  E-value=3.8e-10  Score=87.27  Aligned_cols=58  Identities=26%  Similarity=0.461  Sum_probs=54.9

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCCccC
Q 008556          396 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLSM  453 (561)
Q Consensus       396 IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~~~SL  453 (561)
                      ||||.|+.+.+++++++.+++.+++||+||.+|||+.+|  +++++|..++...+.++||
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            799999999999999999999999999999999999998  5589999999999999886

>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=98.79  E-value=3.3e-09  Score=81.03  Aligned_cols=54  Identities=17%  Similarity=0.244  Sum_probs=51.2

Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhc
Q 008556          394 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT  447 (561)
Q Consensus       394 r~IRlP~~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~  447 (561)
                      ++||+|+|+.+.++|++++.+.+.+++||+||.+|||+.+|+++++|..++...
T Consensus         2 g~IrvPr~~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_           2 GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCEeCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            579999999999999999999999999999999999999999999999988654

>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=98.79  E-value=9.7e-09  Score=87.95  Aligned_cols=55  Identities=24%  Similarity=0.220  Sum_probs=49.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  553 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~l  553 (561)
                      .-||++||+||.+||.    +++|+.|||+.||||+++|+++++||+++||+...+-++
T Consensus        17 ~LLpe~QR~vl~L~~~----e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~ye~kL~l   71 (106)
T d1xsva_          17 SLLTNKQRNYLELFYL----EDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   71 (106)
T ss_dssp             GGSCHHHHHHHHHHHT----SCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HhCCHHHHHHHHHHHH----hCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            3499999999999999    999999999999999999999999999999997554443

>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=98.77  E-value=9.2e-09  Score=88.10  Aligned_cols=54  Identities=24%  Similarity=0.257  Sum_probs=49.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  552 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  552 (561)
                      .-||+++|.||.|+|+    +++|++|||+.||||+++|+.+++||+++||+...+-+
T Consensus        15 ~lLp~~qR~v~~L~y~----~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~e~kL~   68 (106)
T d1s7oa_          15 ALLTDKQMNYIELYYA----DDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLH   68 (106)
T ss_dssp             GGSCHHHHHHHHHHHH----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence            4499999999999999    99999999999999999999999999999998654433

>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=98.55  E-value=4.7e-08  Score=77.68  Aligned_cols=69  Identities=16%  Similarity=0.155  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHH
Q 008556          319 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  389 (561)
Q Consensus       319 ~~Are~LI~~nlrLV~sIArrY~~~g~~~eDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~I  389 (561)
                      ..++++++..|.+.++.+|.++.++..+.+|++||.++.+|+..++|++.  .+|.+|++..+++.+.+++
T Consensus         6 ~~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~   74 (75)
T d1h3la_           6 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSY   74 (75)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHh
Confidence            36799999999999999999999999999999999999999999999964  4699999999999998865

>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=98.32  E-value=5.9e-08  Score=77.94  Aligned_cols=70  Identities=17%  Similarity=0.266  Sum_probs=57.3

Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCccCCCCCCCCCCchhhhhccc
Q 008556          401 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITAD  471 (561)
Q Consensus       401 ~~~~~l~ki~ka~~~l~~e~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~~l~d~l~d  471 (561)
                      .+...++++.++...|.+++||+||.+|||+.|||++++|..++...  ...+|||.++. +++.++.+++++
T Consensus         4 s~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~-d~~~~~~e~lps   75 (77)
T d1rp3a1           4 QVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFR-DFARDYSELIPS   75 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHTTTGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCcc-CCCCchhccCCC
Confidence            34578899999999999999999999999999999999999998653  46789997653 334456666665

>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=98.27  E-value=1.1e-06  Score=69.14  Aligned_cols=55  Identities=13%  Similarity=0.311  Sum_probs=49.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          486 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       486 ~~e~L~~aL~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ..+.+...++.|+|+|++|+.+..     .|+|.+|||..||||..||+....++++||.
T Consensus         2 ~~~~~~~~~~~LT~rE~~vl~~l~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   56 (70)
T d1yioa1           2 TQDQLEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLN   56 (70)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            345678888999999999999876     6999999999999999999999999999983

>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=98.04  E-value=4.2e-06  Score=65.13  Aligned_cols=47  Identities=19%  Similarity=0.301  Sum_probs=43.9

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          494 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       494 L~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      +..|+|+|++|+.+..     +|+|.+|||+.||||..+|++...++++||.
T Consensus         4 l~~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   50 (67)
T d1a04a1           4 VNQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMK   50 (67)
T ss_dssp             GGGSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             cccCCHHHHHHHHHHH-----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence            5689999999999876     6999999999999999999999999999984

>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=97.87  E-value=1.3e-05  Score=61.85  Aligned_cols=45  Identities=27%  Similarity=0.383  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .|+++|++||.+--     +|+|.+|||+.||||..+|+....++++||.
T Consensus         4 ~Lt~rE~~vl~l~~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   48 (65)
T d1l3la1           4 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD   48 (65)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             ccCHHHHHHHHHHH-----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            69999999998875     7999999999999999999999999999984

>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=97.81  E-value=1.7e-05  Score=61.40  Aligned_cols=45  Identities=29%  Similarity=0.378  Sum_probs=41.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .|+++|++|+.+.-     +|+|.+|||+.||+|..+|+....++++||-
T Consensus         4 ~LT~rE~~vl~l~~-----~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~   48 (67)
T d1fsea_           4 LLTKREREVFELLV-----QDKTTKEIASELFISEKTVRNHISNAMQKLG   48 (67)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH-----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            49999999998865     7999999999999999999999999999984

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

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: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=97.48  E-value=7.2e-05  Score=60.90  Aligned_cols=45  Identities=22%  Similarity=0.297  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      .|+++|++|+.+..     .|++.+|||+.||||..+|+....++++||.
T Consensus        22 ~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~   66 (87)
T d1p4wa_          22 RLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG   66 (87)
T ss_dssp             SCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            59999999999987     6999999999999999999999999999984

>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=95.45  E-value=0.012  Score=43.71  Aligned_cols=39  Identities=31%  Similarity=0.479  Sum_probs=34.4

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHHhh
Q 008556          279 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS  317 (561)
Q Consensus       279 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l~~  317 (561)
                      ++.++..+|...+|++||.+|.|+++|++.+++...+..
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            566788899999999999999999999999999876654

>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=95.18  E-value=0.011  Score=45.76  Aligned_cols=43  Identities=16%  Similarity=0.285  Sum_probs=35.7

Q ss_pred             cCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCC-CHHHHHHHHH
Q 008556          496 LLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGL-SKERVRQLES  538 (561)
Q Consensus       496 ~L~erER~VL~L--RyGL~d~e~~Tl~EIAe~LGI-SrerVRqie~  538 (561)
                      .|+++|++||..  .|....|-+-|++|||+.+|+ |..+|+..+.
T Consensus         2 ~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~   47 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   47 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHH
Confidence            589999999876  454455688999999999999 8999987643

>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=94.47  E-value=0.03  Score=43.51  Aligned_cols=38  Identities=39%  Similarity=0.554  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhhhhCCCCcHHHHHHHccCCHHHHHHHH
Q 008556          278 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL  315 (561)
Q Consensus       278 ~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~eL~~~l  315 (561)
                      .+++++...|+..+||+||.+|.|..+||+.+++...+
T Consensus        10 ~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l   47 (77)
T d1rp3a1          10 RRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTL   47 (77)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence            35788999999999999999999999999998887654

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=94.09  E-value=0.034  Score=39.64  Aligned_cols=37  Identities=16%  Similarity=0.251  Sum_probs=30.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL  536 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqi  536 (561)
                      .|++.+.+-++-.+-    .|.|..+||+.||||+.||.+.
T Consensus         5 ~lt~~q~~~a~~l~~----~G~s~~~iA~~~gVSr~TiYry   41 (47)
T d1ijwc_           5 AINKHEQEQISRLLE----KGHPRQQLAIIFGIGVSTLYRY   41 (47)
T ss_dssp             SSCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHhh
Confidence            477777777766665    6899999999999999999765

>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=91.75  E-value=0.2  Score=37.16  Aligned_cols=38  Identities=32%  Similarity=0.567  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHhhhhCCCCcHHHHHHHccC--CHHHHHHHH
Q 008556          278 IRLEKEKSKLQSQFGREPTLIEWAKAIGL--SCRDLKSEL  315 (561)
Q Consensus       278 ~~le~~~~~l~~~~g~~pt~~ewA~a~g~--~~~eL~~~l  315 (561)
                      -++.++..+|...+|++||.+|.|+++|+  +.+.+...+
T Consensus        12 ~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l   51 (60)
T d1ku2a1          12 NKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETL   51 (60)
T ss_dssp             HHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHG
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHH
Confidence            35677889999999999999999999974  566665544

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=91.35  E-value=0.25  Score=36.69  Aligned_cols=40  Identities=20%  Similarity=0.385  Sum_probs=32.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      |++.+++||..--.   +...|+.|||+.+|+|..+|+..+.+
T Consensus         3 lD~~D~~IL~~L~~---~~r~s~~eiA~~l~ls~~~v~~Ri~r   42 (63)
T d2cg4a1           3 IDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVEK   42 (63)
T ss_dssp             CCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            67888888887553   25789999999999999999875543

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=90.89  E-value=0.23  Score=36.92  Aligned_cols=40  Identities=23%  Similarity=0.175  Sum_probs=31.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .|++.++.||..--.  + ...|+.|||+.+|+|+.+|.+++.
T Consensus         2 klD~~D~~IL~~L~~--n-~r~s~~~iA~~lgis~~tv~~Ri~   41 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK--D-SRLSMRELGRKIKLSPPSVTERVR   41 (63)
T ss_dssp             CCCHHHHHHHHHHHH--C-SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            477788888876543  2 578999999999999999986543

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.68  E-value=0.17  Score=38.51  Aligned_cols=43  Identities=9%  Similarity=0.150  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          496 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       496 ~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      .|+..|+.=|..+|-  +|+.++..|||..|||++.+|+.++++-
T Consensus         7 ~LT~~eK~~ii~~~e--~g~k~sq~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           7 QLTFREKSRIIQEVE--ENPDLRKGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             CCCHHHHHHHHHHHH--HCTTSCHHHHHHHHTCCHHHHHHHHHTH
T ss_pred             cCCHHHHHHHHHHHH--cCCcchHHHHHHHhCCChhHHHHHHHHH
Confidence            466666664544443  3456799999999999999999998874

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.62  E-value=0.25  Score=36.35  Aligned_cols=39  Identities=18%  Similarity=0.397  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      |++.++.||.+--.  + ...|+.|||+.+|+|+.+|.+++.
T Consensus         1 lD~~D~kIl~~L~~--n-~r~s~~~lA~~~gls~~~v~~Ri~   39 (60)
T d1i1ga1           1 IDERDKIILEILEK--D-ARTPFTEIAKKLGISETAVRKRVK   39 (60)
T ss_dssp             CCSHHHHHHHHHHH--C-TTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45667788876543  2 567999999999999999987543

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=89.93  E-value=0.15  Score=35.53  Aligned_cols=32  Identities=6%  Similarity=0.207  Sum_probs=26.8

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      +|..|+-     +++.-.+||+.|||++.+|-++++.
T Consensus        10 ~V~~L~~-----~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1          10 AVLNMWQ-----QGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            4666664     7999999999999999999877653

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=89.09  E-value=0.52  Score=34.39  Aligned_cols=39  Identities=18%  Similarity=0.339  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          497 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       497 L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      |++.++.||..--.   +...|+.|||+.+|+|+.+|...++
T Consensus         1 lD~~D~~Il~~L~~---n~r~s~~eiA~~l~ls~~~v~~Ri~   39 (60)
T d2cyya1           1 LDEIDKKIIKILQN---DGKAPLREISKITGLAESTIHERIR   39 (60)
T ss_dssp             CCHHHHHHHHHHHH---CTTCCHHHHHHHHCSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45667777766433   2567999999999999999986543

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.64  E-value=0.26  Score=39.24  Aligned_cols=43  Identities=28%  Similarity=0.277  Sum_probs=34.0

Q ss_pred             cCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhC--CCHHHHHHHHH
Q 008556          496 LLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFG--LSKERVRQLES  538 (561)
Q Consensus       496 ~L~erER~VL~L--RyGL~d~e~~Tl~EIAe~LG--ISrerVRqie~  538 (561)
                      .|++|+++||..  .+.+..|.+-+.++|++.+|  +|..+||..+.
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~   47 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMK   47 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHH
Confidence            489999999875  22355679999999999966  58999998653

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=86.64  E-value=0.49  Score=39.71  Aligned_cols=38  Identities=18%  Similarity=0.174  Sum_probs=28.9

Q ss_pred             CCHHHHH-HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          497 LNPKERC-IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       497 L~erER~-VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      |+...|+ |+.+ |.    ++++..+||+.||||+.+|..++.+
T Consensus        17 Ls~dlR~rIv~~-~~----~G~s~r~iA~~~~VS~~tV~k~l~r   55 (123)
T d1pdnc_          17 LPNNIRLKIVEM-AA----DGIRPCVISRQLRVSHGCVSKILNR   55 (123)
T ss_dssp             CCHHHHHHHHHH-HH----TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH-HH----hcCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4444444 4554 44    6899999999999999999887665

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=86.44  E-value=0.34  Score=37.31  Aligned_cols=28  Identities=25%  Similarity=0.396  Sum_probs=24.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          516 PKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       516 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      ++|.+|||..+|+|+++|.    |++++|++.
T Consensus        30 ~~t~~eiA~~lG~sretvs----r~l~~l~~~   57 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTS----TALNSLIKE   57 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHH----HHHHHHHHT
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            6899999999999999995    677888764

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=86.40  E-value=0.35  Score=35.60  Aligned_cols=25  Identities=12%  Similarity=0.135  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .++|.+|+|+.+|||+.+|+++++.
T Consensus        11 ~gltQ~elA~~lGvs~~tvs~~E~G   35 (62)
T d2ppxa1          11 LKLTQEEFSARYHIPLGTLRDWEQG   35 (62)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence            4699999999999999999999973

>d1nr3a_ d.236.1.1 (A:) DNA-binding protein Tfx {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding protein Tfx
superfamily: DNA-binding protein Tfx
family: DNA-binding protein Tfx
domain: DNA-binding protein Tfx
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=86.08  E-value=0.0069  Score=51.76  Aligned_cols=32  Identities=13%  Similarity=0.280  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +|+|++|||++||.|+..|+.++++|++++++
T Consensus         4 kGltQ~eIA~~LgTSraNIs~IEk~A~eNIek   35 (122)
T d1nr3a_           4 RGWSQKKIARELKTTRQNVSAIERKAMENIEK   35 (122)
T ss_dssp             CSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSS
T ss_pred             ccCCHHHHHHHHCccHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999998875

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.63  E-value=0.34  Score=36.30  Aligned_cols=27  Identities=37%  Similarity=0.506  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          516 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       516 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      ++|.+|||..+|+|+++|.    |.|++|++
T Consensus        29 ~lt~~~lA~~~G~sRetvs----r~L~~l~~   55 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVG----RILKMLED   55 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4899999999999999995    56666665

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.49  E-value=0.43  Score=35.40  Aligned_cols=42  Identities=19%  Similarity=0.364  Sum_probs=30.3

Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          498 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       498 ~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +....+||.+   |.++...|.+|+|+.||||+.+|++.+    ++|++
T Consensus         4 ~~~~~~iL~~---L~~~~~~s~~eLa~~l~vS~~ti~r~i----~~L~~   45 (63)
T d1biaa1           4 NTVPLKLIAL---LANGEFHSGEQLGETLGMSRAAINKHI----QTLRD   45 (63)
T ss_dssp             CHHHHHHHHH---HTTSSCBCHHHHHHHHTSCHHHHHHHH----HHHHH
T ss_pred             cHHHHHHHHH---HHHCCcCCHHHHHHHHCcCHHHHHHHH----HHHHH
Confidence            3445555554   345577899999999999999998654    55654

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=85.46  E-value=0.44  Score=37.49  Aligned_cols=35  Identities=17%  Similarity=0.207  Sum_probs=27.9

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008556          503 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  540 (561)
Q Consensus       503 ~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RA  540 (561)
                      ++|.+..-   ++|+|..+||+.||||..+|+++..+.
T Consensus        13 ~aV~l~~~---~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          13 DAVALYEN---SDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHTT---GGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHH---cCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            46666541   147999999999999999999998765

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=85.46  E-value=1  Score=37.75  Aligned_cols=49  Identities=18%  Similarity=0.194  Sum_probs=37.2

Q ss_pred             HHHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          488 QHVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       488 e~L~~aL--~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      +.+...+  -.|++.+-.|+.+-+. . ++++|..|||+.+|+|+.+|...+.
T Consensus        13 ~~~~~~~~~~Gl~~~~~~i~~~L~~-~-~~plt~~ela~~l~vsk~~vs~~l~   63 (151)
T d1ku9a_          13 ELFSELAKIHGLNKSVGAVYAILYL-S-DKPLTISDIMEELKISKGNVSMSLK   63 (151)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHH-C-SSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHh-C-CCCcCHHHHHHHhCCCcchHHHHHH
Confidence            3344444  3579999999988774 3 3679999999999999999976443

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=85.36  E-value=0.54  Score=36.83  Aligned_cols=49  Identities=16%  Similarity=0.223  Sum_probs=38.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          488 QHVRNLLTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       488 e~L~~aL~~L~erER~VL~LRyGL~d---~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ..|...+..|++.|+.|..+  .+++   -..+|.+|||+..|||..+|-+..+
T Consensus         7 ~~i~~~~~~Ls~~e~~ia~y--il~~~~~~~~~si~~lA~~~~vS~sTi~Rf~k   58 (83)
T d2o3fa1           7 AIIQSMKHKLPPSERKLADY--ILAHPHKAIESTVNEISALANSSDAAVIRLCK   58 (83)
T ss_dssp             HHHHHHGGGSCHHHHHHHHH--HHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHHHH--HHcCHHHHHHccHHHHHHHHCCCHHHHHHHHH
Confidence            45778889999999998754  3332   2478999999999999999976544

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=85.30  E-value=0.42  Score=36.68  Aligned_cols=29  Identities=34%  Similarity=0.491  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      -++|.+|||..+|+|+++|.    |++++|++.
T Consensus        29 ~~lt~~elA~~~g~sretvs----r~l~~l~~~   57 (80)
T d3e5ua1          29 MPLSQKSIGEITGVHHVTVS----RVLASLKRE   57 (80)
T ss_dssp             SCCCHHHHHHHHTCCHHHHH----HHHHHHHHT
T ss_pred             eCCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            46899999999999999995    677777764

>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=84.63  E-value=0.79  Score=34.70  Aligned_cols=40  Identities=20%  Similarity=0.356  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHhCC-CHHHHHHHHHh
Q 008556          407 SKVLEAKRLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFI  446 (561)
Q Consensus       407 ~ki~ka~~~l~~e~gr~Pt~eEIA~~lgi-s~e~v~~ll~~  446 (561)
                      .++-.....+..+.|..|+..|||+.+|+ |...|...+..
T Consensus         8 ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~   48 (71)
T d1jhfa1           8 QEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   48 (71)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            34445556667788999999999999999 78888877654

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.37  E-value=0.61  Score=35.50  Aligned_cols=43  Identities=12%  Similarity=0.108  Sum_probs=37.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-CCCHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-GLSKERVRQLE  537 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~L-GISrerVRqie  537 (561)
                      +.|++.+++|+.+--.-.+.+|.+..||+..| |++...|++..
T Consensus         2 nGLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~ai   45 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAV   45 (69)
T ss_dssp             CCSCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHH
Confidence            36899999999998777777899999999999 89999987643

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=84.14  E-value=0.47  Score=36.32  Aligned_cols=29  Identities=14%  Similarity=0.099  Sum_probs=24.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      -++|.+|||..+|+|+++|.    |++++|++.
T Consensus        28 ~~lt~~eLA~~~G~sretvs----r~L~~l~~~   56 (81)
T d2gaua1          28 IYLSREELATLSNMTVSNAI----RTLSTFVSE   56 (81)
T ss_dssp             CCCCHHHHHHHTTSCHHHHH----HHHHHHHHT
T ss_pred             ecCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            36899999999999999995    677777763

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=84.07  E-value=0.42  Score=36.43  Aligned_cols=28  Identities=7%  Similarity=0.259  Sum_probs=23.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008556          516 PKSLSEVGNIFGLSKERVRQLESRALYRLKQS  547 (561)
Q Consensus       516 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  547 (561)
                      ++|.+|||..+|+|+++|.    |++++|++.
T Consensus        27 ~lt~~elA~~lg~sr~tvs----r~l~~l~~~   54 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNIS----KTLNELQDN   54 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHH----HHHHHHHHT
T ss_pred             ecCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            4799999999999999995    677888763

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=83.10  E-value=2.3  Score=34.96  Aligned_cols=54  Identities=11%  Similarity=0.107  Sum_probs=39.7

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008556          487 RQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  545 (561)
Q Consensus       487 ~e~L~~aL~--~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  545 (561)
                      ...+...+.  .|++.|-.||..-+. .+|.+.|..||++.+|+++.+|..    ++++|-
T Consensus        15 ~~~~~~~l~~~glt~~q~~vL~~l~~-~~~~~it~~ela~~~~~~~~~vs~----~l~~L~   70 (135)
T d3broa1          15 STRFDIFAKKYDLTGTQMTIIDYLSR-NKNKEVLQRDLESEFSIKSSTATV----LLQRME   70 (135)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHH-TTTSCCBHHHHHHHHTCCHHHHHH----HHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH-cCCCCCCHHHHHHHHCcCHhHHHH----HHHHHH
Confidence            334445543  489999999877664 344679999999999999999965    555553

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=83.10  E-value=0.59  Score=36.81  Aligned_cols=42  Identities=17%  Similarity=0.215  Sum_probs=31.7

Q ss_pred             HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH-H----HHHHHHHHhh
Q 008556          504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES-R----ALYRLKQSLG  549 (561)
Q Consensus       504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~-R----ALkKLR~~l~  549 (561)
                      |-.+|--    .++|++++|+.+|||+.+|.++++ +    .+.+|.+.+.
T Consensus        16 i~~~r~~----~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~   62 (89)
T d2o38a1          16 LNAVIDR----ARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLN   62 (89)
T ss_dssp             HHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHH
T ss_pred             HHHHHHH----cCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHH
Confidence            4455555    789999999999999999999997 2    2455555443

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=83.04  E-value=0.64  Score=35.12  Aligned_cols=24  Identities=21%  Similarity=0.342  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .++|..|+|+.||||+.+|.+.+.
T Consensus        13 ~gltQ~elA~~LGvs~~ti~~yE~   36 (67)
T d2auwa1          13 NNLSLTTAAEALGISRRMVSYYRT   36 (67)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Confidence            679999999999999999999876

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=82.87  E-value=0.67  Score=34.58  Aligned_cols=31  Identities=13%  Similarity=0.188  Sum_probs=26.7

Q ss_pred             HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          504 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       504 VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      |-.+|.-    .++|.+|+|+.+||++.+|..+++
T Consensus        11 i~~~r~~----~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          11 LQEHLRN----SGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHT----TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHH----cCCCHHHHHHHHHcCHhHHHHHHc
Confidence            4445555    899999999999999999999986

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=82.54  E-value=0.68  Score=37.37  Aligned_cols=43  Identities=21%  Similarity=0.244  Sum_probs=33.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      -.|++.+..||..-+.  .+.++|..|||+.+|+++.+|+.++.+
T Consensus        17 ~gLs~~~~~iL~~L~~--~~~~~t~~eLa~~~~i~~~tvs~~l~~   59 (109)
T d2d1ha1          17 YKITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVENSLKK   59 (109)
T ss_dssp             HTCCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCcCHHHHHHHHHHHH--cCCCCCHHHHHHHHCccHhHHHHHHHH
Confidence            4699999999865432  124799999999999999999865544

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.86  E-value=0.93  Score=33.67  Aligned_cols=29  Identities=17%  Similarity=0.245  Sum_probs=23.5

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          514 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       514 ~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +..-+..+||+.||||+.+|.+    +++||.+
T Consensus        21 ~~~v~~~~iA~~L~vs~~SVt~----mvkrL~~   49 (63)
T d2isya1          21 GVTPLRARIAERLDQSGPTVSQ----TVSRMER   49 (63)
T ss_dssp             TCCCCHHHHHHHHTCCHHHHHH----HHHHHHH
T ss_pred             CCCCcHHHHHHHhCCCchhHHH----HHHHHHH
Confidence            3568999999999999999965    5666654

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=81.44  E-value=1.7  Score=34.67  Aligned_cols=50  Identities=12%  Similarity=0.230  Sum_probs=33.8

Q ss_pred             HHHHHHhcCCH-HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          489 HVRNLLTLLNP-KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       489 ~L~~aL~~L~e-rER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      .+.+++..|.. .-..||.+-.   + .+++..||++.+|+|+.+|++.+    ++|++
T Consensus        12 ~la~~~kaL~~p~Rl~Il~~L~---~-~~~~v~ela~~l~is~stvS~HL----~~L~~   62 (98)
T d1r1ta_          12 SLAEFFAVLADPNRLRLLSLLA---R-SELCVGDLAQAIGVSESAVSHQL----RSLRN   62 (98)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHT---T-CCBCHHHHHHHHTCCHHHHHHHH----HHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH---c-CCcCHHHHHHHHCcCHHHHHHHH----HHHHH
Confidence            44455555554 4444554332   3 46999999999999999998764    45554

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=81.43  E-value=0.69  Score=34.08  Aligned_cols=24  Identities=25%  Similarity=0.418  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .++|++|+|+.+|||+.+|.++++
T Consensus        13 ~g~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_          13 KKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHhcccCHHHHHHHHc
Confidence            689999999999999999999986

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.35  E-value=1  Score=33.28  Aligned_cols=39  Identities=18%  Similarity=0.209  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          499 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       499 erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      +|...||.+-.  ......|..|+|+.||||+.||++-+..
T Consensus         7 eR~~~Il~~L~--~~~~~vs~~~La~~l~VS~~TI~rdi~~   45 (65)
T d1j5ya1           7 ERLKSIVRILE--RSKEPVSGAQLAEELSVSRQVIVQDIAY   45 (65)
T ss_dssp             HHHHHHHHHHH--HCSSCBCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHH--HcCCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence            44455665432  2224579999999999999999876643

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=80.95  E-value=1.8  Score=34.40  Aligned_cols=51  Identities=22%  Similarity=0.245  Sum_probs=36.1

Q ss_pred             HHHHHHHhcCCHHHH-HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008556          488 QHVRNLLTLLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  546 (561)
Q Consensus       488 e~L~~aL~~L~erER-~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  546 (561)
                      +.+.+++..|...-| .||.+-..    .+++..||++.+|+|+.+|++.+    +.|+.
T Consensus         6 e~~a~~fkaL~d~~Rl~Il~~L~~----~~~~v~el~~~l~~s~~~vS~HL----~~L~~   57 (94)
T d1r1ua_           6 ERVTEIFKALGDYNRIRIMELLSV----SEASVGHISHQLNLSQSNVSHQL----KLLKS   57 (94)
T ss_dssp             HHHHHHHHHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTCCHHHHHHHH----HHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHc----CCccHHHHHHHHCCCHHHHHHHH----HHHHH
Confidence            346667777876555 34443332    57999999999999999998764    45554

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=80.54  E-value=0.89  Score=33.28  Aligned_cols=24  Identities=13%  Similarity=0.297  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .++|++|+|+.+|||+.+|.++++
T Consensus        15 ~gltq~~lA~~~gvs~~ti~~~E~   38 (65)
T d2croa_          15 LKMTQTELATKAGVKQQSIQLIEA   38 (65)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHhHHHHHHC
Confidence            679999999999999999999986

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=80.54  E-value=0.9  Score=33.70  Aligned_cols=24  Identities=25%  Similarity=0.255  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      .++|.+++|+.+|||+.+|.++++
T Consensus        21 ~gltq~~lA~~~gis~~~i~~~E~   44 (69)
T d1y7ya1          21 KGLSQETLAFLSGLDRSYVGGVER   44 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             cCCCHHHHHhHhCCCHHHHHHHHC
Confidence            689999999999999999999986

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=80.26  E-value=0.94  Score=32.85  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008556          515 KPKSLSEVGNIFGLSKERVRQLESR  539 (561)
Q Consensus       515 e~~Tl~EIAe~LGISrerVRqie~R  539 (561)
                      .++|++|+|+.+|||+.+|.++++.
T Consensus        13 ~g~sq~elA~~~gvs~~~is~~E~g   37 (63)
T d1r69a_          13 LGLNQAELAQKVGTTQQSIEQLENG   37 (63)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cCCcHHHHHHHhCcCHHHHHHHHCC
Confidence            6899999999999999999999863

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=80.11  E-value=0.92  Score=37.11  Aligned_cols=41  Identities=22%  Similarity=0.123  Sum_probs=32.5

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008556          495 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  538 (561)
Q Consensus       495 ~~L~erER~VL~LRyGL~d~e~~Tl~EIAe~LGISrerVRqie~  538 (561)
                      ..|+|-|.-.-.-++. +  .++|.++||+.+|+|+.+|++++.
T Consensus        12 ~~L~p~e~A~a~~~l~-~--~g~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_          12 NELTPREIADFIGREL-A--KGKKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             TCCCHHHHHHHHHHHH-H--TTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             cCCCHHHHHHHHHHHH-H--hCCCHHHHHHHHCCcHHHHHHHHH
Confidence            3588887776555543 2  578999999999999999999875