Citrus Sinensis ID: 009567

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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--
Protein Sequence
MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccHHcccccHHHHHHHccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHcccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccEEEEEHHccccccccHHHHHHHccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHcccccccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccHcccccEccccccHHHccccccEcccccccHccHHHHHHHcccccccEEcccEEccEEEcccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccHHHHHHHHHHHccccccccccccccccccHHHccccccccHHHHHHHHccccccccccccccccHHcHHHHHcHHccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHcccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mhneqsapavasvptssvarhfptsvllqeqrdeyrpllhmfkedktsqatsdsrnIETEAFFveeknsgdlDQLVQDLEHqflhwpdlwnlsppmkrgedpsvsltmqslsndteesvdaepfDAVALARKALSASKEAAslaenpklngaeftdisltsslgypleevkqfsqprflerrskkrkvskpqvtnhetynSRKASVKKKLsegfdrndplrlflwgpetrklltaDEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRdlkselhsgnssREKLINANLRLVVHVAKQYqgrgislhdLLQEGSMGLMKSVEkfkpqagcrfasYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIqegnhspdkedlaRRVGITVEKLERLIFITrmplsmqqpvwadqdtTFQEITadtgveipdisVQKQLMRQHVRNLLtllnpkerCIVRLRFgiedgkpkslsevgnIFGLSKERVRQLESRALYRLKQSLggkasygyadlli
Flexible Loop (DISEMBL)
mhneqsapavasvptssvarhfPTSVLLQEQRDEYRPLLHMfkedktsqatsdsrNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAslaenpklngaeFTDISLTSslgypleevkqfsqprflerrskkrkvskpqvtnhetynsrkasvkkklsegfdrndplrlfLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLqsqfgreptLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFqhsrtirlpeNIYTLLSKVLEAKRLYIqegnhspdkedlarRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNlltllnpkerCIVRLRfgiedgkpkslsevgnifglskeRVRQLESRALYrlkqslggkasygyadlli
Low Complexity Region (SEG)
MHNEQsapavasvptssvaRHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDavalarkalsaskeaaslaeNPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered region (IsUnstruct)
*************************************************************FFV******DLDQLVQDLEHQFLHWPDLWNL******************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE*********FGREPTLIEWAKAIGLSCRDL************KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG********LARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY*****
Disordered Region (DISOPRED)
***********SVPTSSVARHFPTSVLLQEQRDEYRPLLHM************************************DLEHQFLH***************************************************************LNGAEF***************************************************************DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS*FGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL*******SPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered Region (DISEMBL)
****************SVARHFPTSVLLQEQRDEYRPLLHMFKED*********RNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQS**********AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLE*************TNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK********SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered Region (DISPRO)
*********VASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM**********************VDAEPFDAVALARKALSASKEAASLAENPKL*****************************************************************DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV*ADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFExxxxxxxxxxxxxxxxxxxxxFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
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	532	2.2.26 [Sep-21-2011]
Q9LD95	547	RNA polymerase sigma fact	yes	no	0.962	0.936	0.555	1e-162
P26683	390	RNA polymerase sigma fact	yes	no	0.629	0.858	0.372	2e-66
O22056	572	RNA polymerase sigma fact	no	no	0.635	0.590	0.381	4e-65
P38023	399	RNA polymerase sigma fact	yes	no	0.560	0.746	0.394	1e-63
P74565	425	RNA polymerase sigma fact	N/A	no	0.582	0.729	0.342	9e-58
P52322	416	RNA polymerase sigma fact	no	no	0.562	0.718	0.345	1e-56
Q31ME3	320	RNA polymerase sigma fact	no	no	0.562	0.934	0.386	7e-56
Q03066	416	RNA polymerase sigma-C fa	no	no	0.563	0.721	0.360	9e-53
Q31QG5	320	RNA polymerase sigma fact	no	no	0.565	0.940	0.382	3e-52
Q59996	404	Probable RNA polymerase s	N/A	no	0.560	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 =  571 bits (1471), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 297/535 (55%), Positives = 381/535 (71%), Gaps = 23/535 (4%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETE 60
           +H++ + P V S   +S++RHFP SVL QE R+E RPL H  ++D+TSQ T + R  +  
Sbjct: 33  LHDQTTTPVVNSRHLNSLSRHFPASVLSQEPREESRPLSHALRDDRTSQLTLERRQFDEL 92

Query: 61  AFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEES 118
               E+          +  E Q LH   LWNL  SP     + P+V   +          
Sbjct: 93  VSSRED----------EKFEQQLLHSTGLWNLLISPLTSETKLPAVVSPL---------- 132

Query: 119 VDAEPFDAVALARKALSASKEAASLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPR 177
            DAE  D VALA+KALSASK+AA L ++ + N ++   D   TSS     E+       R
Sbjct: 133 ADAELCDVVALAQKALSASKQAALLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKR 192

Query: 178 FLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADE 237
            LERR+K R+  K    + E Y  +K S KKK  +G D +D L+LFLWGPET++LLTA E
Sbjct: 193 QLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKE 252

Query: 238 EFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 297
           E ELI+ IQ L++LEK K+KL+SQ G EPT+ EWA+A+G+S   LKS++H G SSREKLI
Sbjct: 253 EAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLI 312

Query: 298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 357
            ANLRLVVH+AKQYQ RG++  DLLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IR
Sbjct: 313 TANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIR 372

Query: 358 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 417
           K+IFQ+SRTIRLPEN+Y LL KV EA++  +QEGN+ P KE+LA  VG++ EKL++L++ 
Sbjct: 373 KSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYN 432

Query: 418 TRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVR 477
           TR PLSMQQP+W+DQDTTFQEIT D+G+E P +SV KQLMR HVRNLL +L+PKER I++
Sbjct: 433 TRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIK 492

Query: 478 LRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 532
           LRFGI+ GK +SLSE+G I+GLSKERVRQLESRALYRLKQ++     + YADLL+
Sbjct: 493 LRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHAYADLLV 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 =  253 bits (647), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 130/349 (37%), Positives = 220/349 (63%), Gaps = 14/349 (4%)

Query: 169 EVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPE 228
           ++ +F +P+  E  +K  K +K +         R  S KK  +E     D +RL+L    
Sbjct: 44  DIDEFLEPQTDEDDAKSGKAAKSR--------RRTQSKKKHYTE-----DSIRLYLQEIG 90

Query: 229 TRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 288
             +LL ADEE EL  +I DL+ LE+ + +L  +  R+P   EWA+A+ L     +  LH 
Sbjct: 91  RIRLLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQLPLPAFRYRLHI 150

Query: 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 348
           G  +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF  + G +F++YA
Sbjct: 151 GRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 210

Query: 349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV 408
            WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P +E++A R+ +T+
Sbjct: 211 TWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTI 270

Query: 409 EKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 468
           EKL  +    ++P+S++ P+  ++D+   +     G E P+  V K L+R+ +  +L  L
Sbjct: 271 EKLRFIAKSAQLPISLETPIGKEEDSRLGDFIESDG-ETPEDQVSKNLLREDLEKVLDSL 329

Query: 469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           +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 (635), Expect = 4e-65,   Method: Compositional matrix adjust.
 Identities = 131/343 (38%), Positives = 215/343 (62%), Gaps = 5/343 (1%)

Query: 177 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 235
           R  ER++++ K  +   +   +  +  +  KK+L ++  D NDPLR       + KLLT 
Sbjct: 216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275

Query: 236 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 295
            EE EL A IQDL++LE+ +++L  + GR+PT  +WA A G+  + L+  +H G   ++K
Sbjct: 276 REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDK 335

Query: 296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355
           +I +N+RLV+ +AK YQG G++L DL+QEG  GL++  EKF    G +F++YA+WW++Q 
Sbjct: 336 MIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQA 395

Query: 356 IRKAIFQHSRTIRLPENIYTLLSKVLEA-KRLYIQEGNHSPDKEDLARRVGITVEKLERL 414
           +RK++   SR IRLP ++     +V EA K+LY + G H P  E++A   G+++++L  +
Sbjct: 396 VRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKH-PKNEEIAEATGLSMKRLMAV 454

Query: 415 IFITRMPLSMQQPVWADQDTTFQEITAD-TGVEIPDISVQKQLMRQHVRNLLTLLNPKER 473
           +   + P S+ Q +  +Q+    E+ AD   V   DI + K+ MRQ +  +L  L  +E+
Sbjct: 455 LLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILI-KEFMRQDLDKVLDSLGTREK 513

Query: 474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
            ++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 (623), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 118/299 (39%), Positives = 199/299 (66%), Gaps = 1/299 (0%)

Query: 218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 277
           D +RL+L      +LL ADEE EL  QI DL+ LE+ + +L  Q  R P+  EWA A+  
Sbjct: 89  DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148

Query: 278 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 337
              + +  L  G  +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF 
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 208

Query: 338 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 397
            + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P +
Sbjct: 209 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTE 268

Query: 398 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 457
           E++A R+ +T+EKL  +    ++P+S++ P+  ++D+   +     G E P+  V K L+
Sbjct: 269 EEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDEVAKNLL 327

Query: 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           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 (573), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 123/359 (34%), Positives = 209/359 (58%), Gaps = 49/359 (13%)

Query: 202 RKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQ 261
           RK +VKKK        D +R++L      +LL A+EE EL  QI DL+ LE  +  L  Q
Sbjct: 59  RKDAVKKKPYT----EDSIRIYLQEIGRIRLLRAEEEIELARQIADLLELELIRDNLTLQ 114

Query: 262 FGREPTLIEWAKAI----------------GLSCRDLKSELHSGNS-------------- 291
             R+P+ +EW K +                    +D+ S L + ++              
Sbjct: 115 LERQPSELEWGKQVWKLETAKQRLVGDKKKEPKKKDIDSYLANPDNELSLENEWSQQPNK 174

Query: 292 --------------SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 337
                         +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF 
Sbjct: 175 NFAAFRRRLFLDRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 234

Query: 338 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 397
            + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P +
Sbjct: 235 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTE 294

Query: 398 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 457
           E++A ++ +T+EKL  +    ++P+S++ P+  ++D+   +     G E P+  V K L+
Sbjct: 295 EEIAEKMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDEVSKNLL 353

Query: 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           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 (562), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 117/339 (34%), Positives = 201/339 (59%), Gaps = 40/339 (11%)

Query: 218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEK------------------------ 253
           D +R++L      +LL A+EE EL  +I DL++LE+                        
Sbjct: 67  DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126

Query: 254 ----EKSK-------LQSQFGRE----PTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 298
               EKS+       +++  G+     P L EW           K  L+ G  ++EK++ 
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186

Query: 299 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 358
           +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF  + G +F++YA WW+RQ I +
Sbjct: 187 SNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITR 246

Query: 359 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 418
           AI   SRTIRLP ++Y  +S++ +  ++  QE    P +E++A ++ +T+EKL  +    
Sbjct: 247 AIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSA 306

Query: 419 RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRL 478
           ++P+S++ P+  ++D+   +     G E P+  V K L+R+ + N+L  L+P+ER ++RL
Sbjct: 307 QLPISLETPIGKEEDSRLGDFIEADG-ETPEDEVSKNLLREDLENVLDTLSPRERDVLRL 365

Query: 479 RFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           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 =  218 bits (556), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 116/300 (38%), Positives = 188/300 (62%), Gaps = 1/300 (0%)

Query: 218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 277
           D +R +L      +LLTA+EE     Q+Q L+ L   +++L+ + G EP+  EWA A+ L
Sbjct: 11  DLVRAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDL 70

Query: 278 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 337
           +  DL  ++  G  ++ K+I ANLRLVV +AK+YQ R +   DL+QEG++GL + VEKF 
Sbjct: 71  NLEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFD 130

Query: 338 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 397
           P  G +F++YAYWW+RQ I +AI Q SRTIRLP +I   L+K+ + +R   Q+   S   
Sbjct: 131 PSKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATA 190

Query: 398 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 457
            +LA  + + +E++   I + R P+S+   V   QDT  QE+  D     P   V+++ +
Sbjct: 191 SELAEVLELPLEQVREYIQMNRQPVSLDVKVGDSQDTELQELLEDEQSS-PSDYVEQESL 249

Query: 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           R+ +RNL+  L P+++ ++ LR+G+++G   SL++VG    +S+ERVR+LE +A+  L++
Sbjct: 250 RRDLRNLMAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAMDHLRR 309

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 (529), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 124/344 (36%), Positives = 190/344 (55%), Gaps = 44/344 (12%)

Query: 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE---------------------KEK 255
            D +RL+L      +LL  DEE     ++Q  ++L                      + +
Sbjct: 59  TDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYLKLRIVLANAVKQGDEVATPYLHLIEVQ 118

Query: 256 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN----------------------SSR 293
            +L S+ G  P+L  WA   G++  DLK  L  G                        S+
Sbjct: 119 ERLASELGHRPSLERWAATAGINLCDLKPILSEGKRRWAEIAKMTVEELEKMQSQGLQSK 178

Query: 294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR 353
           E +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF++YAYWW+R
Sbjct: 179 EHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIR 238

Query: 354 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER 413
           Q I +AI   SRTIRLP +I   L+K+ +A+R   QE   +P  EDLA  + +T  ++  
Sbjct: 239 QGITRAIATSSRTIRLPVHITEKLNKIKKAQRKIAQEKGRTPTLEDLAIELDMTPTQVRE 298

Query: 414 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKER 473
           ++      +S++  V  D+DT   E+    GV  P+  + ++ +++ +++LL  L  +ER
Sbjct: 299 VLLRVPRSVSLETKVGKDKDTELGELLETDGV-TPEEMLMRESLQRDLQHLLADLTSRER 357

Query: 474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
            ++ +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: 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG-REPTLIEWAKAI 275
           +D +R +L       LLT +EE  L  ++Q  ++L++ +  LQS+ G R+P+ +EWA A 
Sbjct: 9   SDLVRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAA 68

Query: 276 GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK 335
           GLS  +L+ + H G  ++ K+I ANLRLVV VAK+Y  R + L DL+QEG++G+ + VEK
Sbjct: 69  GLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEK 128

Query: 336 FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSP 395
           F P  G RF++YAYWW+RQ I +AI + +RTIRLP +I   L+K+ + +R   Q+   + 
Sbjct: 129 FDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKMQRQLSQQLGRTA 188

Query: 396 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 455
              +LA  + +T  ++   +   R PLS+   V  +QDT   ++  +T    P+    + 
Sbjct: 189 TLPELAAALDLTPAQVRDYLEKARHPLSLDLRVGDNQDTELGDLL-ETDCTTPEEFTLQA 247

Query: 456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515
            MR+ +  LL  L  ++R ++ LR+G+EDG+  +L+ +G+   +S+ERVRQLE  AL+ L
Sbjct: 248 SMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRERVRQLEREALHTL 307

Query: 516 KQS 518
           +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: 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK------------------- 257
            D +RL+L       LL  DEE  +  Q+Q  +RL + +++                   
Sbjct: 48  TDLVRLYLQDIGRIPLLKRDEEVHIAQQVQSYLRLVEIQNRAAESDAAIDQYQTAIAVHD 107

Query: 258 -LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN----------------------SSRE 294
            L  Q G  P+   WAK +G +   LK  L SG                       +++ 
Sbjct: 108 QLLVQLGHRPSYERWAKILGQTVATLKQTLKSGKKRWAELAGLTVEELENIEKQGITAKA 167

Query: 295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 354
            +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF++Y+YWW+RQ
Sbjct: 168 HMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYSYWWIRQ 227

Query: 355 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 414
            I +AI   SR IRLP +I   L+K+  A+R   QE  H+P  +++A  +G+T E++  +
Sbjct: 228 GITRAIATQSRMIRLPVHITEKLNKIKRAQRKISQEKGHTPKIDEVAEELGMTPEQVREV 287

Query: 415 IFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERC 474
           +      +S++  V  D+DT   ++  +T  + P+  + ++ ++  ++ +L  L P+E+ 
Sbjct: 288 LTQVPRSVSLELKVGQDKDTELMDLL-ETDTQSPEDELMREALQNDMQEILLDLTPREQE 346

Query: 475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515
           ++ 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	532
297741628	561	unnamed protein product [Vitis vinifera]	0.990	0.939	0.637	0.0
359481391	572	PREDICTED: RNA polymerase sigma factor r	0.990	0.921	0.637	0.0
224068757	535	predicted protein [Populus trichocarpa]	0.943	0.938	0.632	0.0
255556952	548	RNA polymerase sigma factor rpoD, putati	0.960	0.932	0.626	0.0
356536959	571	PREDICTED: RNA polymerase sigma factor r	0.992	0.924	0.588	1e-173
356548319	574	PREDICTED: RNA polymerase sigma factor r	0.996	0.923	0.579	1e-171
449451030	562	PREDICTED: RNA polymerase sigma factor s	0.962	0.911	0.581	1e-168
297827203	546	RNA polymerase sigma-70 factor [Arabidop	0.953	0.928	0.559	1e-160
312282671	547	unnamed protein product [Thellungiella h	0.953	0.926	0.559	1e-160
18404292	547	RNApolymerase sigma-subunit F [Arabidops	0.962	0.936	0.555	1e-160

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

 Score =  686 bits (1771), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 343/538 (63%), Positives = 417/538 (77%), Gaps = 11/538 (2%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETE 60
           M ++Q APAVAS+PT+ +AR FPTSVLLQEQRDEYRP     K+++T QAT + R +E  
Sbjct: 29  MLHDQVAPAVASIPTT-IARKFPTSVLLQEQRDEYRPFPQALKDERTFQATLEKRQMEI- 86

Query: 61  AFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGE-DPSVSLTMQSLSNDTEESV 119
               +E+NS D +Q + + E Q L  P LW   P  + GE  P  S  M+S++ D E S+
Sbjct: 87  VVSADEENSDDHNQYMVNFERQLLLQPGLWYSLPSSQTGEKSPFSSSIMKSITTDIENSM 146

Query: 120 DAEPFDAVALARKALSASKEAASLAENPKLNGAEFTD-----ISLTSSLGYPLEEVKQFS 174
           D +P D +ALA+KALSASK+A SL EN KL GA+  D     +   SS   PLEE K   
Sbjct: 147 DVKPCDVLALAKKALSASKQAVSLYENAKLLGADLEDSPSPSLGAISSPNLPLEE-KTVR 205

Query: 175 QPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLT 234
             R LERRSKKR+   P+V  HE + SR+A V++K++EG+D  DPLRLFLWGPETRKLLT
Sbjct: 206 STRLLERRSKKRR--NPKVAVHENHGSRRAEVQRKINEGYDPKDPLRLFLWGPETRKLLT 263

Query: 235 ADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 294
           A EE ELI QIQ+L+RLE+ K +LQS   REPT++EWA+A+GLSC+ L+S+LHSGN SR+
Sbjct: 264 AKEESELIVQIQELMRLEEVKKRLQSHLKREPTVVEWAEAVGLSCQVLQSQLHSGNRSRQ 323

Query: 295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 354
           KLI ANLR+VVH+AKQYQGRG++L DLLQEGSMGLM SVEKFKP AGCRFASYAYWW+RQ
Sbjct: 324 KLIYANLRMVVHIAKQYQGRGLNLQDLLQEGSMGLMNSVEKFKPNAGCRFASYAYWWIRQ 383

Query: 355 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 414
            +RKAIFQHSRTIRLPEN+Y+LL KV EAKRL+IQEG+H P KE++A RVGIT+EKL+RL
Sbjct: 384 AVRKAIFQHSRTIRLPENMYSLLGKVKEAKRLFIQEGHHDPTKEEIAERVGITIEKLQRL 443

Query: 415 IFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERC 474
           +  TRMPLSMQQPVWADQDTTFQE+TADTG+EIPD+SV KQLMRQHVRNLL +L PKER 
Sbjct: 444 LLHTRMPLSMQQPVWADQDTTFQEVTADTGIEIPDVSVAKQLMRQHVRNLLHVLTPKERR 503

Query: 475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 532
           I+RLRFGI DG P++LSE+G +FG SKERVRQLE RAL++LKQ L       Y DLL+
Sbjct: 504 IIRLRFGIGDGIPRTLSEIGLVFGFSKERVRQLEQRALHKLKQCLSSHGLESYTDLLV 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 =  685 bits (1768), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 343/538 (63%), Positives = 417/538 (77%), Gaps = 11/538 (2%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETE 60
           M ++Q APAVAS+PT+ +AR FPTSVLLQEQRDEYRP     K+++T QAT + R +E  
Sbjct: 40  MLHDQVAPAVASIPTT-IARKFPTSVLLQEQRDEYRPFPQALKDERTFQATLEKRQMEI- 97

Query: 61  AFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGE-DPSVSLTMQSLSNDTEESV 119
               +E+NS D +Q + + E Q L  P LW   P  + GE  P  S  M+S++ D E S+
Sbjct: 98  VVSADEENSDDHNQYMVNFERQLLLQPGLWYSLPSSQTGEKSPFSSSIMKSITTDIENSM 157

Query: 120 DAEPFDAVALARKALSASKEAASLAENPKLNGAEFTD-----ISLTSSLGYPLEEVKQFS 174
           D +P D +ALA+KALSASK+A SL EN KL GA+  D     +   SS   PLEE K   
Sbjct: 158 DVKPCDVLALAKKALSASKQAVSLYENAKLLGADLEDSPSPSLGAISSPNLPLEE-KTVR 216

Query: 175 QPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLT 234
             R LERRSKKR+   P+V  HE + SR+A V++K++EG+D  DPLRLFLWGPETRKLLT
Sbjct: 217 STRLLERRSKKRR--NPKVAVHENHGSRRAEVQRKINEGYDPKDPLRLFLWGPETRKLLT 274

Query: 235 ADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 294
           A EE ELI QIQ+L+RLE+ K +LQS   REPT++EWA+A+GLSC+ L+S+LHSGN SR+
Sbjct: 275 AKEESELIVQIQELMRLEEVKKRLQSHLKREPTVVEWAEAVGLSCQVLQSQLHSGNRSRQ 334

Query: 295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 354
           KLI ANLR+VVH+AKQYQGRG++L DLLQEGSMGLM SVEKFKP AGCRFASYAYWW+RQ
Sbjct: 335 KLIYANLRMVVHIAKQYQGRGLNLQDLLQEGSMGLMNSVEKFKPNAGCRFASYAYWWIRQ 394

Query: 355 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 414
            +RKAIFQHSRTIRLPEN+Y+LL KV EAKRL+IQEG+H P KE++A RVGIT+EKL+RL
Sbjct: 395 AVRKAIFQHSRTIRLPENMYSLLGKVKEAKRLFIQEGHHDPTKEEIAERVGITIEKLQRL 454

Query: 415 IFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERC 474
           +  TRMPLSMQQPVWADQDTTFQE+TADTG+EIPD+SV KQLMRQHVRNLL +L PKER 
Sbjct: 455 LLHTRMPLSMQQPVWADQDTTFQEVTADTGIEIPDVSVAKQLMRQHVRNLLHVLTPKERR 514

Query: 475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 532
           I+RLRFGI DG P++LSE+G +FG SKERVRQLE RAL++LKQ L       Y DLL+
Sbjct: 515 IIRLRFGIGDGIPRTLSEIGLVFGFSKERVRQLEQRALHKLKQCLSSHGLESYTDLLV 572

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  677 bits (1748), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/528 (63%), Positives = 410/528 (77%), Gaps = 26/528 (4%)

Query: 4   EQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFF 63
           EQ+ PAV+S+PT+S A+HFPTSVLLQEQRDE+RPL ++FKED+ SQAT D R  E     
Sbjct: 33  EQATPAVSSIPTTSTAQHFPTSVLLQEQRDEFRPLQNIFKEDRASQATLDRRKTEIGTSG 92

Query: 64  VEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEP 123
            E K+S +LDQLV++ E+Q  HWP  WNL                      T++ +D EP
Sbjct: 93  HEGKDSDELDQLVENFEYQLHHWPAYWNL----------------------TDKLIDVEP 130

Query: 124 FDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRS 183
            + + LA++ALSASK AA LA+N      +  +++ TSS  + LEEVK     R L R+S
Sbjct: 131 TNVINLAKRALSASKHAAFLADN----NTDLDNLASTSSSSFSLEEVKIVRSRRHLARQS 186

Query: 184 KKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIA 243
             R+  K +    ETY+S+ A ++K+LS+GFD NDPLRLFLWGPET++LLTA EEFELIA
Sbjct: 187 LNRRAPKTKDLIFETYDSKSADIQKRLSQGFDPNDPLRLFLWGPETKQLLTAKEEFELIA 246

Query: 244 QIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRL 303
           QIQDL+ LE  K++L+SQFGREPTL+EWA+A+GLSC  LK +LHSGN SREKLINANLR+
Sbjct: 247 QIQDLMNLEGVKNRLESQFGREPTLVEWAQAVGLSCHVLKLQLHSGNRSREKLINANLRM 306

Query: 304 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 363
           VVH+AK+YQ RG+ L DLLQEG++GLMKS+EKFKPQAGCRFA+YAYWW+RQTI KAIFQH
Sbjct: 307 VVHIAKRYQNRGLGLQDLLQEGTVGLMKSIEKFKPQAGCRFATYAYWWIRQTITKAIFQH 366

Query: 364 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLS 423
           SRTIRLPEN+Y LL KV+EAKR YIQEGNH P  E++ARRVGI ++KLE+L+  TR PLS
Sbjct: 367 SRTIRLPENVYGLLGKVMEAKRSYIQEGNHQPTAEEIARRVGIAIDKLEKLLCFTRTPLS 426

Query: 424 MQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIE 483
           MQQ VW+DQ+TTFQEITADT +EIPD+SV KQLMR+H+R LL +L+ KER I+RLRFGIE
Sbjct: 427 MQQTVWSDQNTTFQEITADTEIEIPDMSVAKQLMRKHIRGLLNILSLKERRIIRLRFGIE 486

Query: 484 DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 531
           DGK KSLSE+GN+FGLSKERVRQLESRALY+LKQ +G      YADLL
Sbjct: 487 DGKQKSLSEIGNVFGLSKERVRQLESRALYKLKQCVGSHGLDAYADLL 534

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  667 bits (1721), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/533 (62%), Positives = 408/533 (76%), Gaps = 22/533 (4%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETE 60
           M +EQ+ PAV S PT+S+AR+FPTSVLLQEQRDE+RPLL++FKEDKT QAT D++ ++  
Sbjct: 37  MLHEQAVPAVTSAPTTSIARNFPTSVLLQEQRDEFRPLLNIFKEDKTFQATVDTKQMDPG 96

Query: 61  AFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVD 120
               E   S  LDQL+    H  L W                  SLTMQS++ +T+E + 
Sbjct: 97  TSDQEGICSDVLDQLIL---HSNLSW------------------SLTMQSITTNTDELMV 135

Query: 121 AEPFDAVALARKALSASKEAASLAEN-PKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFL 179
            EP + + LARKALSASKEAA LA+    L+    T +  T    + LEEVK     R L
Sbjct: 136 VEPTNVIDLARKALSASKEAALLAQKCANLDDTVSTGLEPTDLSNFSLEEVKTVRSTRRL 195

Query: 180 ERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEF 239
           ER+SK R+V+K +   HE Y+SR+A V+KK++EGFD  DPLRLFLWGPET++LLTA EE 
Sbjct: 196 ERQSKNRRVTKTKEIFHEPYSSRRAGVQKKINEGFDPKDPLRLFLWGPETKQLLTAKEES 255

Query: 240 ELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINA 299
           ELI Q+QDL+ LE  K K + QFGR+PTL+EWA A+GLS   ++S+LHSGN SREKLINA
Sbjct: 256 ELIGQVQDLMSLENVKEKFKLQFGRDPTLVEWADAVGLSYSVMQSQLHSGNRSREKLINA 315

Query: 300 NLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA 359
           NLR+VVH+AKQYQGRG+SL DLLQEGSMGLMKS+EKFKPQ GCRFA+YAYWW+RQT+RKA
Sbjct: 316 NLRMVVHIAKQYQGRGLSLQDLLQEGSMGLMKSIEKFKPQVGCRFATYAYWWIRQTVRKA 375

Query: 360 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR 419
           IFQHSRTIRLPEN+Y  L KV EAKR YI EGNH+P KE+LA+R+GIT  +LERL+++ R
Sbjct: 376 IFQHSRTIRLPENVYHTLGKVSEAKRSYIMEGNHNPTKEELAKRIGITTVRLERLLYMAR 435

Query: 420 MPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLR 479
           MPLSMQQ VWADQ+TTFQEITAD  VEIP++ V KQLMR+HV +LL +LNP+ER I+RLR
Sbjct: 436 MPLSMQQTVWADQETTFQEITADIEVEIPELCVAKQLMRKHVLSLLNILNPRERKIIRLR 495

Query: 480 FGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 532
           +GIEDGK KSLSE+G++FGLSKERVRQLESRALY+LKQ L       YADLL+
Sbjct: 496 YGIEDGKKKSLSEIGSVFGLSKERVRQLESRALYKLKQCLASHGLEAYADLLV 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 =  613 bits (1582), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 318/540 (58%), Positives = 407/540 (75%), Gaps = 12/540 (2%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETE 60
           M +EQ++P VAS  ++  A++FP SVLL EQRDEYRPLLHM KEDKTSQA   +R ++T 
Sbjct: 36  MLHEQASPTVASWSSNFSAQNFPASVLLPEQRDEYRPLLHMSKEDKTSQAMLSTRQMDTV 95

Query: 61  AFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVD 120
               EE N+ + DQ+V D      HWP+L   S  +  GE  + S T++ +S D E   +
Sbjct: 96  TVH-EENNTENADQVVLDFRKHLHHWPNLQLTSSQI--GE-VAASSTLEHVSVDLERRPN 151

Query: 121 AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTS-SLGYP-LEEVKQFSQPRF 178
              F+ V+LA+KALS SK+ +S+ E+ K   A+    SL S SL  P +   K     R 
Sbjct: 152 GVQFNGVSLAKKALSTSKQESSVVEDLKSIKADDVPFSLASTSLADPSIGRNKTVRSTRL 211

Query: 179 LERRSKKRKVSKPQVTNHETYNSRKASVKKKL------SEGFDRNDPLRLFLWGPETRKL 232
           LERRSK+RKV K +V + ETY +RK   ++KL      +E  D++DPLRLFLWGPET++L
Sbjct: 212 LERRSKQRKVPKSKVIDDETYLARKDDAQEKLRAEKKKNEELDQDDPLRLFLWGPETKQL 271

Query: 233 LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 292
           LT ++E +LI+QIQDL+RLE+ K+ LQSQFGREPT+ EWA+  GL+CR L+S+LHSGN S
Sbjct: 272 LTLEQESQLISQIQDLLRLEEVKTNLQSQFGREPTMAEWAEGAGLNCRLLQSQLHSGNRS 331

Query: 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352
           REKLI ANLR+VVHVAK YQGRG+SL DLLQEGSMGLMKSVEKF P AG RF +YA+WW+
Sbjct: 332 REKLIQANLRMVVHVAKSYQGRGLSLQDLLQEGSMGLMKSVEKFNPLAGSRFGNYAFWWI 391

Query: 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 412
           RQ IRKA+F+HSRTIRLPE ++ LL KV+EAK+LYIQEGN  P KE+LARRVG+TVEK++
Sbjct: 392 RQAIRKAVFRHSRTIRLPEKVFILLGKVMEAKKLYIQEGNLHPTKEELARRVGVTVEKID 451

Query: 413 RLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKE 472
           +L+F  R+P+SMQQ VWADQ+TTFQEITAD  VE  D++V+KQLMR+HV N+L++L+PKE
Sbjct: 452 KLLFSARIPISMQQTVWADQNTTFQEITADPTVEATDVTVEKQLMRRHVLNVLSVLHPKE 511

Query: 473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 532
           R I+RLR+G EDG+ KSLSE+G+IFGLSKERVRQLE RALY+LK+ L  +    Y DLL+
Sbjct: 512 RRIIRLRYGFEDGEQKSLSEIGDIFGLSKERVRQLEIRALYKLKKCLVKQGLDAYVDLLL 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 =  607 bits (1566), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 314/542 (57%), Positives = 402/542 (74%), Gaps = 12/542 (2%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETE 60
           M  EQ++P VAS  ++  A++FP SVLLQEQRDEYRPLLHM KEDKTSQA   +R ++T 
Sbjct: 35  MLREQASPTVASWSSNFSAQNFPASVLLQEQRDEYRPLLHMSKEDKTSQAMLSTRQMDT- 93

Query: 61  AFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVD 120
               EE N+ + DQ+V D      +WP L NL    + GE  S S T+Q +S+D +   +
Sbjct: 94  VMVHEENNTENADQVVLDFRKHLHYWPHLQNLLASSQTGE-ISASSTLQQVSSDLDRHTN 152

Query: 121 AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISL---TSSLGYP-LEEVKQFSQP 176
               + V+LA+KALS SK+ +S+ E+ K   A+   I     ++ L  P +   K     
Sbjct: 153 GVQCNRVSLAKKALSTSKQGSSVVEDLKSIKADDDSIPFGLASTGLADPSIGRNKTVRST 212

Query: 177 RFLERRSKKRKVSKPQVTNHETYNSRKAS------VKKKLSEGFDRNDPLRLFLWGPETR 230
           R LERRSK+RKV K +V + ETY +RK        V+KK +E  D+NDPL  FL GPET+
Sbjct: 213 RLLERRSKQRKVPKSKVIDDETYLARKDDAHEKLRVEKKKNEELDQNDPLCFFLRGPETK 272

Query: 231 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 290
           +LLT ++E +LI+QIQDL+RLE+ K+KLQSQFGREPT+ EWA+ +GL+CR L ++L SG+
Sbjct: 273 QLLTLEQESQLISQIQDLLRLEEVKTKLQSQFGREPTMAEWAEGVGLNCRMLHAQLRSGS 332

Query: 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 350
            SREKLI ANLR+VVHVAK YQGRG+SL DLLQEGSMGLMKSVEKF P  G RF +YA+W
Sbjct: 333 RSREKLIQANLRMVVHVAKSYQGRGLSLQDLLQEGSMGLMKSVEKFNPLVGSRFGNYAFW 392

Query: 351 WVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK 410
           W+RQ IRKA+F+HSRTIRLPE ++ LL KV+EAK+LYIQEGN  P KE+LARRVG+TVEK
Sbjct: 393 WIRQAIRKAVFRHSRTIRLPEKVFILLGKVMEAKKLYIQEGNLHPTKEELARRVGVTVEK 452

Query: 411 LERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 470
           +++L+F  R+P+SMQQ VWADQ+TTFQEITAD  VE  D+SV+KQLMRQHV N+L++L+P
Sbjct: 453 IDKLLFSARIPISMQQTVWADQNTTFQEITADPTVEATDVSVEKQLMRQHVLNVLSILHP 512

Query: 471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADL 530
           KER I+RLR+G EDG+ KSLSE+G+IFGLSKERVRQLE RALY+LK+ L  +    Y DL
Sbjct: 513 KERRIIRLRYGFEDGEQKSLSEIGDIFGLSKERVRQLEIRALYKLKKCLVKQGLDAYVDL 572

Query: 531 LI 532
           L+
Sbjct: 573 LL 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 =  597 bits (1539), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 300/516 (58%), Positives = 387/516 (75%), Gaps = 4/516 (0%)

Query: 16  SSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQL 75
           +S AR+F TS L QEQ  E RP   + K+D++SQ T + R IE  +  ++E +  D D L
Sbjct: 50  ASPARYFSTSFLSQEQHHECRPQSQILKDDRSSQMTLERRLIE-RSVPIDEGSRDDHDHL 108

Query: 76  VQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALS 135
           + +L+HQ + WP L +  PP++  E    S+  +S +   E  V  EP + +ALA+KALS
Sbjct: 109 IWELKHQAVEWPGLLSSWPPVQMEEYKISSIEKESYNAAGEMLVKDEPENVIALAKKALS 168

Query: 136 ASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 195
           ASK+AA L +  +L G      SL  SL    +E +     R  +RRSKKRKV K   T 
Sbjct: 169 ASKQAALLVDETELVGTSLDYSSLDDSLS---KEGRTVRSTRLQDRRSKKRKVPKHVTTI 225

Query: 196 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 255
            E  N R    ++K SE FD NDPLRLFLWGPET+KLLTA EE ELI QIQDL+ L+  K
Sbjct: 226 DEISNFRGKDSRRKTSEKFDPNDPLRLFLWGPETKKLLTAQEESELIVQIQDLMILDNVK 285

Query: 256 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 315
           ++LQSQF REPTL+EWA+A+G++C+ L+S+LH   +SREKLINANLR+VVH+AKQYQGRG
Sbjct: 286 ARLQSQFDREPTLVEWAEALGITCQHLQSQLHVFQTSREKLINANLRMVVHIAKQYQGRG 345

Query: 316 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT 375
           +SLHDLLQ GS+GLMKSVEKFKPQAGCRF SYAYWW+R +I KAIFQHSRTIRLPEN+Y 
Sbjct: 346 LSLHDLLQVGSLGLMKSVEKFKPQAGCRFGSYAYWWIRHSITKAIFQHSRTIRLPENVYA 405

Query: 376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435
           LL KV EAK  +++ GN+ P KE+LA RVGITVE+ ++L+F++R+P S+QQPVWADQ+TT
Sbjct: 406 LLGKVTEAKNYFVRAGNYKPSKEELAARVGITVERFDKLMFMSRIPRSLQQPVWADQETT 465

Query: 436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 495
           FQEITAD+ V+ PD+SV+++LMR+H+RNLL++L+PKER I+RLRFGIEDG+ K+L E+GN
Sbjct: 466 FQEITADSEVDTPDVSVERELMRRHIRNLLSILSPKERRIIRLRFGIEDGREKTLLEIGN 525

Query: 496 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 531
           +FGLSKERVRQLE+RALY+LK+    +    YADLL
Sbjct: 526 MFGLSKERVRQLENRALYKLKRCCNSQGLGAYADLL 561

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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 =  572 bits (1475), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 302/540 (55%), Positives = 384/540 (71%), Gaps = 33/540 (6%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETE 60
           +H + + P V S   +S++RHFP SVL QE R+E RPL H  +ED+TSQ T + R     
Sbjct: 32  LHEQTTTPVVNSRHLNSLSRHFPASVLSQEPREESRPLSHALREDRTSQLTLERRQ---- 87

Query: 61  AFFVEEKNSGDLDQLV-----QDLEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSN 113
                       D+LV     +  E Q LH   LWNL  SP     + P V   +     
Sbjct: 88  -----------FDELVSSREDEKFEQQLLHSAGLWNLLISPLTAETKLPPVVPPL----- 131

Query: 114 DTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQF 173
                 DAE  D VALA+KALSASK+AA LA++ + N ++ T  SL++S    L E    
Sbjct: 132 -----ADAELCDIVALAQKALSASKQAALLADDTEANPSDNTRGSLSTSSSMSLPEKGAI 186

Query: 174 SQP-RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKL 232
            +  R LERR+K R+  K    ++E Y  +K + KKK  +G D +D L+LFLWGPET++L
Sbjct: 187 VRSKRQLERRAKNRRAPKSNDVDNEGYVPQKINAKKKFKQGVDTDDALQLFLWGPETKQL 246

Query: 233 LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 292
           LTA EE ELI+ IQ L++LEK K+KL+SQ G EPT+ EWA+A+G+S  DLKSE+H G SS
Sbjct: 247 LTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPDLKSEIHRGRSS 306

Query: 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352
           REKLI ANLRLVVH+AKQYQ RG++  DLLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+
Sbjct: 307 REKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWI 366

Query: 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 412
           RQ+IRK+IFQ+SRTIRLPEN+Y LL KV EA++  +QEGN+ P KE LA  VG++ EKL+
Sbjct: 367 RQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEQLAGHVGVSTEKLD 426

Query: 413 RLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKE 472
           +L++ TR PLSMQQP+W+DQDTTFQEIT D+G+E P +SV KQ+MR HVRNLL +L+PKE
Sbjct: 427 KLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQMMRNHVRNLLNVLSPKE 486

Query: 473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 532
           R I++LRFGI+ GK +SLSE+G I+GLSKERVRQLESRALYRLKQ +     + YADLL+
Sbjct: 487 RRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQHMNSHGLHAYADLLV 546

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 302/540 (55%), Positives = 380/540 (70%), Gaps = 33/540 (6%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETE 60
           +H + + P V S   +S++RHFP SVL QE R+E +PL H  +ED+TSQ T + R     
Sbjct: 33  LHEQTATPVVNSRHLTSLSRHFPASVLSQELREESKPLSHALREDRTSQLTLERRQ---- 88

Query: 61  AFFVEEKNSGDLDQLV-----QDLEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSN 113
                       D+LV     +  E Q LH   LWNL  SP     + P+V         
Sbjct: 89  -----------FDELVSSREDEKFEQQLLHSAGLWNLLISPLTTEKQLPAV--------- 128

Query: 114 DTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFT-DISLTSSLGYPLEEVKQ 172
               S DA+  D VALA+KALSASK+AA L EN + +  +   D   TSS     E+   
Sbjct: 129 -VSPSADADLCDLVALAQKALSASKQAALLVENSEADPPDNPRDSLSTSSSMSLPEKGTI 187

Query: 173 FSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKL 232
               R LERR+K R+  K    + E Y  +K + KKK+ +GFD +D L+LFLWGPET++L
Sbjct: 188 VRSKRQLERRAKNRRAPKSNNMDSEGYVPQKINAKKKMKQGFDTDDALQLFLWGPETKQL 247

Query: 233 LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 292
           LTA EE ELIA IQ LI+LEK K+KL+SQ G EPT+ EWA+A+GLS   LKSE+H G SS
Sbjct: 248 LTAKEEAELIAHIQHLIKLEKVKTKLESQNGCEPTIGEWAEAMGLSSPVLKSEIHRGRSS 307

Query: 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352
           REKLI ANLRLVVH+AKQYQ RG++  DLLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+
Sbjct: 308 REKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWI 367

Query: 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 412
           RQ+IRK+IFQ+SRTIRLPEN+Y LL KV EA++  IQ+GN+ P KE LA  VG++ EKL+
Sbjct: 368 RQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCIQDGNYRPSKEQLASHVGVSTEKLD 427

Query: 413 RLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKE 472
           +L++ TR PLSMQQP+W+DQDTTFQE+T D+G+E P +SV KQLMR HVRNLL +L+PKE
Sbjct: 428 KLLYNTRTPLSMQQPIWSDQDTTFQEVTPDSGIETPSMSVGKQLMRNHVRNLLNVLSPKE 487

Query: 473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 532
           + I++LRFGI+ GK +SLSE+G I+GLSKERVRQLESRALYRLKQ++       YADLL+
Sbjct: 488 KRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMSSHGLNAYADLLV 547

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

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 =  571 bits (1471), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 297/535 (55%), Positives = 381/535 (71%), Gaps = 23/535 (4%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETE 60
           +H++ + P V S   +S++RHFP SVL QE R+E RPL H  ++D+TSQ T + R  +  
Sbjct: 33  LHDQTTTPVVNSRHLNSLSRHFPASVLSQEPREESRPLSHALRDDRTSQLTLERRQFDEL 92

Query: 61  AFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEES 118
               E+          +  E Q LH   LWNL  SP     + P+V   +          
Sbjct: 93  VSSRED----------EKFEQQLLHSTGLWNLLISPLTSETKLPAVVSPL---------- 132

Query: 119 VDAEPFDAVALARKALSASKEAASLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPR 177
            DAE  D VALA+KALSASK+AA L ++ + N ++   D   TSS     E+       R
Sbjct: 133 ADAELCDVVALAQKALSASKQAALLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKR 192

Query: 178 FLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADE 237
            LERR+K R+  K    + E Y  +K S KKK  +G D +D L+LFLWGPET++LLTA E
Sbjct: 193 QLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKE 252

Query: 238 EFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 297
           E ELI+ IQ L++LEK K+KL+SQ G EPT+ EWA+A+G+S   LKS++H G SSREKLI
Sbjct: 253 EAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLI 312

Query: 298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 357
            ANLRLVVH+AKQYQ RG++  DLLQEGSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IR
Sbjct: 313 TANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIR 372

Query: 358 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 417
           K+IFQ+SRTIRLPEN+Y LL KV EA++  +QEGN+ P KE+LA  VG++ EKL++L++ 
Sbjct: 373 KSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYN 432

Query: 418 TRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVR 477
           TR PLSMQQP+W+DQDTTFQEIT D+G+E P +SV KQLMR HVRNLL +L+PKER I++
Sbjct: 433 TRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIK 492

Query: 478 LRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 532
           LRFGI+ GK +SLSE+G I+GLSKERVRQLESRALYRLKQ++     + YADLL+
Sbjct: 493 LRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHAYADLLV 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	532
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.885	0.861	0.541	6.6e-129
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.665	0.618	0.492	8.3e-90
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.635	0.590	0.381	1.6e-63
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.451	0.382	0.377	1.5e-50
TIGR_CMR|DET_0551	520	DET_0551 "RNA polymerase sigma	0.434	0.444	0.370	6e-48
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.516	0.743	0.357	2.6e-47
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.674	0.622	0.312	1.8e-46
TIGR_CMR|CJE_1081	622	CJE_1081 "RNA polymerase sigma	0.537	0.459	0.310	4.7e-46
TIGR_CMR|GSU_1525	328	GSU_1525 "RNA polymerase sigma	0.447	0.725	0.347	4.7e-46
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.466	0.767	0.382	7.9e-46

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

 Score = 1265 (450.4 bits), Expect = 6.6e-129, P = 6.6e-129
 Identities = 266/491 (54%), Positives = 340/491 (69%)

Query:    48 SQATSDSRNIETEAFFVEEKNSGDLDQLVQD--LEHQFLHWPDLWNL--SPPMKRGEDPS 103
             S A  D R   T    +E +   +L    +D   E Q LH   LWNL  SP     + P+
Sbjct:    71 SHALRDDR---TSQLTLERRQFDELVSSREDEKFEQQLLHSTGLWNLLISPLTSETKLPA 127

Query:   104 VSLTMQSLSNDTEESVDAEPFDXXXXXXXXXXXXXXXXXXXXNPKLNGAE-FTD-ISLTS 161
             V   +  L+       DAE  D                    + + N ++   D +S +S
Sbjct:   128 V---VSPLA-------DAELCDVVALAQKALSASKQAALLVDDTEANPSDNIKDSLSTSS 177

Query:   162 SLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLR 221
             S+  P E+       R LERR+K R+  K    + E Y  +K S KKK  +G D +D L+
Sbjct:   178 SMSLP-EKGNIVRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYKQGADNDDALQ 236

Query:   222 LFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRD 281
             LFLWGPET++LLTA EE ELI+ IQ L++LEK K+KL+SQ G EPT+ EWA+A+G+S   
Sbjct:   237 LFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPV 296

Query:   282 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAG 341
             LKS++H G SSREKLI ANLRLVVH+AKQYQ RG++  DLLQEGSMGLMKSVEKFKPQ+G
Sbjct:   297 LKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSG 356

Query:   342 CRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLA 401
             CRFA+YAYWW+RQ+IRK+IFQ+SRTIRLPEN+Y LL KV EA++  +QEGN+ P KE+LA
Sbjct:   357 CRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELA 416

Query:   402 RRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHV 461
               VG++ EKL++L++ TR PLSMQQP+W+DQDTTFQEIT D+G+E P +SV KQLMR HV
Sbjct:   417 GHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHV 476

Query:   462 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521
             RNLL +L+PKER I++LRFGI+ GK +SLSE+G I+GLSKERVRQLESRALYRLKQ++  
Sbjct:   477 RNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNS 536

Query:   522 KASYGYADLLI 532
                + YADLL+
Sbjct:   537 HGLHAYADLLV 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:   177 RFLERRSKKRKVSKPQVTNHETY--NSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLT 234
             R LERRSK+R   +  + +      NS+K    KK     + ++P +LFL   ET + LT
Sbjct:   216 RLLERRSKRRYAPRASIADVSCSADNSKKKEKSKKYGRVLEPDEPFKLFLRDRETTEFLT 275

Query:   235 ADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 294
             A EE  L ++IQ L+++E+   KL+ Q GREPTL EWA+A+G+S ++L+S + +G   RE
Sbjct:   276 AKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCRE 335

Query:   295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 354
             K+  +N RLV+HVA++Y+G G+ + DL+Q+G  GLMK+ EKF P  GCRF +YAYWW+RQ
Sbjct:   336 KMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQ 395

Query:   355 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERL 414
             +I+K+IF++SR IRLPE++Y LL KV +A+   I EG   P   ++ARR GIT+EKL +L
Sbjct:   396 SIKKSIFKNSRLIRLPESVYALLRKVGKARMECIMEGEQ-PTNANVARRAGITIEKLAKL 454

Query:   415 IFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERC 474
                TR P SMQ  VW+D+  TFQEIT D  VE PD+SV + +MRQ VR+ L +L+P+E+ 
Sbjct:   455 RAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSVDRMMMRQQVRDFLGILSPREKE 514

Query:   475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 531
             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:   177 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 235
             R  ER++++ K  +   +   +  +  +  KK+L ++  D NDPLR       + KLLT 
Sbjct:   216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275

Query:   236 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 295
              EE EL A IQDL++LE+ +++L  + GR+PT  +WA A G+  + L+  +H G   ++K
Sbjct:   276 REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDK 335

Query:   296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355
             +I +N+RLV+ +AK YQG G++L DL+QEG  GL++  EKF    G +F++YA+WW++Q 
Sbjct:   336 MIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQA 395

Query:   356 IRKAIFQHSRTIRLPENIYTLLSKVLEA-KRLYIQEGNHSPDKEDLARRVGITVEKLERL 414
             +RK++   SR IRLP ++     +V EA K+LY + G H P  E++A   G+++++L  +
Sbjct:   396 VRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKH-PKNEEIAEATGLSMKRLMAV 454

Query:   415 IFITRMPLSMQQPVWADQDTTFQEITADT-GVEIPDISVQKQLMRQHVRNLLTLLNPKER 473
             +   + P S+ Q +  +Q+    E+ AD   V   DI + K+ MRQ +  +L  L  +E+
Sbjct:   455 LLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILI-KEFMRQDLDKVLDSLGTREK 513

Query:   474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
              ++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:   288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASY 347
             + N +++++I ANLRLVV +AK+Y  RG+   DL+QEG++GLMK+V+KF  + G +F++Y
Sbjct:   386 TANRAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTY 445

Query:   348 AYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT 407
             A WWVRQ I +AI   +RTIR+P ++   ++K+    R  + E    P  E+L+ R+ I 
Sbjct:   446 ATWWVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPTLEELSARLNIN 505

Query:   408 VEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTL 467
             VEK+ +++ I + P+S++ P+  D  +TF +   D     P+ +     +R+    +L+ 
Sbjct:   506 VEKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLST 565

Query:   468 LNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 526
             L PKE  I+R+RFGI + GK  +L EVG +F +++ER+RQ+E++AL +L+     +   G
Sbjct:   566 LTPKEERILRMRFGIGKSGKDHTLEEVGRLFNVTRERIRQIEAKALRKLRHPSRARKLRG 625

Query:   527 Y 527
             +
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:   285 ELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 344
             E+ +  + R  LI ANLRLVV VAK++ GRG+ L DL+QEG++GL+++VEKF    G +F
Sbjct:   277 EIDAKRAERH-LIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKF 335

Query:   345 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRV 404
             ++YA WW+RQ I +AI   +RTIR+P ++   ++K+L   R   Q+    P  +++A  +
Sbjct:   336 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIAVEM 395

Query:   405 GITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNL 464
              +  EK+  +  ++++P+S++ P+  ++D+   +   D     P  +  +QL+++ +  +
Sbjct:   396 DLPPEKVREIAKVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTV 455

Query:   465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
             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:   237 EEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 296
             +E +L   I + I ++        + GR P L    + I L+ R  K E      ++ KL
Sbjct:    83 DEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTP-EEEIELAKR--KEE--GDEEAKRKL 137

Query:   297 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI 356
               ANLRLVV +AK+Y GRG+   DL+QEG++GL+K+VEKF  + G +F++YA WW+RQ I
Sbjct:   138 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAI 197

Query:   357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF 416
              +AI   +RTIR+P ++   ++K++   R  +QE    P  E++A+ +GI+ +K+  ++ 
Sbjct:   198 TRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEEIAKEMGISEDKVREIMK 257

Query:   417 ITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIV 476
             I + P+S++ P+  ++D+   +   D   + P       L+R+ +  +L  L  +E+ ++
Sbjct:   258 IAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDEVLKTLTEREQKVL 317

Query:   477 RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
             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:   156 DISLTSSLGYPLEEVKQFSQPR---FLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSE 212
             D+ L ++L   LEE    +  R     ER+  K K+++  VT+    +   A + ++L E
Sbjct:   192 DVRL-AALNAELEEESLSASRRQELLAERQELKEKLAE-MVTSLRLKDRHIAKIAQRLKE 249

Query:   213 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQ--IQDLIRLEKEKSKLQSQFGR--EPTL 268
                + D +   +   E    ++AD   E+ A   +   I+L  E ++   +  R  E  L
Sbjct:   250 LSAKVDTIMAEIAAIEKEAGVSADTLKEIAASEAVGKGIKLSLEDAQKHEKKVRSAEKKL 309

Query:   269 IEWAKAIGLSCRDLKSELHS---GNS----SREKLINANLRLVVHVAKQYQGRGISLHDL 321
              +  +  G   R+L   L +   G +    ++ +L+ ANLRLVV +AK+Y  RG+   DL
Sbjct:   310 KKVEEESGFKARELSDALRAIDRGEAKSKLAKSELVEANLRLVVSIAKKYTNRGLQFLDL 369

Query:   322 LQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVL 381
             +QEG++GLMK+V+KF+ Q G +F++YA WW+RQ I +AI   +RTIR+P ++   ++K++
Sbjct:   370 IQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLI 429

Query:   382 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA 441
                R  +QE    P  E++A R+ + ++K+ +++ I + P+S++ P+  ++D+   +   
Sbjct:   430 RTSRQLVQEIGREPSPEEIAERMNLPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIE 489

Query:   442 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 501
             D GV  P  +V K  + +    +L  L P+E  ++R+RFGI +    +L EVG  F +++
Sbjct:   490 DKGVVSPLEAVIKANLSEQTARVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTR 549

Query:   502 ERVRQLESRALYRLK 516
             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:   238 EFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 297
             E  +++   ++ +L + K   +  F  E + +   K I      +K      + ++ ++ 
Sbjct:   333 ETTMVSTYMEIKKLFQTKEASEKSFDLEKSRL---KEI---LEQIKRGKKISDEAKGRMA 386

Query:   298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR 357
              +NLRLVV +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I 
Sbjct:   387 KSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAIS 446

Query:   358 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI 417
             +AI   +RTIR+P ++   ++++ +  R ++Q+    PD   +A+ VG++V+K++++I I
Sbjct:   447 RAIADQARTIRIPIHMIETINQINKIIREHLQKDGKEPDVSVIAKEVGLSVDKVKQVIKI 506

Query:   418 TRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVR 477
             T+ P+S++ P+  + D  F +   D     P   + K  +++ +  +L  LN +E+ ++R
Sbjct:   507 TKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVLDQLNDREKAVIR 566

Query:   478 LRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 529
             +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:   280 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 338
             ++L   +  G+ ++R+K+I +NLRLVV +AK+Y  RG+   DL++EG+MGL+K+VE+FK 
Sbjct:    79 KELAGRIAKGDKAARDKMIESNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKL 138

Query:   339 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 398
                CRF++YA WW+RQ+I +A+   SRTIRLP ++   ++K+L+  R  +Q  N  P  +
Sbjct:   139 SKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDDINKMLKITRELVQRLNREPSVK 198

Query:   399 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 458
             ++A  + +    + RL+ + +   S+++P+  + D    +   DT    P + ++     
Sbjct:   199 EVATEMKVNSAYVRRLMVLLKKTYSIERPMGENSDYFLIDTIEDTSTVSPAVLLEDLNKY 258

Query:   459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
             + 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:   268 LIEWAKAIGLSC-RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGS 326
             L+E  K +G +  RDL + +  G ++R  L+ ANLRLVV +AK+Y GRG+ L DL+QEG+
Sbjct:    61 LLETRKRLGENRKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGN 120

Query:   327 MGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 386
             +GL++++EKF    G +F++YA WW+RQ I + +   SRTIRLP ++   ++K+   KR 
Sbjct:   121 LGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRE 180

Query:   387 YIQE-GNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV 445
               Q  G  + D E+LA   GI ++K+  L+  +R P+S+  PV ++++    +   D   
Sbjct:   181 MHQHLGREATD-EELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEA 239

Query:   446 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 505
                + +V  +L+   +R++L  L+ +E  ++RLRFG++DG+P++L ++G +FGLS+ERVR
Sbjct:   240 MSAENAVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVR 299

Query:   506 QLESRALYRLK 516
             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	0.5551	0.9624	0.9360	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

Your Input:
	fgenesh4_pm.C_scaffold_28000088	hypothetical protein (535 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.28720003	Predicted protein (152 aa)			•				•		0.574
	gw1.XIV.2894.1	hypothetical protein (684 aa)			•						0.452
	fgenesh4_pm.C_LG_X000986	hypothetical protein (932 aa)							•		0.441
	fgenesh4_pg.C_LG_XVII000398	hypothetical protein (677 aa)			•						0.439
	eugene3.17410001	annotation not avaliable (472 aa)			•						0.439
	gw1.321.23.1	annotation not avaliable (657 aa)			•						0.438
	estExt_fgenesh4_pg.C_3210002	hypothetical protein (472 aa)			•						0.438
	eugene3.00001972	hypothetical protein (485 aa)			•						0.426
	eugene3.29520003	annotation not avaliable (742 aa)					•		•		0.425
	gw1.XIV.2088.1	hypothetical protein (955 aa)			•	•			•		0.420

---

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	532
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	6e-97
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	2e-81
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	1e-77
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	9e-75
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	8e-73
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	1e-72
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	3e-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	2e-53
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	2e-44
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	7e-31
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	9e-30
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	2e-27
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	3e-27
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	2e-24
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	8e-22
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	6e-21
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	2e-20
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	8e-19
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	1e-18
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	2e-17
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	1e-16
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	1e-16
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	2e-13
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	1e-12
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	1e-12
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	1e-12
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	6e-12
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	1e-11
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	8e-11
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	2e-10
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	4e-10
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	7e-10
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	9e-10
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	1e-09
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	5e-09
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	2e-08
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	3e-08
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	1e-06
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	4e-06
PRK08295	208	PRK08295, PRK08295, RNA polymerase factor sigma-70	1e-04
TIGR02859	198	TIGR02859, spore_sigH, RNA polymerase sigma-H fact	2e-04
COG1595	182	COG1595, RpoE, DNA-directed RNA polymerase special	0.002
PRK12427	231	PRK12427, PRK12427, flagellar biosynthesis sigma f	0.003

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

 Score =  295 bits (758), Expect = 6e-97
 Identities = 126/285 (44%), Positives = 194/285 (68%), Gaps = 1/285 (0%)

Query: 232 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 291
           LLT +EE EL  Q+Q ++ LE+ + +L+ Q GREP+  EWA A GLS  +L+  L  G  
Sbjct: 15  LLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQR 74

Query: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
           ++EK+I ANLRLVV VAK+YQ RG+ L DL+QEGS+GL ++VEKF P  G +F++YAYWW
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWW 134

Query: 352 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 411
           +RQ I +AI   SRTIRLP +I   L+K+ + +R   Q+   +P + ++A  + +  E++
Sbjct: 135 IRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQV 194

Query: 412 ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 471
             L+   R P+S+  PV  ++DT   ++  D G   P+  V+++ +RQ + +LL  L P+
Sbjct: 195 RELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELTPR 253

Query: 472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           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 =  258 bits (661), Expect = 2e-81
 Identities = 121/317 (38%), Positives = 206/317 (64%), Gaps = 8/317 (2%)

Query: 201 SRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 260
             K   KK  +E     D +R++L      +LL  DEE EL  +I DL+ LE+ + + +S
Sbjct: 51  RIKIGPKKVYTE-----DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFES 105

Query: 261 QFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHD 320
           + GREP+  EWA+ + +     +  L  G  ++EK++ +NLRLVV +AK+Y  RG+S  D
Sbjct: 106 ELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQD 165

Query: 321 LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKV 380
           L+QEGS+GL+++ EKF  + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++
Sbjct: 166 LIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRI 225

Query: 381 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE-I 439
            +  ++  QE    P +E++A  + +T+EKL  +    ++P+S++ P+  ++D+   + I
Sbjct: 226 KKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI 285

Query: 440 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL 499
            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: 500 SKERVRQLESRALYRLK 516
           ++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 =  247 bits (633), Expect = 1e-77
 Identities = 110/306 (35%), Positives = 181/306 (59%), Gaps = 21/306 (6%)

Query: 232 LLTADEEFELIAQIQDLIRLEKEKSKL-QSQFGREPTL---------------IEWAKAI 275
           LL  + E EL  Q++D   L +    L   + GREP+                IE A  +
Sbjct: 23  LLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLL 82

Query: 276 GLS-CRDLKSELHSGNSSRE---KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK 331
                + L   L  G    +   KL+ +NLRLVV +AK+Y GRG+   DL+QEG++GLMK
Sbjct: 83  TPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMK 142

Query: 332 SVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG 391
           +VEKF P+ G +F++YA WW+RQ I +AI   +RTIR+P +   L++K+   KR  +QE 
Sbjct: 143 AVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQEL 202

Query: 392 NHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 451
              P  E++A  +G++ +K+  ++     P+S+  P+  D+D+   +   D     P+ +
Sbjct: 203 GREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELGDFLEDDKSVSPEDA 262

Query: 452 VQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510
           V+++ +++ +  +L   L  +ER ++RLRFG++DG+PK+L E+G  FG+S+ERVRQ+E++
Sbjct: 263 VERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAK 322

Query: 511 ALYRLK 516
           AL +L+
Sbjct: 323 ALRKLR 328

Length = 342

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

 Score =  239 bits (611), Expect = 9e-75
 Identities = 122/294 (41%), Positives = 185/294 (62%), Gaps = 1/294 (0%)

Query: 232 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 291
           LLT ++E     Q+Q ++ L + K  L  + GREP+L EWA+A+ LS  +LK  L  G  
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
           +++K+I ANLRLVV +AK+YQ R +   DL+QEG++GL + VEKF P  G +F++YAYWW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 352 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 411
           +RQ I +AI Q +RTIRLP +I   L+K+ + +R   Q+   S    ++A+ + +   ++
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQI 211

Query: 412 ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 471
              + + R P+S+   V  +QDT   E+  D G   PD  + ++L+RQ + NLL  L P+
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELSELLEDEGPS-PDQYITQELLRQDLNNLLAELTPQ 270

Query: 472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY 525
           +R ++ LRFG+EDGK  SL++VG    LS+ERVRQLE +AL  L++       Y
Sbjct: 271 QREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRRANVKEY 324

Length = 327

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

 Score =  234 bits (598), Expect = 8e-73
 Identities = 121/308 (39%), Positives = 189/308 (61%), Gaps = 1/308 (0%)

Query: 218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 277
           D +R +L       LLT +EE     Q+Q L+ L++ + +L  + GREPT  EWAKA  L
Sbjct: 8   DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKL 67

Query: 278 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 337
           S  +L+S +  G +++ K++ ANLRLVV VAK+Y  R + L DL+QEG++G+ + VEKF 
Sbjct: 68  SEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFD 127

Query: 338 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 397
           P  G RF++YAYWW+RQ I +AI + SRTIRLP +I   L+K+ +A+R   Q+   +   
Sbjct: 128 PTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATI 187

Query: 398 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 457
            +LA  + +T +++   +   R PLS+   V  +QDT   E+  DTG    D + Q  L 
Sbjct: 188 GELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFATQSSL- 246

Query: 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           +  +  L+  L P+++ ++ LRFG+EDG+P +L+++G    +S+ERVRQ+E  AL +L++
Sbjct: 247 QLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306

Query: 518 SLGGKASY 525
                  Y
Sbjct: 307 RKANIQEY 314

Length = 317

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

 Score =  231 bits (590), Expect = 1e-72
 Identities = 91/224 (40%), Positives = 155/224 (69%)

Query: 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352
           +++L+ +NLRLVV +AK+Y  RG+S  DL+QEG++GLMK+VEKF  + G +F++YA WW+
Sbjct: 2   KKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWI 61

Query: 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 412
           RQ I +AI   +RTIR+P ++   ++K+++A+R   QE    P  E+LA R+G+  EK+ 
Sbjct: 62  RQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVR 121

Query: 413 RLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKE 472
            +  I + P+S++ P+  ++D+   +   DT +E PD    K+L+R+ +  +L  L  +E
Sbjct: 122 EIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTERE 181

Query: 473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
             ++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|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated

 Score =  227 bits (580), Expect = 4e-69
 Identities = 128/348 (36%), Positives = 193/348 (55%), Gaps = 55/348 (15%)

Query: 218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKE--------------------KSK 257
           D +RL+L      +LL  DEE     ++Q  ++L                       + +
Sbjct: 60  DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRER 119

Query: 258 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS----------------------SREK 295
           L S+ G  P+L  WAK   +S  DLK  L  G                        ++E 
Sbjct: 120 LTSELGHRPSLERWAKTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEH 179

Query: 296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355
           +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF++YAYWW+RQ 
Sbjct: 180 MIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQG 239

Query: 356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI 415
           I +AI   SRTIRLP +I   L+K+ +A+R   QE   +P  ED+A+ + +T  ++  + 
Sbjct: 240 ITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV- 298

Query: 416 FITRMP--LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRN----LLTLLN 469
            + R+P  +S++  V  D+DT   ++     +E  DIS ++ LMR+ ++     LL  L 
Sbjct: 299 -LLRVPRSVSLETKVGKDKDTELGDL-----LETDDISPEEMLMRESLQRDLQHLLADLT 352

Query: 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
            +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 =  203 bits (519), Expect = 4e-61
 Identities = 111/302 (36%), Positives = 186/302 (61%), Gaps = 17/302 (5%)

Query: 218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 277
           D +R++L G     LLTA +E EL  +I+         + L ++      L+E  K +  
Sbjct: 26  DLVRVYLNGIGKTALLTAADEVELAKRIE---------AGLYAE-----HLLETRKRLSE 71

Query: 278 SC-RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 336
           +  RDL + +  G ++R  L+ ANLRLVV +AK+Y GRG+ L DL+QEG++GL++++EKF
Sbjct: 72  ARKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKF 131

Query: 337 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKR-LYIQEGNHSP 395
               G +F++YA WW+RQ I + +   SRTIRLP ++   ++K+   KR L+ Q G  + 
Sbjct: 132 DYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREAT 191

Query: 396 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 455
           D E+LA   GI  EK+  L+  +R P+S+  PV +D++    +   D+     + +V   
Sbjct: 192 D-EELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAG 250

Query: 456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515
           L+   +R++L  L+ +E+ ++RLRFG++DG+P++L ++G +FGLS+ERVRQ+E   + +L
Sbjct: 251 LLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKL 310

Query: 516 KQ 517
           + 
Sbjct: 311 RN 312

Length = 324

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

 Score =  194 bits (496), Expect = 3e-58
 Identities = 86/228 (37%), Positives = 137/228 (60%)

Query: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
           +R+ +I +NLRLVV +AK Y  RG+ L DL++EG++GLM +VEKF P+ G RF++YA WW
Sbjct: 47  ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWW 106

Query: 352 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 411
           +RQTI +AI   +RTIRLP ++   L+  L A R   ++    P  E++A  +   VE +
Sbjct: 107 IRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDV 166

Query: 412 ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 471
            R++ +     S+  P+  D   +  +  AD     P+  VQ   ++Q +   L  LN +
Sbjct: 167 SRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNER 226

Query: 472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
           +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 =  196 bits (500), Expect = 2e-56
 Identities = 105/290 (36%), Positives = 170/290 (58%), Gaps = 21/290 (7%)

Query: 231 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 290
           KLL A+EE EL        R+E         +  E  L E  K      RDL+     G 
Sbjct: 224 KLLNAEEEVELA------KRIEAG------LYAEE-LLAEGEKLDPELRRDLQWIGRDGK 270

Query: 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 350
            ++  L+ ANLRLVV +AK+Y  RG+S  DL+QEG++GL+K+VEKF    G +F++YA W
Sbjct: 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATW 330

Query: 351 WVRQTIRKAIFQHSRTIRLP----ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI 406
           W+RQ I +A+   +RTIR+P    E I    +K+   +R  +QE    P  E+LA+ +G 
Sbjct: 331 WIRQAITRAMADQARTIRIPVHMVETI----NKLGRIERELLQELGREPTPEELAKEMGF 386

Query: 407 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 466
           T EK+  +    R P+S+ + +  + D+ F +   D+    P  +V   L++  ++ +L 
Sbjct: 387 TPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLE 446

Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
            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 =  190 bits (486), Expect = 3e-56
 Identities = 86/229 (37%), Positives = 144/229 (62%)

Query: 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 350
           ++R+++I +NLRLVV +AK+Y  RG++L DL++EG++GL+++VEKF P+ G RF++YA W
Sbjct: 86  AARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 145

Query: 351 WVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK 410
           W+RQTI +AI   +RTIRLP ++   L+  L A R    + +H P  E++A  +   V+ 
Sbjct: 146 WIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDD 205

Query: 411 LERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 470
           + R++ +     S+  P+  D + +  +I AD     P+ + Q   M+Q +   L  LN 
Sbjct: 206 VSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELND 265

Query: 471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
           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 =  184 bits (470), Expect = 2e-53
 Identities = 103/308 (33%), Positives = 174/308 (56%), Gaps = 42/308 (13%)

Query: 211 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIE 270
             G   NDP+R++L       LLTA+EE EL                             
Sbjct: 89  PPGVKINDPVRMYLKEIGRVPLLTAEEEIEL----------------------------- 119

Query: 271 WAKAIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGL 329
            AK I             G+  ++++L  ANLRLVV +AK+Y GRG+   DL+QEG+MGL
Sbjct: 120 -AKRIE-----------EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGL 167

Query: 330 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQ 389
           MK+VEKF  + G +F++YA WW+RQ I +AI   +RTIR+P ++   ++K++  +R  +Q
Sbjct: 168 MKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQ 227

Query: 390 EGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 449
           E    P  E++A  + +  EK+  ++ I + P+S++ P+  + D+   +   D     P 
Sbjct: 228 ELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPA 287

Query: 450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 509
                +L+++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E+
Sbjct: 288 DHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEA 347

Query: 510 RALYRLKQ 517
           +AL +L+ 
Sbjct: 348 KALRKLRH 355

Length = 367

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

 Score =  165 bits (421), Expect = 2e-44
 Identities = 92/278 (33%), Positives = 167/278 (60%), Gaps = 16/278 (5%)

Query: 244 QIQDLIRLEKEKSKLQSQFGREPT-LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLR 302
              ++ +L++E   ++ + G     L E  + I       K E  +  + +E ++ ANLR
Sbjct: 339 VYDEIKKLQQELEAIEEETGLTIEELKEINRQI------SKGEAKARRAKKE-MVEANLR 391

Query: 303 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 362
           LV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I  
Sbjct: 392 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 451

Query: 363 HSRTIRLP----ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT 418
            +RTIR+P    E I    +K+    R  +QE    P  E+LA R+G+  +K+ +++ I 
Sbjct: 452 QARTIRIPVHMIETI----NKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIA 507

Query: 419 RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRL 478
           + P+S++ P+  D+D+   +   D   E+P  +  ++ +R+   ++L  L P+E  ++R+
Sbjct: 508 KEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRM 567

Query: 479 RFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           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 =  120 bits (302), Expect = 7e-31
 Identities = 64/247 (25%), Positives = 124/247 (50%), Gaps = 19/247 (7%)

Query: 280 RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLH-DLLQEGSMGLMKSVEKFKP 338
             L      G+    +LI   L LV  +A++++ RG S + DL+Q G +GL+K++E++ P
Sbjct: 12  EKLLEYYAEGDEEARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDP 71

Query: 339 QAGCRFASYAYWWVRQTIRKAIFQHSR---TIRLPENIYTLLSKVLEAKRLYIQEGNHSP 395
             G +F++YA     + IR  I  + R   ++++P ++  L  ++ EA     QE    P
Sbjct: 72  SKGTKFSTYA----VRRIRGEILDYLRKNDSVKVPRSLRELGRRIEEAIDELEQELGREP 127

Query: 396 DKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 453
             E++A  +GI  E+    +        LS+ + V  D D    +      +E PD  V+
Sbjct: 128 TDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDDQ-----IENPDDGVE 182

Query: 454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513
           K+ + + ++  +  L  +E+ ++ LR+  E     +  E+  + G+S+ RV +L  +A+ 
Sbjct: 183 KEELLEILKEAIEPLPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVSRLHKKAIK 238

Query: 514 RLKQSLG 520
           +L++ L 
Sbjct: 239 KLRKELN 245

Length = 247

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

 Score =  117 bits (295), Expect = 9e-30
 Identities = 72/240 (30%), Positives = 128/240 (53%), Gaps = 25/240 (10%)

Query: 295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 354
           KL+ ++LR VV +A+ Y+G G+   DL+QEG++GLMK+V++F P+ G R  S+A  W++ 
Sbjct: 39  KLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKA 98

Query: 355 TIRKAIFQHSRTIRLPENIYTLLSKVL------EAKRLYIQEGNHSPDK-EDLARRVGIT 407
            I + I ++ R +++     T   + L        KRL   +G  +P++ E +A  +G++
Sbjct: 99  EIHEYILRNWRLVKVAT---TKAQRKLFFNLRKMKKRL---QGWLNPEEVEAIAEELGVS 152

Query: 408 VEKLERLIFITRMP---LSMQQPVWADQDTTFQEIT--ADTGVEIPDISVQKQ---LMRQ 459
               E     +R+    +S+   +  D+D     I    D   +  D   ++Q   L RQ
Sbjct: 153 ER--EVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDTLEEEQWEELQRQ 210

Query: 460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
            + 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|236033 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed

 Score =  111 bits (279), Expect = 2e-27
 Identities = 67/257 (26%), Positives = 130/257 (50%), Gaps = 49/257 (19%)

Query: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
           +  ++I+A++RLV+ +A +++  G+ ++DL+QEG +GL+++  +F+P    RF++YA WW
Sbjct: 41  ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWW 100

Query: 352 VRQTI------------------RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNH 393
           +R +I                  +KA+F + R +R              A+   + + + 
Sbjct: 101 IRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLR--------------AR---LAQADE 143

Query: 394 SPDKEDLARRV----GITVEKLERLIFITRMP-LSMQQPVWADQDTTFQEITA--DTGVE 446
              K+++ R +    G+++  +E +      P  S+  P   + +   + +    D    
Sbjct: 144 ELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDS-P 202

Query: 447 IPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 502
           +PD  V+     +  R+ +   L  LN +E  I+R R   ED    +L  +G   G+SKE
Sbjct: 203 LPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRED--GATLEALGEELGISKE 260

Query: 503 RVRQLESRALYRLKQSL 519
           RVRQ+E+RAL +L+++L
Sbjct: 261 RVRQIEARALEKLRRAL 277

Length = 289

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

 Score =  109 bits (274), Expect = 3e-27
 Identities = 69/231 (29%), Positives = 121/231 (52%), Gaps = 13/231 (5%)

Query: 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352
           REKL+  NL LV  +A++++ RG    DL+Q G++GL+K++++F P  G +F+++A   +
Sbjct: 5   REKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTI 64

Query: 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 412
              I++     +  +R+P  +  L  K+ +A     Q    SP   ++A R+G++ E++ 
Sbjct: 65  MGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVV 124

Query: 413 RLIFITRM--PLSMQQPVWADQDTTFQEIT-ADT-GVEIPDISVQKQLMRQHVRNLLTLL 468
             +        LS+   +  D       I   DT G E  D +++    R  ++ LL  L
Sbjct: 125 EALEAGNAYQALSLDASIEDDDGD---PIALLDTLGDE--DDALETVEDRLALKPLLAAL 179

Query: 469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
             +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|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed

 Score =  102 bits (257), Expect = 2e-24
 Identities = 71/250 (28%), Positives = 126/250 (50%), Gaps = 38/250 (15%)

Query: 295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 354
           +L+ ++LR VVH+A+ Y+G G+   DL+QEG++GLMK+V++F P+ G R  S+A  W++ 
Sbjct: 52  QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKA 111

Query: 355 TIRKAIFQHSRTIRLPENIYTL---------LSKVLEAKRLYIQEGNHSPDK-EDLARRV 404
            I + I ++ R ++    + T          L K    KRL    G  +P++ E +A  +
Sbjct: 112 EIHEYILRNWRIVK----VATTKAQRKLFFNLRKA--KKRL----GWLNPEEVEMVAEEL 161

Query: 405 GITVE---KLERLIFITRMP---LSMQQPVWADQDTTFQEIT--ADTGVEIPDISVQKQL 456
           G++ E   ++E      R+     S+  P+  D + +        D   +  D+  +   
Sbjct: 162 GVSEEEVREMES-----RLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNW 216

Query: 457 MRQHVRNL---LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513
             Q    L   L  L+ + R I+  R+  +D    +L E+   +G+S ERVRQ+E  A+ 
Sbjct: 217 EDQRRALLADALEGLDERSRDIIEARWLDDD--KSTLQELAAEYGVSAERVRQIEKNAMK 274

Query: 514 RLKQSLGGKA 523
           +LK ++   A
Sbjct: 275 KLKAAIEAAA 284

Length = 284

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

 Score = 94.6 bits (236), Expect = 8e-22
 Identities = 67/244 (27%), Positives = 133/244 (54%), Gaps = 21/244 (8%)

Query: 280 RDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 338
           R+L   + +G   +REKLIN NLRLV+ V +++  RG ++ DL Q G +GLMK+++ F  
Sbjct: 25  RELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDL 84

Query: 339 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 398
               +F++YA   +   IR+ +  ++  IR+  ++  +  K L+ +   I E +  P  E
Sbjct: 85  SQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVE 143

Query: 399 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQ-DTTF--QEITADTGVE---IPDISV 452
           ++A+ + +  E++   +   + P+S+ +P++ D  D  +   +I+ +   +   + +I++
Sbjct: 144 EIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKNKDENWLEEIAL 203

Query: 453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 512
            K+ M++        LN +E+ I+ LRF     + K+  EV    G+S+ +V +LE  AL
Sbjct: 204 -KEAMKK--------LNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAAL 250

Query: 513 YRLK 516
             ++
Sbjct: 251 KHMR 254

Length = 258

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

 Score = 92.2 bits (229), Expect = 6e-21
 Identities = 68/244 (27%), Positives = 128/244 (52%), Gaps = 19/244 (7%)

Query: 280 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 338
           R+L   + SG+ ++REKLIN NLRLV+ V +++  RG  + DL Q G +GLMKS++ F  
Sbjct: 22  RELFIRMQSGDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDL 81

Query: 339 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 398
               +F++YA   +   IR+ + + +  IR+  ++  +  K L+ +   I E +  P   
Sbjct: 82  SQNVKFSTYAVPMIIGEIRRYL-RDNNPIRVSRSLRDIAYKALQVRDKLISENSKEPTVS 140

Query: 399 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 458
           ++A+ + +  E++   +   + P+S+ +P++ D          D    +  IS +K    
Sbjct: 141 EIAKELKVPQEEVVFALDAIQDPVSLFEPIYND--------GGDPIYVMDQISDEKNKDS 192

Query: 459 QHVRNL-----LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513
           Q +  +     +  LN +E+ I+ +RF   +GK +   EV    G+S+ +V +LE  AL 
Sbjct: 193 QWLEGIALKEAMKRLNEREKMILNMRF--FEGKTQ--MEVAEEIGISQAQVSRLEKAALK 248

Query: 514 RLKQ 517
            +++
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 = 90.2 bits (224), Expect = 2e-20
 Identities = 66/236 (27%), Positives = 122/236 (51%), Gaps = 13/236 (5%)

Query: 287 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 345
            +G+  +R+KLI  NLRLV  + K++  RG    DL Q G +GL+K+++KF      +F+
Sbjct: 6   QNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFS 65

Query: 346 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG 405
           +YA   +   I++ + +    I++  ++  L  K+   K    +E    P   +LA  +G
Sbjct: 66  TYAVPMIMGEIKRFL-RDDGIIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALG 124

Query: 406 ITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI--TADTGVEIPDISVQKQLMRQHVRN 463
           ++ E++   +   R P S+   V  D       +   AD G E  D  ++K  +++ +  
Sbjct: 125 VSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKGSEDSDW-LEKIALKEAISK 183

Query: 464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
               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 = 80.3 bits (199), Expect = 8e-19
 Identities = 27/71 (38%), Positives = 44/71 (61%)

Query: 296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 355
           L+   L LV  +A++Y G G    DL+QEG +GL+++VE+F P+ G  F+++ Y  +R  
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 356 IRKAIFQHSRT 366
           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 = 84.8 bits (210), Expect = 1e-18
 Identities = 57/227 (25%), Positives = 103/227 (45%), Gaps = 56/227 (24%)

Query: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
           +R  LI  NLRLV H+ K++   G  + DL+  G++GL+K+++ F P  G R A+YA   
Sbjct: 49  ARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYA--- 105

Query: 352 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 411
             + I   I  H R +                K+                          
Sbjct: 106 -ARCIENEILMHLRAL----------------KK-------------------------- 122

Query: 412 ERLIFITRMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 468
                 T+  +S+Q P+  D+   + +  +I    G  + +  V+  L  + +   L++L
Sbjct: 123 ------TKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQ-VELNLEIKKLYKKLSVL 175

Query: 469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 515
           + +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 = 81.6 bits (202), Expect = 2e-17
 Identities = 65/239 (27%), Positives = 120/239 (50%), Gaps = 17/239 (7%)

Query: 287 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 345
             G+  +R+ L+  NLRLV  V +++  RG    DL Q G +GL+K+V+KF      +F+
Sbjct: 27  QDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFS 86

Query: 346 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG 405
           +YA   +   I++ + +   T+++  ++    +K+ + K    +E    P  E+LA  +G
Sbjct: 87  TYAVPMIIGEIQRFL-RDDGTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLG 145

Query: 406 ITVEKLERLIFITRMPLSMQQPVWADQD---TTFQEITADTGVEIPDISVQKQLMRQHVR 462
           +T E++      +R P S+ + V  +     T   +I   +  +  D    K+ +R+   
Sbjct: 146 VTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSEEDWFDKIALKEAIRE--- 202

Query: 463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 521
                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 = 79.1 bits (195), Expect = 1e-16
 Identities = 63/233 (27%), Positives = 111/233 (47%), Gaps = 56/233 (24%)

Query: 290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAY 349
            S++  LI  NLRLVV++A++++  GI + DL+  G++GL+K+V  F P    + A+YA 
Sbjct: 51  ESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYA- 109

Query: 350 WWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 409
                         SR I   EN      ++L    +Y++  N                 
Sbjct: 110 --------------SRCI---EN------EIL----MYLRRNNK---------------- 126

Query: 410 KLERLIFITRMPLSMQQPV---WADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 466
                   TR  +S  +P+   W   +    ++   T  +I    +++++ R+ +R  L 
Sbjct: 127 --------TRSEVSFDEPLNVDWDGNELLLSDVLG-TDSDIVYKYLEEEVDRELLRKALA 177

Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
            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 = 78.8 bits (195), Expect = 1e-16
 Identities = 56/234 (23%), Positives = 113/234 (48%), Gaps = 19/234 (8%)

Query: 296 LINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352
           LI   L LV  +A +        + L DL+Q G  GL+ ++E++ P  G +F +YA    
Sbjct: 1   LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYA---- 56

Query: 353 RQTIRKAIFQHSRTIR-LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 411
            Q IR A+    R +  +P ++     K+  A R         P +E++A  +G+ +++ 
Sbjct: 57  VQRIRGAMLDELRRLDWVPRSLRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEY 116

Query: 412 ERL---IFITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 466
            +    I    + +S+ + +    D   +  +   D   E P+  ++++ +R+ +   + 
Sbjct: 117 RQALNEINALSL-VSLDE-LLESGDDGGSLIDRIEDDKSEDPEEELEREELREALAEAIE 174

Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520
            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|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed

 Score = 69.9 bits (172), Expect = 2e-13
 Identities = 52/194 (26%), Positives = 95/194 (48%), Gaps = 10/194 (5%)

Query: 293 REKLINANLRLVVHVAKQY-QGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
           R +L+  NL LV   A ++         DL+Q GS+GL++++E+F P  G  F+S+A  +
Sbjct: 27  RNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPY 86

Query: 352 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 411
           +R  I+  +   S T+R+P     L  +  + ++   QE    P  +++A+ + I++E+ 
Sbjct: 87  IRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEW 146

Query: 412 E--RLIFITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDISVQKQLM-RQHVRNLLT 466
           +  +L    R PLS+  PV  D+D  T+  ++  D        S Q     R  ++  L 
Sbjct: 147 QEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPDPRYR----SFQLAQEDRIRLQQALA 202

Query: 467 LLNPKERCIVRLRF 480
            L  + R ++   F
Sbjct: 203 QLEERTREVLEFVF 216

Length = 256

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

 Score = 67.8 bits (166), Expect = 1e-12
 Identities = 61/235 (25%), Positives = 110/235 (46%), Gaps = 17/235 (7%)

Query: 294 EKLINANLRLV-VHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 350
           ++LI   + LV  HV +   G  + +S  DL   G +GL  ++EKF P    +F +YA +
Sbjct: 25  DELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASF 84

Query: 351 WVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 409
                IR AI    R    LP ++     KV  A     Q    +   +++A  +G+T E
Sbjct: 85  ----RIRGAIIDGLRKEDWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEE 140

Query: 410 KLERLI---FITRMPLSM-QQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLL 465
           ++E  +   F   + LS+ ++    D          D     P+  + K+ + + +   +
Sbjct: 141 EVEATMNEGFFANL-LSIDEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKI 199

Query: 466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520
             L+ KE+ ++ L +  E     +L+E+G +  LS  R+ Q+ S+AL++LK+ L 
Sbjct: 200 KQLSEKEQLVISLFYKEE----LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250

Length = 251

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

 Score = 67.5 bits (165), Expect = 1e-12
 Identities = 57/230 (24%), Positives = 113/230 (49%), Gaps = 9/230 (3%)

Query: 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352
           R++++   L L  H+A+++ GRG    DL+Q   +GL+ +V +F  + G  F S+A   +
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTI 101

Query: 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL- 411
              +R+    +S ++++P  +  L  ++  A     Q    +P   +LA  +G+  E++ 
Sbjct: 102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVV 161

Query: 412 ERLIFITRM-PLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 470
           E L+  +    LS+     +  D       ADT  ++ D  + +   R+ +R LL  L  
Sbjct: 162 EGLVAGSAYNTLSIDSGGGSGDDDARA--IADTLGDV-DAGLDQIENREALRPLLAALPE 218

Query: 471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 520
           +ER ++ LRF     +  + +++    G+S+  V +L ++ L RL+  L 
Sbjct: 219 RERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264

Length = 264

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

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 23/74 (31%), Positives = 40/74 (54%)

Query: 376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT 435
           LL+K+  A+R   QE    P  E++A  +GI+ EK+  ++   R P+S+  PV  ++D  
Sbjct: 2   LLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDGE 61

Query: 436 FQEITADTGVEIPD 449
             ++  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|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family

 Score = 63.5 bits (155), Expect = 6e-12
 Identities = 37/178 (20%), Positives = 74/178 (41%), Gaps = 23/178 (12%)

Query: 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 350
            + E+L    L LV   A++Y G      DL+QE  + L++++++F P+    F ++ + 
Sbjct: 1   EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFR 58

Query: 351 WVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK 410
             R  I   + +  R  R  + +  LL      +    Q        E+    +   +EK
Sbjct: 59  IARNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQ--------EEEREALREALEK 110

Query: 411 L---ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLL 465
           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 = 59.4 bits (145), Expect = 1e-11
 Identities = 24/54 (44%), Positives = 36/54 (66%), Gaps = 4/54 (7%)

Query: 464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
            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 = 61.8 bits (151), Expect = 8e-11
 Identities = 55/245 (22%), Positives = 114/245 (46%), Gaps = 24/245 (9%)

Query: 287 HSGNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCR 343
             G   +++L+     LV  +A + + R    + L DL+Q G +GL+++  ++  + G  
Sbjct: 4   AEGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGAS 63

Query: 344 FASYAYWWVRQTIRKAIFQHSRTIRL---PENIYTLLSKVLEAKRLYIQEGNHSPDKEDL 400
           F +YA     Q IR A+    R   L   P ++     +V +A R   QE    P   ++
Sbjct: 64  FETYA----GQRIRGAMLDELR--SLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTEV 117

Query: 401 ARRVGITVEKL-ERLI---FITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQL 456
           A ++G+++E+  E L+         +   +    D     ++   +  ++     ++ + 
Sbjct: 118 AEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQDEDPLQ----QLEDEE 173

Query: 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           +R+ +   +  L  +E+ ++ L +  E     +L E+G + G+S+ RV Q+ S+A+ RL+
Sbjct: 174 LREALVEAIESLPEREQLVLSLYYQEE----LNLKEIGAVLGVSESRVSQIHSQAIKRLR 229

Query: 517 QSLGG 521
             LG 
Sbjct: 230 ARLGE 234

Length = 236

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

 Score = 61.2 bits (149), Expect = 2e-10
 Identities = 57/241 (23%), Positives = 113/241 (46%), Gaps = 25/241 (10%)

Query: 293 REKLINANLRLVVHVAKQYQGR-GISLH------DLLQEGSMGLMKSVEKFKPQAGCRFA 345
           RE LI     LV +VA    GR  + +       DL+  G  GL+ ++EKF P+   +F 
Sbjct: 33  REYLILKYSPLVKYVA----GRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFK 88

Query: 346 SYAYWWVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRV 404
           +YA       IR AIF   R+I  +P ++     ++  A  +       +P  E++A  +
Sbjct: 89  TYAV----TRIRGAIFDELRSIDWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADEL 144

Query: 405 GITVEKLE----RLIFITRMPLSMQQPVWADQDT-TFQEITADTGVEIPDISVQKQLMRQ 459
           GI++E+      +L   + + L+       + D  +  +         PD   +++ +++
Sbjct: 145 GISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKR 204

Query: 460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
            +   +  L  +E+ ++ L +  ED    +L E+G + G+++ R+ QL ++A+ +L+  L
Sbjct: 205 VIVEAIKTLPEREKKVLILYY-YED---LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260

Query: 520 G 520
            
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: 293 REKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAY 349
           R+ LI   L LV +VA +        +   DL   G  GL+++VE+F P+   RF  YA 
Sbjct: 25  RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84

Query: 350 WWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 409
           + ++  I   I    +   +P +++   +K+ +A     Q     P   +L   + I+ +
Sbjct: 85  FLIKAAI---IDDLRKQDWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQ 141

Query: 410 KLERLIFITR----MPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRN 463
           +L       R    + L+ + P  +D +     +E  AD   E     V K+     +  
Sbjct: 142 ELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERIADERAETGYDVVDKKEFSSILAE 201

Query: 464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
            +  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|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed

 Score = 58.8 bits (143), Expect = 7e-10
 Identities = 23/57 (40%), Positives = 37/57 (64%)

Query: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 348
           +R  LI  NLRLV H+ K+++  G  + DL+  G++GL+K++E F    G + A+YA
Sbjct: 50  ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA 106

Length = 233

>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 = 54.0 bits (131), Expect = 9e-10
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           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 = 58.6 bits (142), Expect = 1e-09
 Identities = 61/238 (25%), Positives = 119/238 (50%), Gaps = 28/238 (11%)

Query: 294 EKLINANLRLVVHVAKQYQGRGISLH-DLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352
           EKL+     LV  +A +Y  +G S H DL+Q G +GL+ ++ ++ P  G  F ++A   +
Sbjct: 32  EKLVKHYKNLVESLAYKYS-KGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTI 90

Query: 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK-L 411
              I++ +   + ++ +P  I  L  K+ +A      E   SP   ++A R+G++ E+ L
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVL 150

Query: 412 ERLIFITRM-----PLSMQQPVWADQD---TTFQEITA--DTGVEIPDISVQKQLMRQHV 461
           E +     M      LS+   + AD D    T  +I    + G E      +++++ + +
Sbjct: 151 EAM----EMGKSYQALSVDHSIEADSDGSTVTLLDIVGQQEDGYE----LTEQRMILEKI 202

Query: 462 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
              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 = 56.4 bits (137), Expect = 5e-09
 Identities = 27/69 (39%), Positives = 46/69 (66%), Gaps = 1/69 (1%)

Query: 281 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQ 339
            L ++L  G  + R  LI  NLRLVV++A++++  GI++ DL+  G++GL+K+V  F P+
Sbjct: 41  YLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPE 100

Query: 340 AGCRFASYA 348
              + A+YA
Sbjct: 101 KKIKLATYA 109

Length = 234

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

 Score = 54.6 bits (132), Expect = 2e-08
 Identities = 24/105 (22%), Positives = 59/105 (56%), Gaps = 4/105 (3%)

Query: 418 TRMPLSMQQPVWADQD---TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERC 474
           T+  +S+Q P+  D++    +  +I      ++ +  V+ ++  + +   + +L+ +E+ 
Sbjct: 124 TKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVIEQ-VELKMEVEKLYKKIDILDEREKE 182

Query: 475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
           ++ +R+G+ +GK K+  E+    G+S+  V ++E RAL +L + L
Sbjct: 183 VIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227

Length = 233

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

 Score = 54.5 bits (131), Expect = 3e-08
 Identities = 52/229 (22%), Positives = 111/229 (48%), Gaps = 10/229 (4%)

Query: 293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV 352
           +EKL++    LV  +A +Y   G    DL+Q G +GL+ ++ ++    G  F  +A   +
Sbjct: 31  QEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTI 90

Query: 353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 412
              I++ +   + ++ +P  I  L  K+ +A          SP   ++A  +G++ E++ 
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150

Query: 413 RLIFITR--MPLSMQQPVWADQDTTFQEITADTG-VEIPDISVQKQLMRQHVRNLLTLLN 469
            ++ + +    LS+   + AD D +        G VE      +++++   +  +L +L+
Sbjct: 151 EIMEMGQSYRALSVDDVIEADSDGSTVARLDSVGEVEDGYDQTERRMV---LEKILPILS 207

Query: 470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 518
            +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 = 49.5 bits (119), Expect = 1e-06
 Identities = 22/60 (36%), Positives = 37/60 (61%), Gaps = 4/60 (6%)

Query: 462 RNLLTL----LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           R LL      L+ +E+ I+ LRFG+  G+ K+  EV ++ G+S+  + +LE R + RLK+
Sbjct: 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228

Length = 234

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

 Score = 46.6 bits (111), Expect = 4e-06
 Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 4/90 (4%)

Query: 430 ADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKS 489
             +               P+  ++++  R+ +R  L  L  +ER ++ LR+     +  S
Sbjct: 73  RLRRELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYL----EGLS 128

Query: 490 LSEVGNIFGLSKERVRQLESRALYRLKQSL 519
             E+  I G+S   V++   RA  +L++ L
Sbjct: 129 YKEIAEILGISVGTVKRRLKRARKKLRELL 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|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated

 Score = 43.0 bits (102), Expect = 1e-04
 Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 1/96 (1%)

Query: 287 HSGNS-SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 345
            SG+  + E LI      V   A+ Y   G    D++QEG +GL K++  +       F 
Sbjct: 19  RSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFK 78

Query: 346 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVL 381
           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 = 42.5 bits (100), Expect = 2e-04
 Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 1/104 (0%)

Query: 277 LSCRDLKSELHSGNS-SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK 335
           L   ++      GN+ + E LIN     V   A+ Y   G    D++QEG +GL K++  
Sbjct: 4   LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRD 63

Query: 336 FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSK 379
           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|224511 COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 20/102 (19%), Positives = 37/102 (36%), Gaps = 4/102 (3%)

Query: 425 QQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIED 484
           ++   A  +                  +  +   + +R  L  L P++R    LR+ +E 
Sbjct: 85  RKRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRY-LEG 143

Query: 485 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 526
               S  E+  I G+S   V+    RA  +L++ L      G
Sbjct: 144 ---LSYEEIAEILGISVGTVKSRLHRARKKLREQLEEAGERG 182

Length = 182

>gnl|CDD|183523 PRK12427, PRK12427, flagellar biosynthesis sigma factor; Provisional

 Score = 39.1 bits (91), Expect = 0.003
 Identities = 52/230 (22%), Positives = 98/230 (42%), Gaps = 28/230 (12%)

Query: 295 KLINANLRLVVHVAKQ--YQGRG-ISLHDLLQEGSMGLMKSVEKF-KPQAGCRFASYAYW 350
           K +NA L LV  V +Q  +Q    I   D+ Q   MGL++++ ++  P     FA+YA  
Sbjct: 19  KYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDEQ--FAAYAV- 75

Query: 351 WVRQTIRKAIFQHSRTIRL-PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 409
                IR AI    R +   P  +     K  +A R   +   H P+ E+++  + +T E
Sbjct: 76  ---HRIRGAILDELRELDWRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAE 132

Query: 410 KLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS--VQKQLM-RQHVRNLLT 466
           +                   A    +  E+ A         S  +++ ++   +++  L+
Sbjct: 133 EY----------QEYLLLENAGTLESLDELLALEAHNDILQSRDLEENIIIEDNLKQALS 182

Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
            L+ +E+ I+ L +  E     SL E+  +  L++ R+ QL  +   ++K
Sbjct: 183 QLDEREQLILHLYYQHE----MSLKEIALVLDLTEARICQLNKKIAQKIK 228

Length = 231

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	532
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
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	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
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	100.0
PRK08215	258	sporulation sigma factor SigG; Reviewed	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
PRK08583	257	RNA polymerase sigma factor SigB; Validated	100.0
PRK05572	252	sporulation sigma factor SigF; 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
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.93
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.93
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.92
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.91
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.89
PRK05602	186	RNA polymerase sigma factor; Reviewed	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
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.88
PRK12513	194	RNA polymerase sigma factor; Provisional	99.88
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.88
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.87
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.87
PRK12519	194	RNA polymerase sigma factor; Provisional	99.86
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.86
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.86
PRK12514	179	RNA polymerase sigma factor; Provisional	99.86
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.86
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.86
PRK11922	231	RNA polymerase sigma factor; Provisional	99.85
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.85
PRK12524	196	RNA polymerase sigma factor; Provisional	99.85
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.85
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.85
PRK12537	182	RNA polymerase sigma factor; Provisional	99.85
PRK12538	233	RNA polymerase sigma factor; Provisional	99.85
PRK12534	187	RNA polymerase sigma factor; Provisional	99.85
PRK12526	206	RNA polymerase sigma factor; Provisional	99.84
PRK11924	179	RNA polymerase sigma factor; Provisional	99.84
PRK12542	185	RNA polymerase sigma factor; Provisional	99.84
PRK12515	189	RNA polymerase sigma factor; Provisional	99.84
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.83
PRK12531	194	RNA polymerase sigma factor; Provisional	99.83
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.83
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.83
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.83
PRK12543	179	RNA polymerase sigma factor; Provisional	99.82
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.82
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.82
PRK12522	173	RNA polymerase sigma factor; Provisional	99.82
PRK12536	181	RNA polymerase sigma factor; Provisional	99.81
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.81
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.81
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.81
PRK12520	191	RNA polymerase sigma factor; Provisional	99.81
PRK12539	184	RNA polymerase sigma factor; Provisional	99.81
PRK12512	184	RNA polymerase sigma factor; Provisional	99.8
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.8
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.8
PRK12518	175	RNA polymerase sigma factor; Provisional	99.8
PRK12533	216	RNA polymerase sigma factor; Provisional	99.8
PRK12529	178	RNA polymerase sigma factor; Provisional	99.8
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.79
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.79
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.79
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.79
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.78
PRK12516	187	RNA polymerase sigma factor; Provisional	99.78
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.78
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.78
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.78
PRK12528	161	RNA polymerase sigma factor; Provisional	99.77
PRK12547	164	RNA polymerase sigma factor; Provisional	99.77
PRK12532	195	RNA polymerase sigma factor; Provisional	99.77
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.77
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.77
PRK12541	161	RNA polymerase sigma factor; Provisional	99.77
PRK12545	201	RNA polymerase sigma factor; Provisional	99.76
PRK12530	189	RNA polymerase sigma factor; Provisional	99.76
PRK12544	206	RNA polymerase sigma factor; Provisional	99.76
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.76
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.75
PRK12535	196	RNA polymerase sigma factor; Provisional	99.75
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.75
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.75
PRK12540	182	RNA polymerase sigma factor; Provisional	99.75
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.74
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.74
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.73
PRK12517	188	RNA polymerase sigma factor; Provisional	99.73
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.72
PRK12546	188	RNA polymerase sigma factor; Provisional	99.72
PRK12511	182	RNA polymerase sigma factor; Provisional	99.7
PRK12525	168	RNA polymerase sigma factor; Provisional	99.7
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.69
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.67
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.62
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.62
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.62
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.49
PRK09191	261	two-component response regulator; Provisional	99.47
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.46
PF07638	185	Sigma70_ECF: ECF sigma factor	99.35
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.24
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.23
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	99.09
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	98.92
PRK06930	170	positive control sigma-like factor; Validated	98.65
PRK00118	104	putative DNA-binding protein; Validated	98.44
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.28
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.2
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.18
PRK04217	110	hypothetical protein; Provisional	98.06
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.02
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	97.96
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	97.93
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	97.87
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.85
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.74
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.66
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.54
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.54
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.53
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.5
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.4
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.36
PRK10840	216	transcriptional regulator RcsB; Provisional	97.32
PRK13870	234	transcriptional regulator TraR; Provisional	97.3
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.3
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.28
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.27
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.25
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	97.24
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	97.2
COG2197	211	CitB Response regulator containing a CheY-like rec	97.16
COG4566	202	TtrR Response regulator [Signal transduction mecha	97.09
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	97.09
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	97.05
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.97
PRK09483	217	response regulator; Provisional	96.96
PRK15369	211	two component system sensor kinase SsrB; Provision	96.74
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.7
COG3413	215	Predicted DNA binding protein [General function pr	96.62
PRK01381	99	Trp operon repressor; Provisional	96.59
PRK10651	216	transcriptional regulator NarL; Provisional	96.55
COG1356	143	tfx Transcriptional regulator [DNA replication, re	96.53
PRK09390	202	fixJ response regulator FixJ; Provisional	96.49
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.26
PRK15320	251	transcriptional activator SprB; Provisional	96.21
COG1342	99	Predicted DNA-binding proteins [General function p	96.13
PRK10403	215	transcriptional regulator NarP; Provisional	96.0
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.68
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	95.66
PRK09935	210	transcriptional regulator FimZ; Provisional	95.66
COG4941	415	Predicted RNA polymerase sigma factor containing a	95.52
PRK04841	903	transcriptional regulator MalT; Provisional	95.37
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	95.18
PRK13558	665	bacterio-opsin activator; Provisional	95.08
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	95.06
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	94.97
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	94.86
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	94.73
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.71
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	94.31
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	94.24
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	93.89
PRK15418	318	transcriptional regulator LsrR; Provisional	93.61
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	93.49
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	93.47
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	93.19
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	93.16
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	92.88
PF13730	55	HTH_36: Helix-turn-helix domain	92.57
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	92.55
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.43
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	92.39
PHA00675	78	hypothetical protein	92.23
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	91.97
PRK05901	509	RNA polymerase sigma factor; Provisional	91.96
PF13518	52	HTH_28: Helix-turn-helix domain	91.82
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	91.46
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	91.43
smart00351	125	PAX Paired Box domain.	90.78
PF10668	60	Phage_terminase: Phage terminase small subunit; In	90.7
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	90.67
PRK07598	415	RNA polymerase sigma factor SigC; Validated	90.56
COG3355	126	Predicted transcriptional regulator [Transcription	90.5
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	90.33
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	90.32
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	90.29
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	90.27
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	89.51
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	89.28
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	89.25
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	88.91
PHA02591	83	hypothetical protein; Provisional	88.68
PRK11083	228	DNA-binding response regulator CreB; Provisional	88.66
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	88.51
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	88.21
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	87.74
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	87.71
cd00131	128	PAX Paired Box domain	87.46
PHA02547	179	55 RNA polymerase sigma factor; Provisional	87.45
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	87.23
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	87.18
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	86.97
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	86.91
PRK05949	327	RNA polymerase sigma factor; Validated	86.88
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	86.79
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	86.53
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	86.45
PRK15479	221	transcriptional regulatory protein TctD; Provision	86.43
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	86.33
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	85.84
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	85.72
PRK12423	202	LexA repressor; Provisional	85.62
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	85.26
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	85.25
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	85.12
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	84.64
PF12728	51	HTH_17: Helix-turn-helix domain	84.36
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	84.32
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	84.29
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	84.28
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	84.21
PRK07670	251	RNA polymerase sigma factor SigD; Validated	84.08
PRK07405	317	RNA polymerase sigma factor SigD; Validated	83.88
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	83.87
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	83.85
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	83.8
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	83.69
COG3415	138	Transposase and inactivated derivatives [DNA repli	83.56
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	83.51
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	83.38
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	83.07
PRK10046	225	dpiA two-component response regulator DpiA; Provis	82.97
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	82.9
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	82.87
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	82.67
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	82.32
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	82.31
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	82.18
TIGR01764	49	excise DNA binding domain, excisionase family. An	82.13
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	81.85
PRK13413	200	mpi multiple promoter invertase; Provisional	81.8
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	81.79
CHL00148	240	orf27 Ycf27; Reviewed	81.75
PRK00215	205	LexA repressor; Validated	81.64
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	81.4
PRK11564	426	stationary phase inducible protein CsiE; Provision	80.68
PF13551	112	HTH_29: Winged helix-turn helix	80.37

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=1.6e-65  Score=541.88  Aligned_cols=315  Identities=38%  Similarity=0.651  Sum_probs=299.1

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhhCCCCcHHHHHHHc
Q 009567          216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI  275 (532)
Q Consensus       216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~--------------------le~~~~~l~~~~g~~pt~~ewA~aa  275 (532)
                      ..|+++.||++|++.|+||++||++|+++||.++.                    |++++..|+..+|++||..|||.++
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                    9999999999999999999999555


Q ss_pred             ----------------------cCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhh
Q 009567          276 ----------------------GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV  333 (532)
Q Consensus       276 ----------------------g~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAi  333 (532)
                                            ||++++|+..++.|..|+++||.+|+++|++||++|.++|++++||||||++|||+|+
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                                  4566666777788999999999999999999999999999999999999999999999


Q ss_pred             hhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHH
Q 009567          334 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER  413 (532)
Q Consensus       334 ekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~  413 (532)
                      ++|||++|++|+|||+||||++|.+++++++|+||+|.|+.+.+++++++...+.+++||.|+.+|||+.+||++++|+.
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             HHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHH
Q 009567          414 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV  493 (532)
Q Consensus       414 ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EI  493 (532)
                      ++.....++|||.+++++++..+.+.+.++. .+|++.+....+...|..+|..|||+||.||.+||||+||+++|++||
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            9999999999999999888888888877543 578888888899999999999999999999999999999999999999


Q ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 009567          494 GNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL  531 (532)
Q Consensus       494 Ae~LgISrerVRqie~rALkKLR~~l~~~~l~~yldll  531 (532)
                      |+.||||+++||+++++|++|||+.-....+++|++.|
T Consensus       377 A~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~~~  414 (415)
T PRK07598        377 GRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLELL  414 (415)
T ss_pred             HHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999765

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=9.6e-63  Score=517.09  Aligned_cols=312  Identities=37%  Similarity=0.728  Sum_probs=300.3

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 009567          216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  295 (532)
Q Consensus       216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~  295 (532)
                      ..|++..||++|+++|+||++||++|+++|++++.+++.+.+|+...|++|+..+||.++|++..+|..+++.|..|++.
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             HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH
Q 009567          296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  375 (532)
Q Consensus       296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~  375 (532)
                      ||.+|+++|+++|++|.++|.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+..
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             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 009567          376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  455 (532)
Q Consensus       376 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~  455 (532)
                      .+++++++...+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++++.. .+|++.+...
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            999999999999999999999999999999999999999888888999999998777778889888763 4788888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 009567          456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA  528 (532)
Q Consensus       456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yl  528 (532)
                      .+...|..+|..||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||.......++.|+
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            8999999999999999999999999999889999999999999999999999999999999999999998886

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=5.4e-62  Score=505.05  Aligned_cols=312  Identities=40%  Similarity=0.669  Sum_probs=298.3

Q ss_pred             CCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHH
Q 009567          215 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE  294 (532)
Q Consensus       215 ~~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are  294 (532)
                      ...|++..||++|+++|+||++||++|+++|+.++.++..+..|+..+|++|+..+||.+++|++.+|+..++.|+.|++
T Consensus        15 ~~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~   94 (327)
T PRK05949         15 FSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ   94 (327)
T ss_pred             CCCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH
Q 009567          295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  374 (532)
Q Consensus       295 ~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~  374 (532)
                      .||..|+++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+.
T Consensus        95 ~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~  174 (327)
T PRK05949         95 KMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHIT  174 (327)
T ss_pred             HHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHH
Q 009567          375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  454 (532)
Q Consensus       375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~  454 (532)
                      ..+++++++...+.+++||+|+.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++|.. .+|++.+..
T Consensus       175 ~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~  253 (327)
T PRK05949        175 EKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQ  253 (327)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHH
Confidence            9999999999999999999999999999999999999999998899999999998877778888888765 588988888


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567          455 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  529 (532)
Q Consensus       455 ~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld  529 (532)
                      ..+...|..+|+.||++||.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+.  ...++.|+.
T Consensus       254 ~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~  326 (327)
T PRK05949        254 ELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA  326 (327)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            8899999999999999999999999999999999999999999999999999999999999994  456777764

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

Probab=100.00  E-value=2.7e-61  Score=494.16  Aligned_cols=298  Identities=44%  Similarity=0.755  Sum_probs=286.1

Q ss_pred             hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 009567          218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  297 (532)
Q Consensus       218 d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI  297 (532)
                      |++..||++++++|+||++||.+|+++++.++.++..+.+|+.+.|++||..+||+++|+++.+|...++.|..|++.||
T Consensus         1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv   80 (298)
T TIGR02997         1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI   80 (298)
T ss_pred             CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567          298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  377 (532)
Q Consensus       298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l  377 (532)
                      .+|+++|++||++|.++|.+++|||||||+|||+|+++|||++|++|+|||+||||++|.+++.+++++||+|.++...+
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             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567          378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  457 (532)
Q Consensus       378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l  457 (532)
                      ++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++.++.+.+++. ..+|++.+....+
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            999999999999999999999999999999999999999888999999999776666777877774 4578888888888


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ...|..+|+.||++||+||.+||||+|++++|++|||+.||||++||||++++|++|||
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            99999999999999999999999999999999999999999999999999999999996

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=7.1e-61  Score=495.10  Aligned_cols=311  Identities=38%  Similarity=0.641  Sum_probs=297.1

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 009567          216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  295 (532)
Q Consensus       216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~  295 (532)
                      .+|++..||++|+++|+||++||.+|+++|++++.+++++..|+..+|++|+..+||.++++++..|...++.|..|++.
T Consensus         6 ~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~   85 (317)
T PRK07405          6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK   85 (317)
T ss_pred             CCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH
Q 009567          296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  375 (532)
Q Consensus       296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~  375 (532)
                      ||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
T Consensus        86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~  165 (317)
T PRK07405         86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE  165 (317)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 009567          376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  455 (532)
Q Consensus       376 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~  455 (532)
                      .+++++++...+...+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+.++|.. .+|++.+...
T Consensus       166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~  244 (317)
T PRK07405        166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQS  244 (317)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHH
Confidence            999999999999999999999999999999999999999988888999999998777778888888764 5789888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567          456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  529 (532)
Q Consensus       456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld  529 (532)
                      .++..|..+|+.||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||+.  ...+..|++
T Consensus       245 ~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~  316 (317)
T PRK07405        245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA  316 (317)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            899999999999999999999999999999999999999999999999999999999999995  456777764

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

Probab=100.00  E-value=5.3e-60  Score=485.90  Aligned_cols=313  Identities=36%  Similarity=0.656  Sum_probs=289.1

Q ss_pred             ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hhCCCCcHH---------------HHHHHccCCH-
Q 009567          217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC-  279 (532)
Q Consensus       217 ~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~-~~g~~pt~~---------------ewA~aag~~~-  279 (532)
                      .|.+..|+.+++..+++++++|.++...++....+......|.. ..|..|+..               +|+.....++ 
T Consensus         8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee   87 (342)
T COG0568           8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE   87 (342)
T ss_pred             hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence            57889999999999999999999999999887777667777776 677888876               6665555544 


Q ss_pred             HHHHHHHhhcH---HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567          280 RDLKSELHSGN---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  356 (532)
Q Consensus       280 ~~L~~~l~~g~---~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI  356 (532)
                      ..|..++..|.   .|+.+||.+|+|||++||++|.|+|+++.||||||+||||+|+++|||++||+|||||+||||++|
T Consensus        88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI  167 (342)
T COG0568          88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI  167 (342)
T ss_pred             HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence            56777777773   699999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567          357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  436 (532)
Q Consensus       357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l  436 (532)
                      .++|.+++|+||+|.|+.+.+++++++.+.+.+++|++|+.+|||+.+|+++++|..++.....++|||.|++++++..+
T Consensus       168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l  247 (342)
T COG0568         168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSEL  247 (342)
T ss_pred             HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988899


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          437 QEITADTGVEIPDISVQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~-L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                      +|+++|+...+|++.+....+.+.+...|.. |+|+|+.||++|||++|+++.|++|||+.+|||++|||||+.+|++||
T Consensus       248 ~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KL  327 (342)
T COG0568         248 GDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKL  327 (342)
T ss_pred             HHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence            9999999888999999999999999999999 999999999999999999999999999999999999999999999999


Q ss_pred             HH-HhhcCchhhhhh
Q 009567          516 KQ-SLGGKASYGYAD  529 (532)
Q Consensus       516 R~-~l~~~~l~~yld  529 (532)
                      |. ......+++|++
T Consensus       328 r~~~~~~~~~~~~l~  342 (342)
T COG0568         328 RRHPERSALLRSYLD  342 (342)
T ss_pred             HHhhhhhhHHHHhhC
Confidence            94 445555677864

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=9.3e-60  Score=508.99  Aligned_cols=301  Identities=35%  Similarity=0.613  Sum_probs=277.2

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 009567          216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  295 (532)
Q Consensus       216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~  295 (532)
                      ..|++..||++|+++|+||++||++|+++|+.+...+..   +.       ...+|+.   ....+|+..++.|..|++.
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            468999999999999999999999999999875332221   11       1122442   2457788889999999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH
Q 009567          296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  375 (532)
Q Consensus       296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~  375 (532)
                      ||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+..
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             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 009567          376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  455 (532)
Q Consensus       376 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~  455 (532)
                      .++++.++...+.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|.....|++.+...
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            99999999999999999999999999999999999999999888999999999887777889999998777899989888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567          456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  529 (532)
Q Consensus       456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld  529 (532)
                      .++..|..+|..|+++||.||.+||||++++++|++|||+.||||++|||||+.+||+|||.......|+.|++
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            99999999999999999999999999999999999999999999999999999999999999999999999975

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=1.5e-58  Score=478.45  Aligned_cols=299  Identities=36%  Similarity=0.632  Sum_probs=275.8

Q ss_pred             ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHH
Q 009567          217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  296 (532)
Q Consensus       217 ~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~L  296 (532)
                      +|++..||++++++|+||++||.+|+++|+.+..++..           |+..+|....  ...++...++.|..|++.|
T Consensus        25 ~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~L   91 (324)
T PRK07921         25 ADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHL   91 (324)
T ss_pred             CChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHH
Confidence            57899999999999999999999999999986655542           2233343111  4567888999999999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHH
Q 009567          297 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTL  376 (532)
Q Consensus       297 I~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~  376 (532)
                      |..|+++|+++|++|.++|.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++++++||+|.|+...
T Consensus        92 v~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~  171 (324)
T PRK07921         92 LEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ  171 (324)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHH
Q 009567          377 LSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQL  456 (532)
Q Consensus       377 l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~  456 (532)
                      +++++++...+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+....
T Consensus       172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~  251 (324)
T PRK07921        172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGL  251 (324)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999988888999999998777778899999876678888888888


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 009567          457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA  528 (532)
Q Consensus       457 l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yl  528 (532)
                      ++..|..+|..|+++|+.||.+||||+|++++|++|||+.||||++|||||+.+|++|||.......|+.|+
T Consensus       252 ~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~  323 (324)
T PRK07921        252 LHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA  323 (324)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence            999999999999999999999999999999999999999999999999999999999999998888888885

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=8e-55  Score=458.27  Aligned_cols=276  Identities=37%  Similarity=0.712  Sum_probs=262.7

Q ss_pred             CCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHH
Q 009567          214 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR  293 (532)
Q Consensus       214 ~~~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Ar  293 (532)
                      ...+|+++.||++|+++|+||++||.+|+.+++.               |                         +..|+
T Consensus        92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~---------------G-------------------------d~~A~  131 (367)
T PRK09210         92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE---------------G-------------------------DEEAK  131 (367)
T ss_pred             cccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh---------------h-------------------------HHHHH
Confidence            3457899999999999999999999999988764               2                         35899


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567          294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  373 (532)
Q Consensus       294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~  373 (532)
                      +.||..|+++|+++|++|.++|.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|++++|+||+|.|+
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             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 009567          374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  453 (532)
Q Consensus       374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~  453 (532)
                      ...++++.++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|....+|++.+.
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            99999999999999999999999999999999999999999998888999999998877778999999887778999999


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567          454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  529 (532)
Q Consensus       454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld  529 (532)
                      ...++..|..+|..||++||.||.+||||+||+++|++|||+.||||++|||||+.+||+|||.+.....|+.|++
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=1.7e-52  Score=467.19  Aligned_cols=274  Identities=34%  Similarity=0.633  Sum_probs=252.3

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 009567          219 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  298 (532)
Q Consensus       219 ~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~  298 (532)
                      .+..||.++...+.||++|+..++++++.               |+                      .....|+++||.
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            34556666666666777776666666653               22                      112378999999


Q ss_pred             HHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHH
Q 009567          299 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  378 (532)
Q Consensus       299 ~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~  378 (532)
                      +|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+...++
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             HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHH
Q 009567          379 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR  458 (532)
Q Consensus       379 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l~  458 (532)
                      +++++...+.+++||+||.+|||+.+|+++++|..++.....++|||.|++++++..+.++++|....+|++.+....++
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            99999999999999999999999999999999999999888999999999888888899999998888899999888999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567          459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  529 (532)
Q Consensus       459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld  529 (532)
                      ..|..+|..||++|+.||++||||++++++|++|||+.||||++|||||+.+|++|||.+.....|+.|+|
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=2.5e-48  Score=385.86  Aligned_cols=238  Identities=39%  Similarity=0.753  Sum_probs=227.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567          292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  371 (532)
Q Consensus       292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~  371 (532)
                      |+++||.+|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+|+|.
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             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567          372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  451 (532)
Q Consensus       372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~  451 (532)
                      ++...++++.++...+.+++|++||.+|||+.+|+++++|..++......+|||.+++++++.++.+.++|+...+|++.
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            99999999999999999999999999999999999999999998888789999999977766678888888877789888


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567          452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  529 (532)
Q Consensus       452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld  529 (532)
                      +...++...|..+|..||++||.||.++|||++++++|++|||+.||||+++|+|++.+|++|||..+....++.|+|
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            888888999999999999999999999999998899999999999999999999999999999999999999999975

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.

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=6.2e-45  Score=371.08  Aligned_cols=264  Identities=27%  Similarity=0.470  Sum_probs=225.6

Q ss_pred             CCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHH
Q 009567          214 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR  293 (532)
Q Consensus       214 ~~~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Ar  293 (532)
                      ..+.+++..|+++++++|+||.++|.+|+.+++.                                       .++..|+
T Consensus        10 ~~~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~   50 (284)
T PRK06596         10 LSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAA   50 (284)
T ss_pred             CCCccHHHHHHHHHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHH
Confidence            3456799999999999999999999999887532                                       2346899


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567          294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  373 (532)
Q Consensus       294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~  373 (532)
                      +.||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.+++++++++|++|.+.
T Consensus        51 ~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~  130 (284)
T PRK06596         51 KQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTK  130 (284)
T ss_pred             HHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998889999976


Q ss_pred             HH--HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh-cCCCcccCCCCCCCCC--cchhhhcccCCCCCh
Q 009567          374 YT--LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI-TRMPLSMQQPVWADQD--TTFQEITADTGVEIP  448 (532)
Q Consensus       374 ~~--~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~-~~~~iSLD~~v~~d~~--~~l~d~i~d~~~~~p  448 (532)
                      ..  ...++.+....+.  .+++|+.+|||+.+|+++++|..++.. ....+|||.+++++++  .++.+.++|.. .+|
T Consensus       131 ~~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p  207 (284)
T PRK06596        131 AQRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDP  207 (284)
T ss_pred             HHHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCc
Confidence            42  3344444444443  458999999999999999999998753 3468999999865532  45778888764 467


Q ss_pred             hHHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          449 DISVQKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       449 ee~~~~~----~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ++.++..    .++..|..+|+.||++||.||.+|||. + +++|++|||+.||||++||||++++|++|||..+..
T Consensus       208 ~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~  282 (284)
T PRK06596        208 ADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA  282 (284)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            7666554    357789999999999999999999973 2 799999999999999999999999999999998764

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=9.1e-45  Score=370.77  Aligned_cols=264  Identities=26%  Similarity=0.451  Sum_probs=226.9

Q ss_pred             hHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHH
Q 009567          218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  297 (532)
Q Consensus       218 d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI  297 (532)
                      +..+.||+++.++|+||+++|.+|+++++.                                       .++..|++.||
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            466789999999999999999999997642                                       23468999999


Q ss_pred             HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH--
Q 009567          298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT--  375 (532)
Q Consensus       298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~--  375 (532)
                      ..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|.+|+|||+||||++|.++++++++++|+|.+...  
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--chhhhcccCCCCChh
Q 009567          376 LLSKVLEAKRLYIQ---EGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQEITADTGVEIPD  449 (532)
Q Consensus       376 ~l~ki~ka~~~l~~---~~gr~Pt~eEIA~~lgis~e~v~~ll~-~~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~~pe  449 (532)
                      ...++++.+..+.+   .+|+.|+.+|||+.+|+++++|..+.. ....++|||.+++++++.  ++.+.+.|+.. +|+
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            33445555555444   689999999999999999999988753 345789999998765443  57888887653 566


Q ss_pred             HHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          450 ISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       450 e~~~~----~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      +.+..    .+....|..+|..||++||.||.+||+.  ++++|++|||+.||||+++|+|++++|++|||..+..+.
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            65443    3456678999999999999999999962  379999999999999999999999999999999987654

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=100.00  E-value=1.2e-44  Score=375.53  Aligned_cols=272  Identities=35%  Similarity=0.567  Sum_probs=253.8

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHH
Q 009567          216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  295 (532)
Q Consensus       216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~  295 (532)
                      ..|.++.|+++|+..|+||+++|..|+.+++.                                        ++..|++.
T Consensus        51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~   90 (325)
T PRK05657         51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR   90 (325)
T ss_pred             cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence            46788999999999999999999999987763                                        34689999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHH
Q 009567          296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  375 (532)
Q Consensus       296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~  375 (532)
                      ||..|.++|+++|++|.+++.+++||+|||++|+|+++++||+.+|++|+|||+||||++|.++++++.+.|++|.++..
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             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHH
Q 009567          376 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  455 (532)
Q Consensus       376 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~  455 (532)
                      .++.+.++...+.+.+|+.|+.+|||..+|+++++|..++.......|+|.++..+...++.+.+.+....+|+..+...
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            99989999999999999999999999999999999999998877889999998777767788888887666888888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 009567          456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY  527 (532)
Q Consensus       456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~y  527 (532)
                      +....|..+|..||+++|.||.+||||.+.+++|++|||+.||||+++|++++++|+++||+.+...++..+
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            888999999999999999999999999888999999999999999999999999999999999998887543

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=3.5e-44  Score=362.87  Aligned_cols=258  Identities=28%  Similarity=0.501  Sum_probs=217.8

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 009567          219 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  298 (532)
Q Consensus       219 ~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~  298 (532)
                      ++..||++++.+|+|++++|.+|+.++..                                       .++..|++.||.
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            57789999999999999999999886431                                       234689999999


Q ss_pred             HHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH--HH
Q 009567          299 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL  376 (532)
Q Consensus       299 ~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~--~~  376 (532)
                      .|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++++.++++|+|.+..  ..
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            9999999999999999999999999999999999999999999999999999999999999999888899998654  33


Q ss_pred             HHHHHHHHHHHHHhcCCCC-CHHHHHHHhCCCHHHHHHHHHhc-CCCcccCCCCCCCCC--cchhhhcccCCCCChhHHH
Q 009567          377 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQD--TTFQEITADTGVEIPDISV  452 (532)
Q Consensus       377 l~ki~ka~~~l~~~~gr~P-t~eEIA~~lgis~e~v~~ll~~~-~~~iSLD~~v~~d~~--~~l~d~i~d~~~~~pee~~  452 (532)
                      ..++.++...+.  +++.| +.+|||+.+|+++++|..+.... ...+|||.+++++++  ..+.+.+.|.. .+|++.+
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            445555544442  33556 69999999999999999986533 347999999866543  25677777765 3677666


Q ss_pred             HHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          453 QKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       453 ~~~----~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      ...    .++..|..+|..||++||.||.+||+.  ++++|++|||+.||||+++|+|++.+|++|||..+.
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  368999999999999999999999999999999764

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=1.8e-43  Score=356.86  Aligned_cols=221  Identities=24%  Similarity=0.391  Sum_probs=201.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567          291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  370 (532)
Q Consensus       291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP  370 (532)
                      .++++||.+|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+|
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--chhhhcccCCCC
Q 009567          371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDT--TFQEITADTGVE  446 (532)
Q Consensus       371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~  446 (532)
                      .++...+++++++...+.+++|+.||.+|||+.+|+++++|..++..  ...++|||.+++++++.  .+.+.++     
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  45689999998654332  3333332     


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      +++..++..+....|..+|..||+++|.||.++|+    +++|++|||+.||||.++|++++++|+++||..++
T Consensus       195 ~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~  264 (264)
T PRK07122        195 DVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE  264 (264)
T ss_pred             CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcC
Confidence            34555666677888999999999999999999998    89999999999999999999999999999999763

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=8.4e-42  Score=343.09  Aligned_cols=227  Identities=25%  Similarity=0.408  Sum_probs=201.5

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  367 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~-g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I  367 (532)
                      +..|++.||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++++.++|
T Consensus        23 d~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~v  102 (256)
T PRK07408         23 SIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTV  102 (256)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCee
Confidence            45899999999999999999999875 67799999999999999999999999999999999999999999999999999


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc--chhhhcccC
Q 009567          368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT--TFQEITADT  443 (532)
Q Consensus       368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~iSLD~~v~~d~~~--~l~d~i~d~  443 (532)
                      |+|.++...+++++++...+.+.+|++|+.+|||+.+|+++++|..+..  .....+|||.+++++++.  .+.+.++++
T Consensus       103 r~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d~  182 (256)
T PRK07408        103 RIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPDP  182 (256)
T ss_pred             eeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCCc
Confidence            9999999999999999999999999999999999999999999999865  345688999988654332  455666655


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          444 GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       444 ~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      ... +..  ...+....|..+|..||+++|.||.++|+    +++|++|||+.||+|.++|++++.+|++|||..+...
T Consensus       183 ~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~  254 (256)
T PRK07408        183 RYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE  254 (256)
T ss_pred             ccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence            432 111  23345667999999999999999999998    8999999999999999999999999999999988654

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=6.1e-41  Score=341.58  Aligned_cols=271  Identities=35%  Similarity=0.572  Sum_probs=248.5

Q ss_pred             CCCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHH
Q 009567          214 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR  293 (532)
Q Consensus       214 ~~~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Ar  293 (532)
                      ....|.+++||.+|+.+|.||.++|.+|+..++.               |                         +..|+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~a~   48 (285)
T TIGR02394         9 TRVADVTQLYLREIGFKPLLTAEEEIAYARRALA---------------G-------------------------DFEAR   48 (285)
T ss_pred             cCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHH
Confidence            3467899999999999999999999999887664               3                         36899


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567          294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  373 (532)
Q Consensus       294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~  373 (532)
                      +.||..|.++|+++|++|.+++.+.+||+|||++|||+|+++||+.+|++|+||+.|||+.+|.+++.++.+.+++|.++
T Consensus        49 ~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~  128 (285)
T TIGR02394        49 KVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHV  128 (285)
T ss_pred             HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 009567          374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  453 (532)
Q Consensus       374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~  453 (532)
                      ...++.+.+..+.+.+..|+.|+.+++|..+|++++++..++......+|+|.++..+...++.+.+.++...+|++.+.
T Consensus       129 ~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~~  208 (285)
T TIGR02394       129 IKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQ  208 (285)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHHH
Confidence            99999988888888888999999999999999999999999988888899998876665555666666666567888888


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ..+....|..+|..||+++|.||.++|||.+.+++|++|||+.||+|.++|++++++|+++||+.+...++
T Consensus       209 ~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~  279 (285)
T TIGR02394       209 NDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV  279 (285)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            88889999999999999999999999988888999999999999999999999999999999999987654

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=9.6e-40  Score=327.50  Aligned_cols=243  Identities=27%  Similarity=0.444  Sum_probs=215.9

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 009567          227 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  306 (532)
Q Consensus       227 i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~s  306 (532)
                      .+++|+||++||.+|+.+++.                                        ++..|++.|+..|.++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence            468899999999999877653                                        2368999999999999999


Q ss_pred             HHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHH
Q 009567          307 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  386 (532)
Q Consensus       307 IAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~  386 (532)
                      +|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .||+|.++...++++.++...
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             HHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 009567          387 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL  464 (532)
Q Consensus       387 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~~pee~~~~~~l~~~L~~~  464 (532)
                      +.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++.  ++.+.+.|+.. .++    ....+..|..+
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            999999999999999999999999999998888889999988644432  45666666432 122    22344578999


Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      +..||+++|.||.++|+    +++|++|||+.||+|+++|++++.+|++|||..+
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    8999999999999999999999999999999853

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=6e-40  Score=329.91  Aligned_cols=227  Identities=26%  Similarity=0.391  Sum_probs=204.9

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhc
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  364 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~~---~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~  364 (532)
                      ++..|++.||..|+|+|+++|++|.+   .+++++||+|||+||||+|+++|||++|++|+|||+||||++|.+++++..
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            34589999999999999999999862   356799999999999999999999999999999999999999999999986


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCC--CC--Ccchhh
Q 009567          365 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--DQ--DTTFQE  438 (532)
Q Consensus       365 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~iSLD~~v~~--d~--~~~l~d  438 (532)
                      +   +|+++...++++.++...+.+.+|+.|+.+|||+.+|+++++|..++....  .++|||.++..  ++  +.++.+
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            4   899999999999999999999999999999999999999999999886554  46899987643  21  235678


Q ss_pred             hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          439 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       439 ~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      .++|.....|++.+...+....|..+|..||++||.||.++|+    +++|++|||+.||+|+++|++++.+|+++||+.
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            8888766678888888888889999999999999999999998    999999999999999999999999999999998


Q ss_pred             hhc
Q 009567          519 LGG  521 (532)
Q Consensus       519 l~~  521 (532)
                      +..
T Consensus       253 l~~  255 (257)
T PRK05911        253 LSA  255 (257)
T ss_pred             HHh
Confidence            754

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

Probab=100.00  E-value=6e-39  Score=319.01  Aligned_cols=221  Identities=27%  Similarity=0.508  Sum_probs=202.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCC-CHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~g~-~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      ..++ .||+.|+|||.+||++|.+++. +++||+|-|+|||++|+++|||++|.+|+|||...|+++|.+++|++. .++
T Consensus        23 ~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~v~  100 (247)
T COG1191          23 EEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVK  100 (247)
T ss_pred             HHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-Ccc
Confidence            5788 9999999999999999998877 999999999999999999999999999999999999999999999999 999


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCCCCCcchhhhcccCCCC
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTGVE  446 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~iSLD~~v~~d~~~~l~d~i~d~~~~  446 (532)
                      +|+.+....+++..+...+.+++||+||.+|||+.+|++.+++...+....  ..+|+|..+..+++..     .++...
T Consensus       101 vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~~~  175 (247)
T COG1191         101 VPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQIE  175 (247)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhccc
Confidence            999999999999999999999999999999999999999999999987664  6788887765544433     223345


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      +|.+.++..+....|.+++..|++|||.||.+||.    +++|++|||+.||||+.+|+|++++|++|||..+..
T Consensus       176 ~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~  246 (247)
T COG1191         176 NPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK  246 (247)
T ss_pred             cchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence            77778888888888999999999999999999998    999999999999999999999999999999998754

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=100.00  E-value=2.3e-38  Score=318.13  Aligned_cols=243  Identities=27%  Similarity=0.463  Sum_probs=215.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 009567          227 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  306 (532)
Q Consensus       227 i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~s  306 (532)
                      ..++|+|+++|+..|+.+++.                                        ++..|++.||..|.++|++
T Consensus        13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~   52 (258)
T PRK08215         13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS   52 (258)
T ss_pred             CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence            467889999999998887653                                        3468999999999999999


Q ss_pred             HHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHH
Q 009567          307 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  386 (532)
Q Consensus       307 IAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~  386 (532)
                      +|++|.+++.+.+||+|||++|||+++++|||.+|++|+||+++||++.|.++++++. .||+|.++.....++.++...
T Consensus        53 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~  131 (258)
T PRK08215         53 VIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREK  131 (258)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999985 889999999999999999999


Q ss_pred             HHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 009567          387 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL  464 (532)
Q Consensus       387 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~~pee~~~~~~l~~~L~~~  464 (532)
                      +.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++.  ++.+.++++.. .++    .......+..+
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            999999999999999999999999999988777888999988655433  34555555431 222    22334578899


Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      +..||++++.||.++|+    +++|++|||+.||+|.++|++++++|+++||+.+
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    8999999999999999999999999999999876

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=100.00  E-value=3.6e-37  Score=311.16  Aligned_cols=250  Identities=20%  Similarity=0.353  Sum_probs=221.8

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHH
Q 009567          227 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  306 (532)
Q Consensus       227 i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~s  306 (532)
                      .+++|+||.++|.+|+..++.                                       .++..+++.|+..|.++|+.
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                                       23468999999999999999


Q ss_pred             HHHHhh-C--CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHH
Q 009567          307 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA  383 (532)
Q Consensus       307 IAkrY~-~--~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka  383 (532)
                      +|++|. +  .+.+++||+|||++|||+++++||+.+|++|+||++|||++.|.+++++.   +++|.++....++++++
T Consensus        47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~~~p~~~~~~~~~i~~~  123 (268)
T PRK06288         47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---DWIPRSVRQKARQIERA  123 (268)
T ss_pred             HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---CccCHHHHHHHHHHHHH
Confidence            999986 3  56789999999999999999999999999999999999999999999865   46899999999999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCC---CcchhhhcccCCCCChhHHHHHHHHH
Q 009567          384 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMR  458 (532)
Q Consensus       384 ~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~iSLD~~v~~d~---~~~l~d~i~d~~~~~pee~~~~~~l~  458 (532)
                      ...+.+.+|+.||.+|||+.+|++.+++..++...  ...+|||.++..++   ..++.+.++++...+|++.+...+..
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            99999999999999999999999999999988644  45789988764222   23566777777667888888888888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      ..|..+|..||+++|.||.++|+    +++|++|||+.||+|.++|++++.+|+++||.++...
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    8999999999999999999999999999999998643

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=100.00  E-value=1.6e-36  Score=303.93  Aligned_cols=244  Identities=23%  Similarity=0.356  Sum_probs=215.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHH
Q 009567          231 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ  310 (532)
Q Consensus       231 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkr  310 (532)
                      |.||++||.+|+.+++.                                       .++..|++.|+..|.++|+.+|++
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            66899999888887653                                       123689999999999999999999


Q ss_pred             hhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHh
Q 009567          311 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE  390 (532)
Q Consensus       311 Y~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~  390 (532)
                      |.+++.+.+||+|||++|||+++++||++.|.+|+||+++||++.|.+++++..+.+++|.++....++++++...+.+.
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--CCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC
Q 009567          391 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL  468 (532)
Q Consensus       391 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L  468 (532)
                      +|+.|+.+|+|+.+|++.+++..++...  ....|||.++..+++......+ + ...+|++.+...+....+..+|+.|
T Consensus       129 ~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L  206 (255)
T TIGR02941       129 LQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARL-D-SVGEVEDGYDQTERRMVLEKILPIL  206 (255)
T ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccc-c-ccCCcchHHHHHHHHHHHHHHHHcC
Confidence            9999999999999999999998887653  4578999988765443322221 1 1224666677777778899999999


Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       469 ~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      |+++|.||.++|+    +++|++|||+.||+|.++|++++.+|+++||..+
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=1.5e-36  Score=299.58  Aligned_cols=223  Identities=29%  Similarity=0.469  Sum_probs=199.3

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567          287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  366 (532)
Q Consensus       287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~  366 (532)
                      .++..|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .
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            345689999999999999999999999999999999999999999999999999999999999999999999999986 8


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCC
Q 009567          367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTG  444 (532)
Q Consensus       367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~--~l~d~i~d~~  444 (532)
                      |++|.++....+++.++...+..++|+.||.+|||+.+|++++++..++.......|||.+++++++.  ++.+.+.++.
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            99999999999999999999999999999999999999999999999988888889999988655432  3556666543


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          445 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       445 ~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      .  +++.   ...+..+..+++.||+++++||.++|+    +++|++|||+.||||+++|++++++|++|||..+
T Consensus       166 ~--~~~~---~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l  231 (231)
T TIGR02885       166 S--EDSD---WLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL  231 (231)
T ss_pred             c--cHHh---HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence            2  2222   223557889999999999999999998    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=4.1e-36  Score=295.51  Aligned_cols=221  Identities=28%  Similarity=0.452  Sum_probs=199.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  369 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl  369 (532)
                      ..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+|+++||+++|.+|+||+++||++.|.++++++.+.+++
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--cchhhhcccCCC
Q 009567          370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQD--TTFQEITADTGV  445 (532)
Q Consensus       370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~--~iSLD~~v~~d~~--~~l~d~i~d~~~  445 (532)
                      |.++...+++++++...+.+.+|+.|+.+|+|+.+|++.+++..++.....  ..|||.++.++++  ..+.+.+.    
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~----  157 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG----  157 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence            999999999999999999999999999999999999999999998876554  8999998863322  12233322    


Q ss_pred             CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          446 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       446 ~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                       +++..+...+....|..+|..||+++++||.++|+    +++|++|||+.||+|.++|+++.++|+++||+.+
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=2.9e-35  Score=294.54  Aligned_cols=225  Identities=24%  Similarity=0.369  Sum_probs=202.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  365 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~---~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r  365 (532)
                      +..|++.||..|.++|+++|++|.+   ++.+.+||+|||++|||+++++|||.+|.+|+||+++||++.|.++++++. 
T Consensus        20 d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~-   98 (251)
T PRK07670         20 DPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED-   98 (251)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-
Confidence            4589999999999999999999975   678999999999999999999999999999999999999999999999876 


Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc-chhhhccc
Q 009567          366 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT-TFQEITAD  442 (532)
Q Consensus       366 ~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~iSLD~~v~~d~~~-~l~d~i~d  442 (532)
                        ++|.++...+++++++...+.+.+|+.|+.+|||+.+|++.++|..++.  ....+.|||.++.++++. .+...+.+
T Consensus        99 --~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~  176 (251)
T PRK07670         99 --WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRD  176 (251)
T ss_pred             --CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhcC
Confidence              6999999999999999999999999999999999999999999999876  345689999988655443 23344455


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          443 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       443 ~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      ....+|++.+...+....|..+|..||+++|+||.++|+    +++|++|||+.||+|.++|++++++|+++||.++.
T Consensus       177 ~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~  250 (251)
T PRK07670        177 DKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE  250 (251)
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            555678888888888889999999999999999999998    99999999999999999999999999999999875

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=1.7e-34  Score=289.66  Aligned_cols=243  Identities=24%  Similarity=0.355  Sum_probs=214.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHH
Q 009567          231 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ  310 (532)
Q Consensus       231 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkr  310 (532)
                      |.|+++||.+|..+++.                                       .++..|++.||..|.++|+++|++
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            77999999888876653                                       134689999999999999999999


Q ss_pred             hhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHh
Q 009567          311 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE  390 (532)
Q Consensus       311 Y~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~  390 (532)
                      |.+++.+.+||+||||+|||+++++||+.+|.+|+||+++||++.|.++++++.+.+++|.++....+++.++...+...
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---chhhhcccCCCCChhHHHHHHHHHHHHHHHH
Q 009567          391 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDT---TFQEITADTGVEIPDISVQKQLMRQHVRNLL  465 (532)
Q Consensus       391 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~iSLD~~v~~d~~~---~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L  465 (532)
                      .++.|+.+++|+.+|++.+++..+....  ....|+|.+++.+++.   .+.+..     ..|++.+...+....+..+|
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  3578899887654332   122222     24566666667777899999


Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ..||+++|+||.++|+    +++|++|||+.||||.++|+++.++|+++||..+..
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

>PRK05572 sporulation sigma factor SigF; Validated

Probab=100.00  E-value=2.3e-34  Score=288.17  Aligned_cols=244  Identities=28%  Similarity=0.430  Sum_probs=213.3

Q ss_pred             hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHH
Q 009567          225 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV  304 (532)
Q Consensus       225 ~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV  304 (532)
                      +.-...|.||.+++.+|...++.                                        ++..|++.|+..|.++|
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            34567899999999888776542                                        23689999999999999


Q ss_pred             HHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHH
Q 009567          305 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK  384 (532)
Q Consensus       305 ~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~  384 (532)
                      +++|++|.+++.+.+||+|||++++|+++++|++.+|.+|.||+++||++.|.+++++.. .|++|.++....++++++.
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            999999999999999999999999999999999998889999999999999999999874 7899999999999999999


Q ss_pred             HHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhhcccCCCCChhHHHHHHHHHHHHH
Q 009567          385 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVR  462 (532)
Q Consensus       385 ~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~--~l~d~i~d~~~~~pee~~~~~~l~~~L~  462 (532)
                      ..+..++|+.|+.+|+|+.+|++++++..+......+.||+.++.+++..  ++.+.+.++..   +    .......|.
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            99999999999999999999999999999888877889999887654332  23344443321   1    123356788


Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       463 ~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      .++..||+++++||.++|+    +++|++|||+.+|+|.++|++++++|+++||..+.
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            9999999999999999997    89999999999999999999999999999998774

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

Probab=100.00  E-value=9.2e-35  Score=285.74  Aligned_cols=217  Identities=23%  Similarity=0.419  Sum_probs=196.0

Q ss_pred             HHHHHHHHHHHHHHHhhC---CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567          296 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  372 (532)
Q Consensus       296 LI~~nlrLV~sIAkrY~~---~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~  372 (532)
                      |+..|.++|+++|++|.+   ++.+++||+|||++|||+++++|||++|++|+||+++||++.|.+++++..   ++|.+
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            588999999999999986   789999999999999999999999999999999999999999999998865   58999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCC-CCcchhhhcccCCCCChh
Q 009567          373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWAD-QDTTFQEITADTGVEIPD  449 (532)
Q Consensus       373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~iSLD~~v~~d-~~~~l~d~i~d~~~~~pe  449 (532)
                      ....++++.++...+.+.+|+.|+.+|+|+.+|+++++|..++..  ....+|+|....++ +..++.+.++++...+|+
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE  157 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence            999999999999999999999999999999999999999999864  34567888766543 334566667665666888


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      +.+...+....|..+|+.||+++|+||.++|+    +++|++|||+.||+|.++|++++++|+++||.++
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=1.5e-34  Score=286.49  Aligned_cols=209  Identities=21%  Similarity=0.335  Sum_probs=179.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhC---CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567          293 REKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  369 (532)
Q Consensus       293 re~LI~~nlrLV~sIAkrY~~---~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl  369 (532)
                      ...|+..|+|+|.++|++|.+   .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..+   +
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            346788899999999999875   4679999999999999999999998666 89999999999999999998653   6


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567          370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITADTGVEI  447 (532)
Q Consensus       370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~  447 (532)
                      |+++....++++++...+.+++|+.|+.+|||+.+|+++++|..++..  .....|||.+++++++..   .+.+   ..
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            888899999999999999999999999999999999999999998764  456899999986654322   2221   12


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      +++..   .....|..++..||+++|.||.++|+    +++|++|||+.||||.++|+|++++|++|||..
T Consensus       167 ~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~  230 (231)
T PRK12427        167 LEENI---IIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF  230 (231)
T ss_pred             HHHHH---HHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            33222   24557899999999999999999998    899999999999999999999999999999964

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=100.00  E-value=2.8e-33  Score=277.49  Aligned_cols=225  Identities=23%  Similarity=0.410  Sum_probs=198.6

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhh---CCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhc
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  364 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~---~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~  364 (532)
                      .|.-+++.|+..|.++|+++|++|.   +++.+.+||+|||++|||+++++|||++|.+|+||+++||++.|.++++++.
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             cccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCcchhhhccc
Q 009567          365 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITAD  442 (532)
Q Consensus       365 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~iSLD~~v~~d~~~~l~d~i~d  442 (532)
                      +   +|.++.....++.++...+.+.+|++|+.+|||+.+|++.++|..++...  ...+|++..++++++. +.. ..+
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   68888888888889999999999999999999999999999999988753  3567888877554432 222 223


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          443 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       443 ~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      +...+|++.+...+....|..+|..||+++|.||.++|.    +++|++|||+.||||.++|++++.+|+++||+.+..
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            334567788888888889999999999999999999998    899999999999999999999999999999998764

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.96  E-value=6.6e-28  Score=238.78  Aligned_cols=210  Identities=25%  Similarity=0.451  Sum_probs=171.7

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 009567          219 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  298 (532)
Q Consensus       219 ~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~  298 (532)
                      .|..|+.+++..|+||+++|..|+..++.                                        ++..|++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence            56789999999999999999888776542                                        34689999999


Q ss_pred             HHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHH
Q 009567          299 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  378 (532)
Q Consensus       299 ~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~  378 (532)
                      .|.++|+++|.+|.+++.+.+||+|||++++|+++++||+++|.+|.||+++|+++.+.+++++..+..           
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---CCcchhhhcccCCCCChhHHHHHH
Q 009567          379 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQ  455 (532)
Q Consensus       379 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d---~~~~l~d~i~d~~~~~pee~~~~~  455 (532)
                                                               ...+++.+.+.+   ....+.+...+. .+++++.+...
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 009567          456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ...+.|..+|..||+++|+||.++|++.+.+++|++|||+.||+|.++|++++.+|+++||+.+..
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            777889999999999999999999987666999999999999999999999999999999998764

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.93  E-value=4.3e-24  Score=210.86  Aligned_cols=199  Identities=28%  Similarity=0.527  Sum_probs=156.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHH
Q 009567          228 ETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV  307 (532)
Q Consensus       228 ~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sI  307 (532)
                      +..+.|++.+|..|+..++.                                        ++..|++.|+..|.++|+++
T Consensus        25 ~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~af~~l~~~y~~~v~~~   64 (227)
T TIGR02846        25 SFPQPLSEEEEKKYLDRLKE----------------------------------------GDEEARNVLIERNLRLVAHI   64 (227)
T ss_pred             hCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHHH
Confidence            45666888888888776653                                        33689999999999999999


Q ss_pred             HHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHH
Q 009567          308 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLY  387 (532)
Q Consensus       308 AkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l  387 (532)
                      |.+|.++..+.+||+||+++++|+++++|+++.+.+|.||+++|+++.+.+++++..+..+                   
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            9999999999999999999999999999999988899999999999999999987642110                   


Q ss_pred             HHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC---CCcchhhhcccCCCCChhHHHHHHHHHHHHHHH
Q 009567          388 IQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQLMRQHVRNL  464 (532)
Q Consensus       388 ~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d---~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~  464 (532)
                                                       ..+++.....+   ....+.+...+ ....+++.+...+..+.|..+
T Consensus       126 ---------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~  171 (227)
T TIGR02846       126 ---------------------------------EVSLQDPIGVDKEGNEISLIDILGS-DGDSVIEQVELNLEIKKLYKK  171 (227)
T ss_pred             ---------------------------------ceeccccccCCcccCcccHHHHhcC-CCCChHHHHHHHHHHHHHHHH
Confidence                                             01111111000   01112222222 123556666666666789999


Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      |+.||+++|+||.++|.++..+++|++|||+.||+|.++|++++++|+++||+.+
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            9999999999999999765558999999999999999999999999999999875

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.

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.93  E-value=6e-24  Score=210.23  Aligned_cols=180  Identities=28%  Similarity=0.536  Sum_probs=139.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      +..|++.|+..|.++|+.+|++|.+++.+.+|++||+|+++|+++++|++..+++|.||+++++++.+.++++++.+.. 
T Consensus        50 d~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~-  128 (234)
T PRK08301         50 DEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK-  128 (234)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc-
Confidence            3589999999999999999999999999999999999999999999999988889999999999999999998764210 


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC--C-CcchhhhcccCCC
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD--Q-DTTFQEITADTGV  445 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d--~-~~~l~d~i~d~~~  445 (532)
                                                                         ...+++.+...+  . ...+.+...+. .
T Consensus       129 ---------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  156 (234)
T PRK08301        129 ---------------------------------------------------AEVSFDEPLNIDWDGNELLLSDVLGTD-N  156 (234)
T ss_pred             ---------------------------------------------------cccccccccccccCCCcccHHHhccCc-c
Confidence                                                               001112111100  0 01111222211 1


Q ss_pred             CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          446 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       446 ~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ..++...........|..+|+.||+++|+||.++|+|...+++|++|||+.||||.++|+++.++|+++||+.+..
T Consensus       157 ~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~  232 (234)
T PRK08301        157 DIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK  232 (234)
T ss_pred             cchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            2333344445556679999999999999999999965444899999999999999999999999999999998753

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.92  E-value=5e-23  Score=204.18  Aligned_cols=180  Identities=30%  Similarity=0.545  Sum_probs=140.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      +..|++.|+..|.+.|+.+|++|.+++.+.+|++||+++++|+++++|++..+++|.||++.++++.+.++++++.+...
T Consensus        50 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~  129 (234)
T TIGR02835        50 DESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRS  129 (234)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccC
Confidence            46899999999999999999999999999999999999999999999999888899999999999999999987653100


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC---CCCCcchhhhcccCCC
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW---ADQDTTFQEITADTGV  445 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~---~d~~~~l~d~i~d~~~  445 (532)
                                                                          ..+++.++.   .+......+.. ++..
T Consensus       130 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~-~~~~  156 (234)
T TIGR02835       130 ----------------------------------------------------EVSFDEPLNVDWDGNELLLSDVL-GTDS  156 (234)
T ss_pred             ----------------------------------------------------cccccccccCCCCCCcchHHHhc-CCCC
Confidence                                                                011111110   00001111111 1111


Q ss_pred             CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          446 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       446 ~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      +.+++.+........|..+|..||+++|.||.++|++.+++++|++|||+.||+|..+|+++..+|+++||+.+..
T Consensus       157 ~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~  232 (234)
T TIGR02835       157 DIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR  232 (234)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            2333444555556779999999999999999999976555899999999999999999999999999999998754

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=1.3e-22  Score=195.94  Aligned_cols=195  Identities=22%  Similarity=0.329  Sum_probs=150.9

Q ss_pred             CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          277 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       277 ~~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      ++++.+...++.| ..|++.|+..|.++|+.+|.+|.+++.+.+|++||++++||+++.+||+.+|.+|.||++.++++.
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            4556666666555 499999999999999999999999999999999999999999999999988789999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT  434 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~-d~~~  434 (532)
                      +.+++++..+..+.+.                                               ....|.+.++.+ +.+.
T Consensus        89 ~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~  121 (208)
T PRK08295         89 IITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDR  121 (208)
T ss_pred             HHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccch
Confidence            9999876542111110                                               011233333222 2222


Q ss_pred             chhhhcccCCCCChhHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567          435 TFQEITADTGVEIPDISVQKQLMRQHV-RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  513 (532)
Q Consensus       435 ~l~d~i~d~~~~~pee~~~~~~l~~~L-~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk  513 (532)
                      .+.+.+.++...+|+..+...+....+ ..++..||+++|+||.+ |.    +++|.+|||+.||+|.++|+....||++
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            344444444445677666555555555 45679999999999999 76    8999999999999999999999999999


Q ss_pred             HHHHHhhcCc
Q 009567          514 RLKQSLGGKA  523 (532)
Q Consensus       514 KLR~~l~~~~  523 (532)
                      +||+++....
T Consensus       197 ~Lr~~l~~~~  206 (208)
T PRK08295        197 KLEKYLENRE  206 (208)
T ss_pred             HHHHHHHhhc
Confidence            9999987653

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.89  E-value=1e-21  Score=188.19  Aligned_cols=191  Identities=23%  Similarity=0.323  Sum_probs=146.0

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      |++..|...++.|+ .|++.|+..|.+.|+.+|+++.++..+.+||+||+++++|+++.+|++..|..|.||++.+|++.
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            45677777777765 99999999999999999999999999999999999999999999999988789999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT  434 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~-d~~~  434 (532)
                      +.++++...+..+.+.                                               ....|++.+... +++.
T Consensus        84 ~~~~~r~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~  116 (198)
T TIGR02859        84 IITAIKTATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESDR  116 (198)
T ss_pred             HHHHHHHHHHhcccch-----------------------------------------------hhhcCcccccccccccc
Confidence            9888865431111000                                               011233332211 1122


Q ss_pred             chhhhcccCCCCChhHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567          435 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  513 (532)
Q Consensus       435 ~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L-~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk  513 (532)
                      ++.+.+.+....+|++.+...+....|..+|..| ++.++.|+. +|.    +++|++|||+.||+|.++|+...+||++
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            3334333223346777777777778899999985 566666665 465    8999999999999999999999999999


Q ss_pred             HHHHHh
Q 009567          514 RLKQSL  519 (532)
Q Consensus       514 KLR~~l  519 (532)
                      +||+.+
T Consensus       192 ~L~~~l  197 (198)
T TIGR02859       192 KLEKYL  197 (198)
T ss_pred             HHHHhc
Confidence            999876

Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.89  E-value=7.7e-22  Score=187.99  Aligned_cols=176  Identities=16%  Similarity=0.250  Sum_probs=144.0

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      ++++.|...++.|+ .|++.|+..|.++|+.+|++|.+++.+.+|++||+|+++|+++.+|++. +.+|.+|++..+++.
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            45666777666665 9999999999999999999999999999999999999999999999986 457999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  435 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~  435 (532)
                      +.++++++.+.                                                        +.+. .   .   
T Consensus        84 ~~d~~R~~~~~--------------------------------------------------------~~~~-~---~---  100 (186)
T PRK05602         84 CYDRLRRRREV--------------------------------------------------------PVED-A---P---  100 (186)
T ss_pred             HHHHHHhcCCC--------------------------------------------------------Cccc-c---c---
Confidence            99998765310                                                        0000 0   0   


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                        + ..+. ...++..+...+....+..+|..||+++|+||.++|.    +++|++|||+.||+|..+|++..+||+++|
T Consensus       101 --~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~L  172 (186)
T PRK05602        101 --D-VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVDALESLLARGRRAL  172 (186)
T ss_pred             --c-cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence              0 0011 1135555555666678999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCch
Q 009567          516 KQSLGGKAS  524 (532)
Q Consensus       516 R~~l~~~~l  524 (532)
                      |+.+...+.
T Consensus       173 r~~l~~~~~  181 (186)
T PRK05602        173 RAQLADLPG  181 (186)
T ss_pred             HHHHHhccc
Confidence            999987654

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.88  E-value=2.4e-21  Score=183.75  Aligned_cols=180  Identities=17%  Similarity=0.253  Sum_probs=140.1

Q ss_pred             HHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHH
Q 009567          280 RDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  358 (532)
Q Consensus       280 ~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~  358 (532)
                      +.|...+..| ..|+..|+..|.++|+.+|++|.+++.+.+|++||+++++|+++.+|++..  .|.+|++..+++.+.+
T Consensus         6 ~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~   83 (187)
T TIGR02948         6 KKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTID   83 (187)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHH
Confidence            3344455544 599999999999999999999999999999999999999999999999865  5999999999999999


Q ss_pred             HHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 009567          359 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE  438 (532)
Q Consensus       359 ~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d  438 (532)
                      ++++..+...                                                       ++.....++...+.+
T Consensus        84 ~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~  108 (187)
T TIGR02948        84 RLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMES  108 (187)
T ss_pred             HHHhhccccc-------------------------------------------------------ccccccCcccccccc
Confidence            9876432100                                                       000000000111111


Q ss_pred             hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          439 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       439 ~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      ...+. .+.|++.+...+....+..+|..|||++|.||.++|.    +++|++|||+.||+|.++|++.+.||+++||..
T Consensus       109 ~~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  183 (187)
T TIGR02948       109 QLAAD-EAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ  183 (187)
T ss_pred             ccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            11111 2356666666677778999999999999999999988    899999999999999999999999999999998


Q ss_pred             hhc
Q 009567          519 LGG  521 (532)
Q Consensus       519 l~~  521 (532)
                      +..
T Consensus       184 l~~  186 (187)
T TIGR02948       184 LRH  186 (187)
T ss_pred             hhc
Confidence            753

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

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.88  E-value=4.1e-21  Score=183.42  Aligned_cols=171  Identities=23%  Similarity=0.317  Sum_probs=137.9

Q ss_pred             HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCC----CCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          281 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       281 ~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~----g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      .|...+..| ..|++.|+..|.+.|+.+|.++.++    +.+.+|++||+++++|+++.+|++. +..|.+|++..+++.
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            355555555 4999999999999999999998765    3689999999999999999999864 457999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  435 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~  435 (532)
                      +.++++++.+....                                                     ..+. +       
T Consensus        92 ~~d~~r~~~r~~~~-----------------------------------------------------~~~~-~-------  110 (189)
T PRK09648         92 VADAHRAAGRDKAV-----------------------------------------------------PTEE-V-------  110 (189)
T ss_pred             HHHHHHHhCCCccc-----------------------------------------------------cccc-c-------
Confidence            99999876531100                                                     0000 0       


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                       .+...  ...+|++.+...+..+.|..+|..||+++|+||.++|+    +++|++|||+.||+|..+|++...||+++|
T Consensus       111 -~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L  183 (189)
T PRK09648        111 -PERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGSTPGAVRVAQHRALARL  183 (189)
T ss_pred             -ccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence             00000  11256666666777788999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhh
Q 009567          516 KQSLG  520 (532)
Q Consensus       516 R~~l~  520 (532)
                      |+.+.
T Consensus       184 r~~l~  188 (189)
T PRK09648        184 RAEIE  188 (189)
T ss_pred             HHHhc
Confidence            99864

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.88  E-value=2.9e-21  Score=183.20  Aligned_cols=180  Identities=15%  Similarity=0.233  Sum_probs=141.7

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHH
Q 009567          280 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  358 (532)
Q Consensus       280 ~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~  358 (532)
                      +.|...++.|+ .+++.++..|.++|+++|+++.++..+++|++||++++||+++++|++..  .|.+|++..+++.+.+
T Consensus         6 ~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d   83 (187)
T PRK09641          6 KRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTID   83 (187)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHH
Confidence            44555555554 99999999999999999999999999999999999999999999999853  7999999999999999


Q ss_pred             HHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 009567          359 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE  438 (532)
Q Consensus       359 ~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d  438 (532)
                      ++++..+..                                                       +++.....++.....+
T Consensus        84 ~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~~  108 (187)
T PRK09641         84 RLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLTMYS  108 (187)
T ss_pred             HHHhcCccc-------------------------------------------------------cccccccCCcchhhhc
Confidence            988754210                                                       0011110111111111


Q ss_pred             hcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          439 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       439 ~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      .+.+. ..+|++.+...+....+..+|..||+++++||.++|.    ++++++|||+.||||.++|++..+||+++||+.
T Consensus       109 ~~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  183 (187)
T PRK09641        109 QLAAD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ  183 (187)
T ss_pred             ccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            11111 2246666677777778999999999999999999998    899999999999999999999999999999998


Q ss_pred             hhc
Q 009567          519 LGG  521 (532)
Q Consensus       519 l~~  521 (532)
                      +..
T Consensus       184 l~~  186 (187)
T PRK09641        184 LRH  186 (187)
T ss_pred             Hhc
Confidence            753

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=1.8e-21  Score=186.65  Aligned_cols=181  Identities=18%  Similarity=0.241  Sum_probs=146.0

Q ss_pred             CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          277 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       277 ~~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      +++..+...+..| ..|++.|+..|.+.|+++|+++.++..+.+|++||+++++|+++++|++.  ..|.+|++.++++.
T Consensus        11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~   88 (194)
T PRK12513         11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL   88 (194)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence            3456667666666 49999999999999999999999999999999999999999999999974  36999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  435 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~  435 (532)
                      +.+++++..+....+.                                                     +.    +.  .
T Consensus        89 ~~~~~R~~~~~~~~~~-----------------------------------------------------~~----~~--~  109 (194)
T PRK12513         89 LIDHWRRHGARQAPSL-----------------------------------------------------DA----DE--Q  109 (194)
T ss_pred             HHHHHHHhcccccccc-----------------------------------------------------cc----ch--h
Confidence            9999987653211100                                                     00    00  0


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                      + ....+ ....|+..+...+....+..+|..||+++|.||.++|.    +++|++|||+.||+|.++|+++..||+++|
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 009567          516 KQSLGGKAS  524 (532)
Q Consensus       516 R~~l~~~~l  524 (532)
                      |..+...++
T Consensus       184 r~~l~~~~~  192 (194)
T PRK12513        184 RELLAEEVA  192 (194)
T ss_pred             HHHHHHhhc
Confidence            999876554

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.88  E-value=2.7e-21  Score=185.94  Aligned_cols=176  Identities=16%  Similarity=0.189  Sum_probs=139.7

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567          278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  356 (532)
Q Consensus       278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI  356 (532)
                      +...|...+..| ..|++.|+..|.++|+++|.+|.++..+.+|++||+++++|+++++||+.+| .|.+|++..+++.+
T Consensus        16 ~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~   94 (194)
T PRK09646         16 DLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRA   94 (194)
T ss_pred             cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHH
Confidence            345566665555 4999999999999999999999999999999999999999999999998765 69999999999999


Q ss_pred             HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567          357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  436 (532)
Q Consensus       357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l  436 (532)
                      .++++++.+..+.                                                       +.....   .  
T Consensus        95 ~d~~r~~~~~~~~-------------------------------------------------------~~~~~~---~--  114 (194)
T PRK09646         95 VDRVRSEQAASQR-------------------------------------------------------EVRYGA---R--  114 (194)
T ss_pred             HHHHHhhcccccc-------------------------------------------------------cccccc---c--
Confidence            9999876521100                                                       000000   0  


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                       +.  +.....+++.+...+..+.|..+|..||+++|+||.++|.    +++|++|||+.||+|..+|+++++||+++||
T Consensus       115 -~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr  187 (194)
T PRK09646        115 -NV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPLGTVKTRMRDGLIRLR  187 (194)
T ss_pred             -cc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence             00  0011123344444555678999999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhhc
Q 009567          517 QSLGG  521 (532)
Q Consensus       517 ~~l~~  521 (532)
                      ..+..
T Consensus       188 ~~l~~  192 (194)
T PRK09646        188 DCLGV  192 (194)
T ss_pred             HHhcc
Confidence            98854

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.87  E-value=1e-20  Score=177.42  Aligned_cols=172  Identities=19%  Similarity=0.236  Sum_probs=137.2

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567          287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  366 (532)
Q Consensus       287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~  366 (532)
                      .++..|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+  .+.+|.+|++..+++.+.+++++..+.
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            345689999999999999999999999999999999999999999999999  456899999999999999998775432


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567          367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  446 (532)
Q Consensus       367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~  446 (532)
                      ...+                                                    +++  ..+.++....+...+  ..
T Consensus        84 ~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~~--~~  107 (182)
T PRK09652         84 PPAS----------------------------------------------------DVD--AEEAEDFDLADALRD--IS  107 (182)
T ss_pred             CCcc----------------------------------------------------ccc--ccccccccccccccc--cc
Confidence            1100                                                    000  000000011111111  12


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      +|++.+...+....+..+|..|||++|+||.++|.    .++|.+|||+.||+|..+|++.+.+|+++||+.+.
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            56666777777788999999999999999999987    89999999999999999999999999999999875

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

Probab=99.87  E-value=1.1e-20  Score=176.23  Aligned_cols=163  Identities=20%  Similarity=0.344  Sum_probs=134.3

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  367 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I  367 (532)
                      ++..|++.|+..|.+.+++++.++.++..+.+|++||+++.+|+++++|+...+ .|.+|++..+++.+.++++++.+..
T Consensus         8 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~   86 (170)
T TIGR02952         8 REEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHP   86 (170)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCC
Confidence            446999999999999999999999988899999999999999999999997555 8999999999999999998765311


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567          368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  447 (532)
Q Consensus       368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~  447 (532)
                      ..                                                     +.+.         ..+...  ...+
T Consensus        87 ~~-----------------------------------------------------~~~~---------~~~~~~--~~~~  102 (170)
T TIGR02952        87 LF-----------------------------------------------------SLDV---------FKELLS--NEPN  102 (170)
T ss_pred             CC-----------------------------------------------------cHHH---------HhhcCC--CCCC
Confidence            00                                                     0000         000000  1124


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      |++.+...+....+..+|..|||++|+||.++|.    +|+|++|||+.||+|..+|++...||+++||+.+
T Consensus       103 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l  170 (170)
T TIGR02952       103 PEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFRAIKKLARQM  170 (170)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            5666666667788999999999999999999998    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.

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.3e-20  Score=180.48  Aligned_cols=175  Identities=23%  Similarity=0.288  Sum_probs=137.7

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567          278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  356 (532)
Q Consensus       278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI  356 (532)
                      +...|...+..| ..|++.|+..|.+.|+.+++++.++..+.+|++||+++++|+. ..|++..+ .|.||++.++++.+
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            345566655555 5999999999999999999999999899999999999999976 67887654 79999999999999


Q ss_pred             HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567          357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  436 (532)
Q Consensus       357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l  436 (532)
                      .++++++.+.....                           .+.                        +.        . 
T Consensus        93 ~d~~Rk~~~~~~~~---------------------------~~~------------------------~~--------~-  112 (194)
T PRK12519         93 IDRLRSRRSRQRLL---------------------------ERW------------------------QQ--------E-  112 (194)
T ss_pred             HHHHHhcccccchh---------------------------hhh------------------------hh--------h-
Confidence            99998765311000                           000                        00        0 


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                        ...+.....+++.+...+....|..+|..||+++++||.++|.    +++|++|||+.||+|.++|++++.||+++||
T Consensus       113 --~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr  186 (194)
T PRK12519        113 --LLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGIPLGTVKARARQGLLKLR  186 (194)
T ss_pred             --hcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence              0000011245555555666677899999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhh
Q 009567          517 QSLG  520 (532)
Q Consensus       517 ~~l~  520 (532)
                      +.+.
T Consensus       187 ~~l~  190 (194)
T PRK12519        187 ELLQ  190 (194)
T ss_pred             HHHH
Confidence            9875

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.86  E-value=1.9e-20  Score=178.00  Aligned_cols=176  Identities=18%  Similarity=0.270  Sum_probs=135.2

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567          278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  356 (532)
Q Consensus       278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI  356 (532)
                      ++..+...++.| ..|++.|+..|.+.|+.++++|.+++.+.+|++||+++++|+++++|++.. ..|.+|++..+++.+
T Consensus         9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~~   87 (186)
T PRK13919          9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHAA   87 (186)
T ss_pred             CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHHH
Confidence            456666666555 499999999999999999999999999999999999999999999998754 369999999999999


Q ss_pred             HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567          357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  436 (532)
Q Consensus       357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l  436 (532)
                      .+++++..+..+                                                    ..+.+     ......
T Consensus        88 ~d~~rk~~~~~~----------------------------------------------------~~~~~-----~~~~~~  110 (186)
T PRK13919         88 VDHVRRRAARPQ----------------------------------------------------PLEPD-----EREPEA  110 (186)
T ss_pred             HHHHHhhhcccc----------------------------------------------------ccccc-----cccccc
Confidence            999977542100                                                    00000     000000


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .+ .+     .+............|..+|..||+++|+||.++|.    +++|++|||+.||+|..+|+..++||+++||
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     11111122233456889999999999999999998    9999999999999999999999999999999


Q ss_pred             HHhhc
Q 009567          517 QSLGG  521 (532)
Q Consensus       517 ~~l~~  521 (532)
                      ..+..
T Consensus       181 ~~l~~  185 (186)
T PRK13919        181 EVLRE  185 (186)
T ss_pred             HHhcC
Confidence            98753

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.86  E-value=1.4e-20  Score=173.18  Aligned_cols=151  Identities=20%  Similarity=0.237  Sum_probs=123.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  369 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl  369 (532)
                      ..|++.|+..|.++|+.+++++ +...+.+|++|||++++|+++++|++..| .|.+|++..+++.+.++++++.+..  
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 56678999999999999999999998766 7999999999999999998753100  


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567          370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  449 (532)
Q Consensus       370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe  449 (532)
                                            .                           .. .      .+              +.|+
T Consensus        79 ----------------------~---------------------------~~-~------~~--------------~~~~   88 (154)
T PRK06759         79 ----------------------E---------------------------KC-V------CV--------------GEYE   88 (154)
T ss_pred             ----------------------c---------------------------cc-c------cc--------------CCCc
Confidence                                  0                           00 0      00              0111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      +.....+....|..+|..||+++|+||.++|+    +++|.+|||+.||+|..+|+++..||+++||+.
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            12222334567899999999999999999998    999999999999999999999999999999974

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=2.7e-20  Score=176.11  Aligned_cols=173  Identities=14%  Similarity=0.158  Sum_probs=137.7

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567          278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  356 (532)
Q Consensus       278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI  356 (532)
                      +...|...+..| ..|+..|+..|.+.|+.+|.+|.++..+.+|++||+++++|+++++|++.. ..|.||++..+++.+
T Consensus         5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~~   83 (179)
T PRK12514          5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNHA   83 (179)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHH
Confidence            344555555555 589999999999999999999999999999999999999999999999754 369999999999999


Q ss_pred             HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567          357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  436 (532)
Q Consensus       357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l  436 (532)
                      .+++++..+.. .                                                     .++.      .   
T Consensus        84 ~d~~R~~~~~~-~-----------------------------------------------------~~~~------~---  100 (179)
T PRK12514         84 IDRLRARKAVA-V-----------------------------------------------------DIDE------A---  100 (179)
T ss_pred             HHHHHhcCCcc-c-----------------------------------------------------cccc------c---
Confidence            99997654210 0                                                     0000      0   


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .+ ..+. ...|++.+...+....|..+|..||+++|+||.++|.    +|+|++|||+.||+|..+|++.+.||+++||
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 0001 1245555554555567899999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhh
Q 009567          517 QSLG  520 (532)
Q Consensus       517 ~~l~  520 (532)
                      +++.
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=99.86  E-value=3.1e-20  Score=177.82  Aligned_cols=175  Identities=14%  Similarity=0.181  Sum_probs=141.6

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCC---CCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHH
Q 009567          277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV  352 (532)
Q Consensus       277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g---~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wI  352 (532)
                      ++++.|+..+..|+ .|++.|+..|.+.|+.++.++.+++   .+.+|++||+++++|+++++|++..+ .|.||++..+
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            45667777777765 8999999999999999999998863   46899999999999999999997654 7999999999


Q ss_pred             HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 009567          353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ  432 (532)
Q Consensus       353 r~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~  432 (532)
                      ++.+.++++++.+....                                                    .+.+.      
T Consensus        82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------  103 (189)
T PRK06811         82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------  103 (189)
T ss_pred             HHHHHHHHHHhcccccc----------------------------------------------------ccchh------
Confidence            99999999876531100                                                    00000      


Q ss_pred             CcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          433 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       433 ~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      .      .. ....+|++.+...+....|..+|..|||++|.||.++|.    +++|.+|||+.||+|..+|++.+.||+
T Consensus       104 ~------~~-~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~lgis~~~V~~~l~Ra~  172 (189)
T PRK06811        104 F------IL-ISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKKLGLTRSAIDNRLSRGR  172 (189)
T ss_pred             h------hh-cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            0      00 011245666666677778999999999999999999997    899999999999999999999999999


Q ss_pred             HHHHHHhhc
Q 009567          513 YRLKQSLGG  521 (532)
Q Consensus       513 kKLR~~l~~  521 (532)
                      ++||...-+
T Consensus       173 ~~Lr~~~~~  181 (189)
T PRK06811        173 KKLQKNKLN  181 (189)
T ss_pred             HHHHHcccC
Confidence            999986543

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.86  E-value=3.9e-20  Score=175.86  Aligned_cols=181  Identities=16%  Similarity=0.210  Sum_probs=141.2

Q ss_pred             CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567          278 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  356 (532)
Q Consensus       278 ~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI  356 (532)
                      ++..|...+..|+ .+++.|+..|.+.|+.+|+++.+...+.+|++||+++++|+++++|++.  ..|.+|++...++.+
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            4556666666554 8999999999999999999999999999999999999999999999975  369999999999999


Q ss_pred             HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567          357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  436 (532)
Q Consensus       357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l  436 (532)
                      .+++++..+.....                                                  ..+.+.      ...+
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 009567          437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .+........+|++.+...+....|..+|..||+++|+||.++|.    +++|++|||+.||+|..+|++..+||+++||
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            000000011256666666677788999999999999999999997    8999999999999999999999999999999


Q ss_pred             HHhh
Q 009567          517 QSLG  520 (532)
Q Consensus       517 ~~l~  520 (532)
                      +++.
T Consensus       184 ~~l~  187 (190)
T TIGR02939       184 IRLR  187 (190)
T ss_pred             HHhh
Confidence            9886

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.

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=4.2e-20  Score=182.84  Aligned_cols=173  Identities=18%  Similarity=0.235  Sum_probs=137.9

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  367 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I  367 (532)
                      ++..|++.|+..|.+.|+++|+++.+.+.+.+|++||+++++|+++++|++.  ..|.+|++..+++.+.+++++..+..
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            3468999999999999999999999999999999999999999999999985  47999999999999999988765322


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567          368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  447 (532)
Q Consensus       368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~  447 (532)
                      .++.                            .                      . +..... ++  ...... ....+
T Consensus       105 ~~~~----------------------------~----------------------~-~~~~~~-~~--~~~~~~-~~~~~  129 (231)
T PRK11922        105 NLAE----------------------------M----------------------V-MASTIA-GG--ERTPLA-DPAED  129 (231)
T ss_pred             cchh----------------------------c----------------------c-cccccc-cc--cccccC-cccCC
Confidence            1100                            0                      0 000000 00  000011 11235


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      |++.+...+..+.|..+|..||+++|+||.++|.    +++|++|||+.||+|.++|++.+.||+++||+.+..
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            6677777777888999999999999999999987    899999999999999999999999999999999865

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.85  E-value=5.9e-20  Score=175.85  Aligned_cols=180  Identities=15%  Similarity=0.203  Sum_probs=140.5

Q ss_pred             HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHH
Q 009567          279 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  357 (532)
Q Consensus       279 ~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~  357 (532)
                      ++.|...++.| ..+++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++..  .|.+|++..+++.+.
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            44555555555 599999999999999999999999989999999999999999999999864  499999999999999


Q ss_pred             HHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 009567          358 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  437 (532)
Q Consensus       358 ~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~  437 (532)
                      ++++++.+....                                                  ....++.....++.    
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 009567          438 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       438 d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ..+.  ....|++.+...+..+.+..+|..||+++|.||.++|.    +|+|.+|||+.||+|..+|++...||+++||.
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  12356666667777788999999999999999999987    89999999999999999999999999999999


Q ss_pred             Hhh
Q 009567          518 SLG  520 (532)
Q Consensus       518 ~l~  520 (532)
                      ++.
T Consensus       185 ~l~  187 (193)
T PRK11923        185 ALQ  187 (193)
T ss_pred             HHH
Confidence            886

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=5.3e-20  Score=177.26  Aligned_cols=177  Identities=19%  Similarity=0.211  Sum_probs=143.0

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      +++..|+..+..|+ .|++.|+..|.+.|+.+|.++.++..+.+|++||+++++|+.+.+|++.. ..|.+|++..+++.
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            35667777776664 99999999999999999999999999999999999999999999998533 47999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  435 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~  435 (532)
                      +.++++++.+..                                                      ..++. .   .   
T Consensus        90 ~~d~~Rk~~~~~------------------------------------------------------~~~~~-~---~---  108 (196)
T PRK12524         90 CTDRLRRRRRAS------------------------------------------------------VDLDD-A---P---  108 (196)
T ss_pred             HHHHHHhhcCCC------------------------------------------------------CCccc-c---c---
Confidence            999987653200                                                      00000 0   0   


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                        +. .+. ...+++.+...+....|..+|+.||+++|+||.|+|.    ++++++|||+.||||..+|+++++||+++|
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 1235555666667778999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCc
Q 009567          516 KQSLGGKA  523 (532)
Q Consensus       516 R~~l~~~~  523 (532)
                      |.++...+
T Consensus       181 r~~l~~~~  188 (196)
T PRK12524        181 AALLAGQR  188 (196)
T ss_pred             HHHHHhcc
Confidence            99987543

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.85  E-value=2.3e-20  Score=178.52  Aligned_cols=173  Identities=20%  Similarity=0.290  Sum_probs=136.5

Q ss_pred             cCCHHHHHHHHhh----cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHH
Q 009567          276 GLSCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW  351 (532)
Q Consensus       276 g~~~~~L~~~l~~----g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~w  351 (532)
                      .++++.|+..++.    +..|++.|+..|.+.|+++|.+|.++..+.+|++||+++.+|+++++|++.  ..|.+|++.+
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            4667778877764    469999999999999999999999999999999999999999999999863  4799999999


Q ss_pred             HHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC
Q 009567          352 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD  431 (532)
Q Consensus       352 Ir~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d  431 (532)
                      +++.+.+++++..+....                          .                           .+...   
T Consensus        85 a~n~~~d~~R~~~~~~~~--------------------------~---------------------------~~~~~---  108 (188)
T PRK09640         85 TYNECITQYRKERRKRRL--------------------------M---------------------------DALSL---  108 (188)
T ss_pred             HHHHHHHHHHHhcccccC--------------------------c---------------------------chhhh---
Confidence            999999999864421000                          0                           00000   


Q ss_pred             CCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          432 QDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       432 ~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                            +...++.    ++.....+....|..+|..||+++|+||.++|.    +++|++|||+.||||..+|+..+.||
T Consensus       109 ------~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra  174 (188)
T PRK09640        109 ------DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIMHMGLSATKMRYKRA  174 (188)
T ss_pred             ------ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence                  0000000    000111233456899999999999999999998    89999999999999999999999999


Q ss_pred             HHHHHHHhh
Q 009567          512 LYRLKQSLG  520 (532)
Q Consensus       512 LkKLR~~l~  520 (532)
                      +++||..+.
T Consensus       175 ~~~Lr~~l~  183 (188)
T PRK09640        175 LDKLREKFA  183 (188)
T ss_pred             HHHHHHHHH
Confidence            999999874

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

Probab=99.85  E-value=1.3e-19  Score=171.87  Aligned_cols=180  Identities=19%  Similarity=0.196  Sum_probs=138.8

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhh
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  363 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~~----~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~  363 (532)
                      ++..|++.|+..|.+.|+.+|++|.+    +..+.+|++||+++.+|+++.+|++..+.+|.+|++..+++.+.+++++.
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            44699999999999999999999853    56789999999999999999999986667899999999999999998764


Q ss_pred             cc-ccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC-CCCCcchhhhcc
Q 009567          364 SR-TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW-ADQDTTFQEITA  441 (532)
Q Consensus       364 ~r-~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~-~d~~~~l~d~i~  441 (532)
                      .+ -.+                         .+                       ....+++.+.. ++....+.+.+.
T Consensus        84 ~~~~~r-------------------------~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~  115 (189)
T TIGR02984        84 LGAQKR-------------------------DI-----------------------RREQSLDAGGRLDESSVRLAAQLA  115 (189)
T ss_pred             HHHHhh-------------------------hc-----------------------ccccCCCcccccCCcchhHHHHcc
Confidence            20 000                         00                       00112222111 111122333333


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          442 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       442 d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      +. ..+|++.+...+....|..+|..|||++|+||.++|+    +++|++|||+.||||.++|++..+||+++||+.+.
T Consensus       116 ~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l~  189 (189)
T TIGR02984       116 AD-GPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQILE  189 (189)
T ss_pred             CC-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhC
Confidence            32 3356777777777788999999999999999999998    89999999999999999999999999999998763

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).

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=6.5e-20  Score=174.47  Aligned_cols=172  Identities=13%  Similarity=0.164  Sum_probs=136.9

Q ss_pred             CHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567          278 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  356 (532)
Q Consensus       278 ~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI  356 (532)
                      +...|...+.+|+ .|++.|+..|.+.|+.++.++.++..+.+|++||+|+.+|+.+++|++.. ..|.+|++..+++.+
T Consensus         9 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~~   87 (182)
T PRK12537          9 DYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHLA   87 (182)
T ss_pred             hHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHHH
Confidence            4455666666554 99999999999999999999999999999999999999999999998644 379999999999999


Q ss_pred             HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567          357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  436 (532)
Q Consensus       357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l  436 (532)
                      .+++++..+...+                                                       +.     ..   
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 009567          437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .+...+  ...+++..........+..+|+.||+++|+||.++|.    +++|++|||+.||||.++|+....||+++||
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  1123333344445567899999999999999999998    9999999999999999999999999999999


Q ss_pred             HHh
Q 009567          517 QSL  519 (532)
Q Consensus       517 ~~l  519 (532)
                      .++
T Consensus       179 ~~l  181 (182)
T PRK12537        179 ECM  181 (182)
T ss_pred             HHh
Confidence            986

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=5.5e-20  Score=182.78  Aligned_cols=174  Identities=14%  Similarity=0.222  Sum_probs=139.7

Q ss_pred             CHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567          278 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  356 (532)
Q Consensus       278 ~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI  356 (532)
                      ++..|...+..| ..|++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+++|++..+ .|.+|++..+++.+
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            445566666555 4899999999999999999999999999999999999999999999987544 79999999999999


Q ss_pred             HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567          357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  436 (532)
Q Consensus       357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l  436 (532)
                      .++++++.+. .                                                       ++. . .+     
T Consensus       128 id~~Rk~~~~-~-------------------------------------------------------~~~-~-~~-----  144 (233)
T PRK12538        128 IDLRRKPRTE-N-------------------------------------------------------VDA-V-PE-----  144 (233)
T ss_pred             HHHHHhhccc-c-------------------------------------------------------ccc-c-cc-----
Confidence            9988753210 0                                                       000 0 00     


Q ss_pred             hhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                        . .+ ....+++.+...+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|+++++||+++||
T Consensus       145 --~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr  216 (233)
T PRK12538        145 --V-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVAAVESLLKRGRQQLR  216 (233)
T ss_pred             --c-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence              0 00 01133444555566678999999999999999999998    9999999999999999999999999999999


Q ss_pred             HHhhcCc
Q 009567          517 QSLGGKA  523 (532)
Q Consensus       517 ~~l~~~~  523 (532)
                      +.+...+
T Consensus       217 ~~l~~~~  223 (233)
T PRK12538        217 DLLRRHE  223 (233)
T ss_pred             HHHHHhh
Confidence            9987554

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=7.2e-20  Score=174.39  Aligned_cols=172  Identities=15%  Similarity=0.161  Sum_probs=135.8

Q ss_pred             HHHHHHh-hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHH
Q 009567          281 DLKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  359 (532)
Q Consensus       281 ~L~~~l~-~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~  359 (532)
                      .+...+. ++..+++.|+..|.++|+.+|.+|.++..+.+|++||+++++|+++++|++.++ .|.+|++..+++.+.++
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            3444444 445999999999999999999999999999999999999999999999998654 58899999999999999


Q ss_pred             HHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhh
Q 009567          360 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI  439 (532)
Q Consensus       360 ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~  439 (532)
                      +++..+...                                                    ..+++.         ....
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 009567          440 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       440 i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      . +. ..++++.....+....|..+|..||++++.|+.++|.    +++|++|||+.||+|.++|+++++||+++||..+
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 1123344445566678999999999999999999998    8999999999999999999999999999999987


Q ss_pred             h
Q 009567          520 G  520 (532)
Q Consensus       520 ~  520 (532)
                      .
T Consensus       186 ~  186 (187)
T PRK12534        186 E  186 (187)
T ss_pred             c
Confidence            4

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.2e-19  Score=176.60  Aligned_cols=171  Identities=12%  Similarity=0.156  Sum_probs=133.0

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567          287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  366 (532)
Q Consensus       287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~  366 (532)
                      .++..+++.|+..|.+.|+.++.++.++..+.+|++||+++.+|++++.|++.++ .|.||++.++++.+.+++++..+.
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            3456999999999999999999999999889999999999999999999998665 599999999999999999876531


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567          367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  446 (532)
Q Consensus       367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~  446 (532)
                      ....                                                     ..    . +...+.+.+.+. ..
T Consensus       113 ~~~~-----------------------------------------------------~~----~-~~~~~~~~~~~~-~~  133 (206)
T PRK12526        113 KEQN-----------------------------------------------------LG----D-DIWPIEQALAES-QS  133 (206)
T ss_pred             cccc-----------------------------------------------------cc----c-ccchhhhhcccc-cC
Confidence            1000                                                     00    0 000000111111 11


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      .+. ..........|..+|..||+++|+||.++|+    +++|++|||+.||+|.++|+..++||+++||+.+...
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    9999999999999999999999999999999998654

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.2e-19  Score=169.68  Aligned_cols=168  Identities=16%  Similarity=0.176  Sum_probs=138.6

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567          287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  366 (532)
Q Consensus       287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~  366 (532)
                      .++..|++.|+..|.+.|+++|+++.++..+.+|++||++++||++.++|+  .+..|.+|++..+++.+.+++++..+.
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            344699999999999999999999999999999999999999999999998  345899999999999999998765421


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567          367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  446 (532)
Q Consensus       367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~  446 (532)
                      ...                                                     ..+ ..   .     +...+....
T Consensus        87 ~~~-----------------------------------------------------~~~-~~---~-----~~~~~~~~~  104 (179)
T PRK11924         87 KAV-----------------------------------------------------LSD-DA---L-----EPEFAETAE  104 (179)
T ss_pred             ccc-----------------------------------------------------Ccc-cc---c-----ccccCCccC
Confidence            100                                                     000 00   0     000000224


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      +|++.+...+....+..+|..||++++.||.++|.    +++|..|||+.||+|+.+|+++..+|+++||+.+..+
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            67778888888889999999999999999999998    8999999999999999999999999999999988754

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=8.3e-20  Score=174.02  Aligned_cols=175  Identities=17%  Similarity=0.201  Sum_probs=139.0

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567          287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  366 (532)
Q Consensus       287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~  366 (532)
                      .++..|++.|+..|.+.++.+|.++.++..+.+|++||+++.+|+++++|++..+..|.||++..+++.+.++++++.+.
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            34569999999999999999999999999999999999999999999999875555899999999999999999876421


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567          367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  446 (532)
Q Consensus       367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~  446 (532)
                      ...                  .                                    +. .   ..    +.... ..+
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 009567          447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG  526 (532)
Q Consensus       447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~  526 (532)
                      .+++..........|..+|..|||++|+||.++|.    +++|++|||+.||+|..+|+..+.||+++||..+....-..
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            23333333444567899999999999999999998    89999999999999999999999999999999998887777


Q ss_pred             hh
Q 009567          527 YA  528 (532)
Q Consensus       527 yl  528 (532)
                      |+
T Consensus       178 ~~  179 (185)
T PRK12542        178 FK  179 (185)
T ss_pred             HH
Confidence            74

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=2.2e-19  Score=171.70  Aligned_cols=177  Identities=19%  Similarity=0.270  Sum_probs=143.4

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      ++++.|...+..|+ .|++.|+..|.+.++.++.++.++..+.+|++||+++.+|++.++|++.  ..|.+|++..+++.
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            46667777666554 8999999999999999999999999999999999999999999999974  47999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  435 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~  435 (532)
                      +.+++++..+..                                                        +..    +.   
T Consensus        85 ~~d~~r~~~~~~--------------------------------------------------------~~~----~~---  101 (189)
T PRK12515         85 ALSALRRRKHEE--------------------------------------------------------IDD----EA---  101 (189)
T ss_pred             HHHHHHccCCCC--------------------------------------------------------Ccc----cc---
Confidence            999987543100                                                        000    00   


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                       .....+ ...+|+......+....+..+|..||+++|+||.++|.    +++|++|||+.||+|..+|++...||+++|
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 009567          516 KQSLGGKAS  524 (532)
Q Consensus       516 R~~l~~~~l  524 (532)
                      |..+...+.
T Consensus       176 r~~l~~~~~  184 (189)
T PRK12515        176 AELLKAAGV  184 (189)
T ss_pred             HHHHHHhcc
Confidence            999887654

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

Probab=99.83  E-value=2.5e-19  Score=161.18  Aligned_cols=157  Identities=24%  Similarity=0.389  Sum_probs=131.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567          292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  371 (532)
Q Consensus       292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~  371 (532)
                      |++.++..|.++|+++++++.+++.+.+|++|||+++++++++.|++.  .+|.+|+.+++++.+.++++++.+ .  +.
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  689999999999999999988764 1  10


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567          372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  451 (532)
Q Consensus       372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~  451 (532)
                      ..                                                   .      ..    .... .....++..
T Consensus        77 ~~---------------------------------------------------~------~~----~~~~-~~~~~~~~~   94 (158)
T TIGR02937        77 EL---------------------------------------------------D------LL----EELL-DSDPSPEEE   94 (158)
T ss_pred             ch---------------------------------------------------h------hh----hhcc-cccCCHHHH
Confidence            00                                                   0      00    0000 111245556


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      .........|..++..||++++.||.++|+    .|+|..|||+.+|+|+.+|+++..+++++||+.+
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            666677778999999999999999999987    7999999999999999999999999999999864

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=3e-19  Score=171.72  Aligned_cols=176  Identities=12%  Similarity=0.148  Sum_probs=134.1

Q ss_pred             HHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHH
Q 009567          282 LKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  360 (532)
Q Consensus       282 L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~i  360 (532)
                      ++..+..| ..|++.|+..|.+.|+.+|.++.++..+.+|++||+++.+|+..++|++.++ .|.+|++..+++.+.+++
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            45555555 5999999999999999999999999889999999999999999999997554 699999999999999999


Q ss_pred             HhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhc
Q 009567          361 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT  440 (532)
Q Consensus       361 r~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i  440 (532)
                      ++..+....                         .                           ..+... .+..  ....+
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 009567          441 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       441 ~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      .+  ...++..    .....+..++..||+++|+||.++|.    +++|.+|||+.||||.++|+..+++|+++||..+.
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  0122222    23356888999999999999999998    99999999999999999999999999999999987


Q ss_pred             cCc
Q 009567          521 GKA  523 (532)
Q Consensus       521 ~~~  523 (532)
                      ...
T Consensus       191 ~~~  193 (194)
T PRK12531        191 AES  193 (194)
T ss_pred             hcc
Confidence            654

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.83  E-value=2.2e-19  Score=169.14  Aligned_cols=172  Identities=13%  Similarity=0.192  Sum_probs=133.8

Q ss_pred             CCHHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          277 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       277 ~~~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      |++..+...+..| ..|++.|+..|.+.|+.+|++|.++..+.+|++||+++++|+++++|++.  .+|.+|++..+++.
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            3455565555555 49999999999999999999999999999999999999999999999874  47999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  435 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~  435 (532)
                      +.+++++..+.....                           +.+                       .+.         
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 009567          436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                          ..+.  ... +..........|..+|..||+++|+||.++|.    +++|++|||+.||+|..+|+....||+++|
T Consensus       102 ----~~~~--~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~~V~~~l~ra~~~l  170 (176)
T PRK09638        102 ----TLRK--EKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNIPEGTVKSRVHHGIKQL  170 (176)
T ss_pred             ----cCCc--cch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence                0000  000 11122233456889999999999999999987    899999999999999999999999999999


Q ss_pred             HHHhh
Q 009567          516 KQSLG  520 (532)
Q Consensus       516 R~~l~  520 (532)
                      |+.+.
T Consensus       171 ~~~l~  175 (176)
T PRK09638        171 RKEWG  175 (176)
T ss_pred             HHHhc
Confidence            99774

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.83  E-value=4.7e-19  Score=170.36  Aligned_cols=172  Identities=16%  Similarity=0.163  Sum_probs=138.7

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      +++..+...+..|+ .+++.|+..|.+.|++++.++.++..+.+|++||+++.+|+++++|++.  ..|.+|++..+++.
T Consensus        12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~   89 (192)
T PRK09643         12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNA   89 (192)
T ss_pred             cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHH
Confidence            35666766666554 9999999999999999999999999999999999999999999999975  36999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  435 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~  435 (532)
                      +.+++++..+..+.                                                     +++.    ..   
T Consensus        90 ~~d~~Rk~~~~~~~-----------------------------------------------------~~~~----~~---  109 (192)
T PRK09643         90 CLDRLRRAKARPTV-----------------------------------------------------PLDD----VY---  109 (192)
T ss_pred             HHHHHHccccCCCC-----------------------------------------------------Cccc----cc---
Confidence            99999875421100                                                     0000    00   


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                        +. .    ..+++.+...+....|..+|..||+++|+||.++|.    +++|++|||+.||+|..+|+....||+++|
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    012223344455667999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhc
Q 009567          516 KQSLGG  521 (532)
Q Consensus       516 R~~l~~  521 (532)
                      |+.+..
T Consensus       179 r~~l~~  184 (192)
T PRK09643        179 AELLGY  184 (192)
T ss_pred             HHHHHH
Confidence            998864

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

Probab=99.83  E-value=2.6e-19  Score=164.44  Aligned_cols=160  Identities=18%  Similarity=0.188  Sum_probs=129.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567          292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  371 (532)
Q Consensus       292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~  371 (532)
                      |++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++.  .+|.+|++.++++.+.+++++..+....  
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~--   77 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKY--   77 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHH--
Confidence            789999999999999999999998999999999999999999999874  4799999999999999998775421000  


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567          372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  451 (532)
Q Consensus       372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~  451 (532)
                                               ...+                        .    ++..       ......++++.
T Consensus        78 -------------------------~~~~------------------------~----~~~~-------~~~~~~~~~~~   97 (161)
T TIGR02985        78 -------------------------QEEI------------------------L----EIEV-------DELSENDPEEE   97 (161)
T ss_pred             -------------------------HHHH------------------------H----hhcc-------cccCCCCcHHH
Confidence                                     0000                        0    0000       00011245556


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      +...+....|..++..||+++++||.++|.    +++|..|||+.||+|+++|+++..+|+++||+.+
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            666677778999999999999999999987    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.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=4.6e-19  Score=168.18  Aligned_cols=166  Identities=16%  Similarity=0.197  Sum_probs=132.9

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  367 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I  367 (532)
                      ++..|++.|+..|.+.|+.++++|.++..+.+|++||+++.+|+++.+|++..  .|.+|++..+++.+.++++...+..
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            34589999999999999999999999999999999999999999999999864  6999999999998888876543110


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567          368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  447 (532)
Q Consensus       368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~  447 (532)
                      +.                                                      ++... +..     +   ......
T Consensus        82 ~~------------------------------------------------------~~~~~-~~~-----~---~~~~~~   98 (179)
T PRK12543         82 RI------------------------------------------------------FEKAE-EQR-----K---PVSIDF   98 (179)
T ss_pred             cc------------------------------------------------------ccccc-ccc-----c---cccccC
Confidence            00                                                      00000 000     0   001113


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      |+. +...+....|..+|..|||++|+||.++|.    +++|++|||+.||||..+|+..++||+++||+.+....
T Consensus        99 ~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  169 (179)
T PRK12543         99 SED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE  169 (179)
T ss_pred             hHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444 555666778999999999999999999998    99999999999999999999999999999999987643

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

Probab=99.82  E-value=4.9e-19  Score=166.01  Aligned_cols=167  Identities=18%  Similarity=0.213  Sum_probs=132.3

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      |+++.+...+..|+ .|++.++..|.+.|++++.++.++..+.+|++||+++.+|+..++|++.  .+|.+|++..+++.
T Consensus         1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~   78 (169)
T TIGR02954         1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE   78 (169)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence            34556666665554 9999999999999999999999999999999999999999999999975  36999999999999


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  435 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~  435 (532)
                      +.+++++..+...                                                       ++.....+    
T Consensus        79 ~~d~~R~~~~~~~-------------------------------------------------------~~~~~~~~----   99 (169)
T TIGR02954        79 CIDLLKKKKKVIP-------------------------------------------------------FDPNTSIE----   99 (169)
T ss_pred             HHHHHHhcCCcCc-------------------------------------------------------cccccccc----
Confidence            9999876542100                                                       00000000    


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                            +.   .++.  .. .....+..+|..||+++|+||.++|.    +|+|.+|||+.||||..+|+....||+++|
T Consensus       100 ------~~---~~~~--~~-~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L  163 (169)
T TIGR02954       100 ------KG---ECET--HA-DSRLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVKTYLHRALKKL  163 (169)
T ss_pred             ------cc---hhhh--ch-HHHHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                  00   0000  00 11236888999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhh
Q 009567          516 KQSLG  520 (532)
Q Consensus       516 R~~l~  520 (532)
                      |..+.
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.

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.82  E-value=8.3e-19  Score=164.90  Aligned_cols=165  Identities=14%  Similarity=0.126  Sum_probs=131.2

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  367 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I  367 (532)
                      .+..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+..++|++.. ..|.+|++..+++.+.++++++.+..
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            34689999999999999999999999888999999999999999999997532 47999999999999999998654210


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567          368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  447 (532)
Q Consensus       368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~  447 (532)
                      ..                                                     ..+      +..   + .++.   .
T Consensus        85 ~~-----------------------------------------------------~~~------~~~---~-~~~~---~   98 (173)
T PRK09645         85 VE-----------------------------------------------------GGD------DVL---G-VPEQ---S   98 (173)
T ss_pred             cc-----------------------------------------------------ccc------ccc---c-CCCC---C
Confidence            00                                                     000      000   0 0000   1


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      +++.+........|..+|+.||+++|+||.|+|.    +++|.+|||+.||+|..+|+..++||+++||+.+...+
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            2222333334457889999999999999999998    99999999999999999999999999999999987654

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=9e-19  Score=165.00  Aligned_cols=167  Identities=16%  Similarity=0.193  Sum_probs=130.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567          291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  370 (532)
Q Consensus       291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP  370 (532)
                      ..++.|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++..  +|.+|++..+++.+.++++++.+....+
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            45899999999999999999999999999999999999999999999853  7999999999999999998765321000


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567          371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  450 (532)
Q Consensus       371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee  450 (532)
                      ...                                                  .+.    +   ...+.........++.
T Consensus        81 ~~~--------------------------------------------------~~~----~---~~~~~~~~~~~~~~~~  103 (173)
T PRK12522         81 LDL--------------------------------------------------FHK----E---DGGEIEFADDVNISEE  103 (173)
T ss_pred             ccc--------------------------------------------------cch----h---hhhhhccccCCCChHH
Confidence            000                                                  000    0   0000000001112333


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       451 ~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                       ....+..+.+..+|..||+++++|+.++|.    +++|++|||+.||+|..+|+..+.||+++||+.+..
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    999999999999999999999999999999998754

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=6.1e-19  Score=167.64  Aligned_cols=170  Identities=15%  Similarity=0.146  Sum_probs=130.5

Q ss_pred             HHHHHHHh-hcHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHH
Q 009567          280 RDLKSELH-SGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  357 (532)
Q Consensus       280 ~~L~~~l~-~g~~Are~LI~~nlrLV~sIAkrY~~-~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~  357 (532)
                      ..+...+. ++..|++.|+..|.+.|+.++.++.+ ...+.+|++||+++.||+.++.|++.  ..|.+|++..++|.+.
T Consensus         9 ~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~   86 (181)
T PRK12536          9 RALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLM   86 (181)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHH
Confidence            33444444 45599999999999999999998765 57899999999999999999999974  4699999999999999


Q ss_pred             HHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 009567          358 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  437 (532)
Q Consensus       358 ~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~  437 (532)
                      +++++..+...                                                       .+....+     ..
T Consensus        87 d~~Rk~~~~~~-------------------------------------------------------~~~~~~~-----~~  106 (181)
T PRK12536         87 DFLRSRARREA-------------------------------------------------------LHDPLDD-----ES  106 (181)
T ss_pred             HHHHHHhcccc-------------------------------------------------------ccCCccc-----hh
Confidence            99987542100                                                       0000000     00


Q ss_pred             hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          438 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       438 d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +...+.   .++.    .+....+..+|..||+++|.||.++|.    +++|.+|||+.||+|+++|+...++|+++||+
T Consensus       107 ~~~~~~---~~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~  175 (181)
T PRK12536        107 ELFATS---DDEA----AEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGIHRGLKALAA  175 (181)
T ss_pred             hhcCCC---Ccch----HHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            000011   1111    123446889999999999999999998    99999999999999999999999999999999


Q ss_pred             HhhcC
Q 009567          518 SLGGK  522 (532)
Q Consensus       518 ~l~~~  522 (532)
                      .+...
T Consensus       176 ~l~~~  180 (181)
T PRK12536        176 KIRGE  180 (181)
T ss_pred             HhcCC
Confidence            88653

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

Probab=99.81  E-value=6.5e-19  Score=162.83  Aligned_cols=158  Identities=18%  Similarity=0.218  Sum_probs=125.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567          292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  371 (532)
Q Consensus       292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~  371 (532)
                      |++.++..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++..  .|.+|++..+++.+.++++++.+.... .
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            7899999999999999999999999999999999999999999999763  599999999999999999876532100 0


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567          372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  451 (532)
Q Consensus       372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~  451 (532)
                                               .++.                                    .+.+.+..  ++.+.
T Consensus        79 -------------------------~~~~------------------------------------~~~~~~~~--~~~~~   95 (159)
T TIGR02989        79 -------------------------DDEL------------------------------------LEALAAEA--EATEA   95 (159)
T ss_pred             -------------------------CHHH------------------------------------HHHHHhhc--ccchH
Confidence                                     0000                                    00000000  11111


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      .........|..+++.||++++.||.++|.    +|+|.+|||+.||||.++|+...+||+++||+++
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            222334467889999999999999999987    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).

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.81  E-value=1.1e-18  Score=165.64  Aligned_cols=164  Identities=16%  Similarity=0.180  Sum_probs=134.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      +..|++.|+..|.+.|++++.++.++..+.+|++||+++.+|+++++|++.  ..|.+|++..+++.+.+++++..+-..
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            358999999999999999999999998999999999999999999999874  369999999999999999887532100


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  448 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p  448 (532)
                      .                                                     +.+.        ......  ....+|
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 009567          449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ++.+...+....|..+|..||+++|+||.++|.    +|+|++|||+.||||.++|++.+.||+++||+.+..
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

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

Probab=99.81  E-value=1.6e-18  Score=173.49  Aligned_cols=180  Identities=16%  Similarity=0.195  Sum_probs=141.1

Q ss_pred             CCHHHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHH-------hhhhhCCcCCCchhhHH
Q 009567          277 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFASYA  348 (532)
Q Consensus       277 ~~~~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLik-------AiekFDp~kG~rFSTYA  348 (532)
                      .++..|...++.|+ .|+..|+..|.+.|+.++.++.++..+.+|++||.|+.+|.       .+.+|++.  ..|.||+
T Consensus        24 ~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL  101 (244)
T TIGR03001        24 AADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWV  101 (244)
T ss_pred             ccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHH
Confidence            46677888777776 99999999999999999999999999999999999999994       78889864  3699999


Q ss_pred             HHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCC
Q 009567          349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV  428 (532)
Q Consensus       349 ~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v  428 (532)
                      +..++|.+.++++++.+...+                                                       +   
T Consensus       102 ~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~---  123 (244)
T TIGR03001       102 RIVATRIALELQAQERRHSPV-------------------------------------------------------E---  123 (244)
T ss_pred             HHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c---
Confidence            999999999999765421100                                                       0   


Q ss_pred             CCCCCcchhhhcccCCCCChhHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHH
Q 009567          429 WADQDTTFQEITADTGVEIPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERV  504 (532)
Q Consensus       429 ~~d~~~~l~d~i~d~~~~~pee~~~~----~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerV  504 (532)
                       +++  ...+. .+. ..+|++.+..    .+....|..+|+.||+++|+||.++|.    +++|++|||++||||.++|
T Consensus       124 -~~~--~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~----eg~S~~EIA~~Lgis~~TV  194 (244)
T TIGR03001       124 -EPT--ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV----DGLSMDRIGAMYQVHRSTV  194 (244)
T ss_pred             -ccc--ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHH
Confidence             000  00000 011 1134433332    235567999999999999999999998    9999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCchh
Q 009567          505 RQLESRALYRLKQSLGGKASY  525 (532)
Q Consensus       505 Rqie~rALkKLR~~l~~~~l~  525 (532)
                      +..+.||+++||+.+.+....
T Consensus       195 k~rl~RAr~~Lr~~l~~~~~~  215 (244)
T TIGR03001       195 SRWVAQARERLLERTRRRLAE  215 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999998775443

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=99.81  E-value=1.1e-18  Score=167.01  Aligned_cols=182  Identities=16%  Similarity=0.158  Sum_probs=136.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567          292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  371 (532)
Q Consensus       292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~  371 (532)
                      +++.|+..|.+.|+.+|.++.++..+.+|++||.++.+|+.+++|++.  .+|.+|++..+++.+.++++++.+....+.
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            688999999999999999999999999999999999999999999864  369999999999999999987653221100


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567          372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  451 (532)
Q Consensus       372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~  451 (532)
                      ....                  ....+++                       ++... . .+ ......++. ..+|++.
T Consensus        81 ~~~~------------------~~~~~~~-----------------------~~~~~-~-~~-~~~~~~~~~-~~~~~~~  115 (191)
T PRK12520         81 DDAD------------------EQSDDDL-----------------------FDALF-A-AD-GHYREPPSD-WGDPDAA  115 (191)
T ss_pred             cccc------------------cchhhhh-----------------------hhhhc-c-cc-cccccCccc-cCCHHHH
Confidence            0000                  0000000                       00000 0 00 000001111 2356776


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      +...+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|++.+.||+++||+++...+.
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=99.81  E-value=2e-18  Score=164.50  Aligned_cols=170  Identities=16%  Similarity=0.181  Sum_probs=130.7

Q ss_pred             HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHH----hhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHH
Q 009567          279 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQ----YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  353 (532)
Q Consensus       279 ~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkr----Y~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr  353 (532)
                      ...|...+..| ..|++.|+..|.+.|+.+|++    +.++..+.+|++||+++.+|++++.|++..  .|.+|++..++
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            34455555555 599999999999999999874    557788999999999999999999999753  69999999999


Q ss_pred             HHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 009567          354 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD  433 (532)
Q Consensus       354 ~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~  433 (532)
                      +.+.+++++..+.. .                                                   ..+.+.     ..
T Consensus        86 n~~~d~~R~~~~~~-~---------------------------------------------------~~~~~~-----~~  108 (184)
T PRK12539         86 YKLIDHLRRTRASL-A---------------------------------------------------DVPIDD-----AD  108 (184)
T ss_pred             HHHHHHHHHHhccc-c---------------------------------------------------ccChhh-----hc
Confidence            99999988754210 0                                                   000000     00


Q ss_pred             cchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567          434 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  513 (532)
Q Consensus       434 ~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk  513 (532)
                          ...       +.+.....+....|..++..||+++|+|+.++|.    +|+|++|||+.||+|..+|+....||++
T Consensus       109 ----~~~-------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~  173 (184)
T PRK12539        109 ----ELV-------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRGLK  173 (184)
T ss_pred             ----ccc-------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                000       0001112233457899999999999999999998    8999999999999999999999999999


Q ss_pred             HHHHHhhcC
Q 009567          514 RLKQSLGGK  522 (532)
Q Consensus       514 KLR~~l~~~  522 (532)
                      +||+.+...
T Consensus       174 ~Lr~~l~~~  182 (184)
T PRK12539        174 ALAALIGRE  182 (184)
T ss_pred             HHHHHHhhc
Confidence            999988643

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.7e-18  Score=163.11  Aligned_cols=166  Identities=19%  Similarity=0.241  Sum_probs=128.5

Q ss_pred             HHHHHh-hcHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHH
Q 009567          282 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  356 (532)
Q Consensus       282 L~~~l~-~g~~Are~LI~~nlrLV~sIAkrY~~~----g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI  356 (532)
                      +...+. ++..|++.|+..|.+.|+.+|.++.++    ..+.+|++||+++.+|...++|++.  ..|.+|++..+++.+
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            333444 456999999999999999999998763    3689999999999999999999874  479999999999999


Q ss_pred             HHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 009567          357 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  436 (532)
Q Consensus       357 ~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l  436 (532)
                      .++++++.+....                                                     +++.         +
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 009567          437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       437 ~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .+.+++..   +.+    ......+..+|+.||+++|+||.++|.    +++|++|||+.||+|..+|+...++|+++||
T Consensus       108 ~~~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr  176 (184)
T PRK12512        108 AETLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVRVALHRGLAALA  176 (184)
T ss_pred             cccccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence            00011100   001    122346788999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhhcC
Q 009567          517 QSLGGK  522 (532)
Q Consensus       517 ~~l~~~  522 (532)
                      ..+.+.
T Consensus       177 ~~l~~~  182 (184)
T PRK12512        177 AKFRSE  182 (184)
T ss_pred             HHhhcC
Confidence            998764

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

Probab=99.80  E-value=2.4e-18  Score=163.03  Aligned_cols=171  Identities=19%  Similarity=0.265  Sum_probs=125.6

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCC-----CHhhHHHHHHHHHHH-hhhhhCCcCCCchhhHHHHHH
Q 009567          280 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWWV  352 (532)
Q Consensus       280 ~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~-----~~eDLiQEG~iGLik-AiekFDp~kG~rFSTYA~~wI  352 (532)
                      ..|...++.|+ .|++.|+..|.+.|+.+|.+|.++..     +.+|++||+|+.+|+ ...+|++.  ..|.+|++.++
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 78889764  36999999999


Q ss_pred             HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 009567          353 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ  432 (532)
Q Consensus       353 r~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~  432 (532)
                      ++.+.+++++..+..+.                      .                           .  ..+...    
T Consensus        83 ~n~~~d~~R~~~~~~~~----------------------~---------------------------~--~~~~~~----  107 (183)
T TIGR02999        83 RRILVDHARRRRAQKRG----------------------G---------------------------G--AVRVPL----  107 (183)
T ss_pred             HHHHHHHHHHHHHHhcc----------------------C---------------------------C--cccccc----
Confidence            99999998765321000                      0                           0  000000    


Q ss_pred             CcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          433 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       433 ~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                          .+..++.   .++.. ......+.+...|..||+++|+||.|+|.    +++|++|||+.||+|..+|+..+.||+
T Consensus       108 ----~~~~~~~---~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar  175 (183)
T TIGR02999       108 ----DEVLPDA---EADLD-EELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIAELLGVSVRTVERDWRFAR  175 (183)
T ss_pred             ----ccccCCC---CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence                0000000   11111 11111223444567799999999999998    999999999999999999999999999


Q ss_pred             HHHHHHh
Q 009567          513 YRLKQSL  519 (532)
Q Consensus       513 kKLR~~l  519 (532)
                      ++||+.+
T Consensus       176 ~~Lr~~l  182 (183)
T TIGR02999       176 AWLADEL  182 (183)
T ss_pred             HHHHHHh
Confidence            9999976

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.

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.80  E-value=3.6e-18  Score=168.14  Aligned_cols=118  Identities=18%  Similarity=0.265  Sum_probs=105.0

Q ss_pred             HhhcHHHHHHHHHHHHHHHHHHHHHhhCCC--CCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhh
Q 009567          286 LHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  363 (532)
Q Consensus       286 l~~g~~Are~LI~~nlrLV~sIAkrY~~~g--~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~  363 (532)
                      ++.|+..++.||..|.|+|.++|++|.++.  .+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++|+.
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            345554599999999999999999998775  589999999999999999999999999999999999999999999987


Q ss_pred             c---cccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 009567          364 S---RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR  403 (532)
Q Consensus       364 ~---r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~  403 (532)
                      .   +.+++|....+....+..+...+..+.++.|+.+||+..
T Consensus        84 ~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~  126 (218)
T TIGR02895        84 QKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY  126 (218)
T ss_pred             ccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence            7   567899776666777788888899999999999999754

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).

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.3e-18  Score=161.98  Aligned_cols=166  Identities=17%  Similarity=0.162  Sum_probs=127.7

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567          287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  366 (532)
Q Consensus       287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~  366 (532)
                      .++..+++.|+..|.+.|+.+++++.+. .+.+|++||+++.+|+.++.|++.  ..|.+|++..+++.+.+++++..+.
T Consensus         7 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~   83 (175)
T PRK12518          7 RGDRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQR   83 (175)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcc
Confidence            3446999999999999999999998753 688999999999999999999974  4699999999999999998764321


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567          367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  446 (532)
Q Consensus       367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~  446 (532)
                      -..                                                      .+... ....      ....   
T Consensus        84 ~~~------------------------------------------------------~~~~~-~~~~------~~~~---   99 (175)
T PRK12518         84 PSR------------------------------------------------------IQDDS-LNDQ------PSRP---   99 (175)
T ss_pred             ccc------------------------------------------------------hhccc-cccc------ccCC---
Confidence            000                                                      00000 0000      0000   


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      .++......+....+..+|+.||+++|+||.++|+    +|+|++|||+.||+|..+|+....||+++||+.+...+
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            11112222233456889999999999999999998    89999999999999999999999999999999987654

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=4.5e-18  Score=167.29  Aligned_cols=172  Identities=18%  Similarity=0.167  Sum_probs=136.7

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567          287 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  366 (532)
Q Consensus       287 ~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~  366 (532)
                      .....++..|+..|.+.++.++.++.++..+.+|++||+|+.+|+.+++|++.   .|.+|++..++|.+.++++++.+.
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            34468999999999999999999999999999999999999999999999853   499999999999999998876421


Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCC
Q 009567          367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  446 (532)
Q Consensus       367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~  446 (532)
                      ...                                                     ........  ...... . ++...
T Consensus        91 ~~~-----------------------------------------------------~~~~~~~~--~~~~~~-~-~~~~~  113 (216)
T PRK12533         91 HEV-----------------------------------------------------AAPDTLDD--ADSLDD-W-QPAGE  113 (216)
T ss_pred             ccc-----------------------------------------------------cccccccc--cccccc-c-ccCCC
Confidence            100                                                     00000000  000000 0 11123


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          447 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       447 ~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      +|++.+...+....|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|+++++||+++||+.+...
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    8999999999999999999999999999999998654

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=3.3e-18  Score=162.47  Aligned_cols=166  Identities=9%  Similarity=0.023  Sum_probs=130.1

Q ss_pred             hhcHHHHHHHHHHHHHHHHHHHHHhhC--CCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhc
Q 009567          287 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  364 (532)
Q Consensus       287 ~~g~~Are~LI~~nlrLV~sIAkrY~~--~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~  364 (532)
                      .++..+++.|+..|.+.|+.++..+.+  +..+.+|++||.|+.+|+..++|++.....|.||++..+++.+.++++++.
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            455699999999999999998766665  357899999999999999999998544457999999999999999887543


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCC
Q 009567          365 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG  444 (532)
Q Consensus       365 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~  444 (532)
                      +..                  ..                                    .+.         ..+ ..+..
T Consensus        89 ~~~------------------~~------------------------------------~~~---------~~~-~~~~~  104 (178)
T PRK12529         89 LEL------------------AW------------------------------------LEA---------LAT-LPEPL  104 (178)
T ss_pred             HHh------------------hh------------------------------------hhH---------hhh-ccCcC
Confidence            100                  00                                    000         000 00011


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          445 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       445 ~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      ..+|++.+...+....|..+|..||+++|.||.|+|.    +++|++|||+.||+|.++|+...++|+.+|++.+.
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            1255655655666678999999999999999999998    99999999999999999999999999999998753

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

Probab=99.79  E-value=6.5e-18  Score=160.90  Aligned_cols=171  Identities=20%  Similarity=0.285  Sum_probs=136.1

Q ss_pred             HHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhh
Q 009567          284 SELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  363 (532)
Q Consensus       284 ~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~  363 (532)
                      ....++..++..++..|.+.++.+++++.++..+.+||+||+++.+|+++..| .. +..|.||++.+++|.+.+++++.
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~   85 (182)
T COG1595           8 EALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKR   85 (182)
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHh
Confidence            34455669999999999999999999999988899999999999999999999 33 34799999999999999999887


Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccC
Q 009567          364 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADT  443 (532)
Q Consensus       364 ~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~  443 (532)
                      .+....                                                      .+     +.+  ......+.
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  00000000


Q ss_pred             CCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          444 GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       444 ~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      ..+.+ +.+...+....|..+|..||+++|++|.++|+    +|+|++|||+.||||.++|+..+++|+++||..+...
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            00011 24555667778999999999999999999998    9999999999999999999999999999999988754

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.79  E-value=2.8e-18  Score=159.30  Aligned_cols=157  Identities=13%  Similarity=0.044  Sum_probs=125.9

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567          298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  377 (532)
Q Consensus       298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l  377 (532)
                      ..|.+.|+.+|.++.++..+.+|++||+++.+|+++++|++.   .|.+|++..+++.+.+++++..+..+.        
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            568999999999999999999999999999999999999863   499999999999999999875421000        


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567          378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  457 (532)
Q Consensus       378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l  457 (532)
                                                                  ..+.    . ..   .+...  ...+|++.+...+.
T Consensus        71 --------------------------------------------~~~~----~-~~---~~~~~--~~~~~~~~~~~~e~   96 (160)
T PRK09642         71 --------------------------------------------LSLC----K-ET---EENIK--SSHNIEDLLLTKEQ   96 (160)
T ss_pred             --------------------------------------------cccc----h-hh---hhhcc--CCCChHHHHHHHHH
Confidence                                                        0000    0 00   00000  11245555666667


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      ...|..+|+.||+++|+||.++|.    +++|.+|||+.||+|.++|+....||+++||+.+....
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    99999999999999999999999999999999986554

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.79  E-value=4.2e-18  Score=162.85  Aligned_cols=169  Identities=17%  Similarity=0.122  Sum_probs=128.5

Q ss_pred             HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHH
Q 009567          281 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  359 (532)
Q Consensus       281 ~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~  359 (532)
                      .|...+..| ..|++.|+..|.+.++.++. +.++..+.+|++||.|+.+|+..++|++.  ..|.+|++..+++.+.++
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            355555544 59999999999999999995 67888899999999999999999999964  469999999999999999


Q ss_pred             HHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhh
Q 009567          360 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI  439 (532)
Q Consensus       360 ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~  439 (532)
                      +++..+..+.                                                     +.+.     ..    +.
T Consensus        90 ~Rk~~~~~~~-----------------------------------------------------~~~~-----~~----~~  107 (185)
T PRK09649         90 IRHVRSRPRT-----------------------------------------------------TRGA-----RP----EH  107 (185)
T ss_pred             HHHhcccccc-----------------------------------------------------cccc-----ch----hh
Confidence            9875421100                                                     0000     00    00


Q ss_pred             cccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          440 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       440 i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      ..+.     +......+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|+..+.||+++||+.+
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    9999999999999999999999999999999966


Q ss_pred             hcCc
Q 009567          520 GGKA  523 (532)
Q Consensus       520 ~~~~  523 (532)
                      ....
T Consensus       179 ~~~~  182 (185)
T PRK09649        179 EPDD  182 (185)
T ss_pred             Cccc
Confidence            5443

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

Probab=99.79  E-value=2.7e-18  Score=164.71  Aligned_cols=172  Identities=18%  Similarity=0.199  Sum_probs=130.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  369 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl  369 (532)
                      ..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+.+|++.  ..|.+|++..++|.+.++++++.+....
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            48899999999999999999999998999999999999999999999864  4699999999999999999876531100


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567          370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  449 (532)
Q Consensus       370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe  449 (532)
                      .                         ..+++.           ..        .+.    ....      ........++
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      0000111233


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ...........|..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|+.++.||+++||+.+..
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    999999999999999999999999999999998864

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.

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.78  E-value=6.2e-18  Score=158.09  Aligned_cols=158  Identities=15%  Similarity=0.107  Sum_probs=130.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567          293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  372 (532)
Q Consensus       293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~  372 (532)
                      ++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|+++++|++.   .|.+|++..+++.+.+++++..+....   
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   599999999999999999876421100   


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567          373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  452 (532)
Q Consensus       373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~  452 (532)
                                             ..+++                                     +.+.   ..+|++.+
T Consensus        77 -----------------------~~~~~-------------------------------------~~~~---~~~~~~~~   93 (165)
T PRK09644         77 -----------------------GTDEI-------------------------------------EAIQ---AESTEEYV   93 (165)
T ss_pred             -----------------------chhHH-------------------------------------hhhc---ccChHHHH
Confidence                                   00000                                     0000   01355555


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      ...+....+..+|..||+++|+||.++|.    +++|.+|||+.||+|..+|+..+.||+++||+.+....
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    99999999999999999999999999999999987544

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=6.8e-18  Score=162.03  Aligned_cols=161  Identities=20%  Similarity=0.197  Sum_probs=128.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      +..++..|+..|.+.++.+|.++.++..+.+|++||.++.+|+..++|+..  ..|.+|++..+++.+.++++++.+...
T Consensus         8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~   85 (187)
T PRK12516          8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQ   85 (187)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence            458999999999999999999999999999999999999999999999864  359999999999999999887542100


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  448 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p  448 (532)
                      .                                                      .+..        +.+... .   .+
T Consensus        86 ~------------------------------------------------------~~~~--------~~~~~~-~---~~   99 (187)
T PRK12516         86 D------------------------------------------------------TDGM--------FTEQLA-V---HP   99 (187)
T ss_pred             c------------------------------------------------------cccc--------cccccC-C---Cc
Confidence            0                                                      0000        000000 0   01


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      +.  ........|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|+..+.||+++||+.+...+
T Consensus       100 ~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~  168 (187)
T PRK12516        100 SQ--YGTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG  168 (187)
T ss_pred             ch--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            10  01112346889999999999999999998    99999999999999999999999999999999998654

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

Probab=99.78  E-value=7.2e-18  Score=156.70  Aligned_cols=158  Identities=19%  Similarity=0.211  Sum_probs=127.5

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  367 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I  367 (532)
                      ++..+++.|+..|.+.|+.+|.++.++..+.+|++||+++.+|+..++|+.  ...|.+|++..+++.+.+++++..+. 
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            456999999999999999999999999999999999999999999999964  34799999999999999998765420 


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567          368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  447 (532)
Q Consensus       368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~  447 (532)
                      .+                                                     . +...            ++..   
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 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ++.........+.|..+|..||+++|+||.++|.    +++|.+|||+.||+|.++|++...||+++||+.+..
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            0001122334567889999999999999999997    899999999999999999999999999999998764

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.

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.78  E-value=6.6e-18  Score=159.14  Aligned_cols=162  Identities=14%  Similarity=0.084  Sum_probs=127.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      +..++..|+..|.+.|+.++.++.++..+.+|++||+++.+|+. ..|+..  ..|.+|++.++++.+.++++++.+.. 
T Consensus         8 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~-   83 (172)
T PRK12523          8 HSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQ-   83 (172)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHH-
Confidence            34999999999999999999999999999999999999999986 446543  36999999999999999998754100 


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  448 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p  448 (532)
                                       ..         ..++                        ..             ........|
T Consensus        84 -----------------~~---------~~~~------------------------~~-------------~~~~~~~~~  100 (172)
T PRK12523         84 -----------------AY---------LAEL------------------------AL-------------VPEAEQPSP  100 (172)
T ss_pred             -----------------HH---------HHHH------------------------hh-------------cccccCCCh
Confidence                             00         0000                        00             000001134


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      +......+....+..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|++.+.+|+++||..+..
T Consensus       101 ~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~  169 (172)
T PRK12523        101 EEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG  169 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            444444444457999999999999999999998    999999999999999999999999999999998764

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.78  E-value=1.3e-17  Score=162.24  Aligned_cols=166  Identities=20%  Similarity=0.290  Sum_probs=135.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      +..+++.|+..|.+.++.++.++.++..+.+|++||+++.+|+...+|++  + .|.+|++..+++.+.+++++..+ .+
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            35899999999999999999999999999999999999999999999985  3 69999999999999999987542 10


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  448 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p  448 (532)
                      .                                                    ..++      .+  + +... ....+|
T Consensus       102 ~----------------------------------------------------~~~~------~~--~-~~~~-~~~~~~  119 (203)
T PRK09647        102 M----------------------------------------------------EALP------ED--Y-DRVP-GDEPNP  119 (203)
T ss_pred             c----------------------------------------------------cccc------cc--c-cccC-CCCCCH
Confidence            0                                                    0000      00  0 0001 112245


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      +..+...+....|..+|..||+++|+||.++|+    ++++++|||+.||+|..+|++.+.||+++||+.+...+-
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    999999999999999999999999999999999876543

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=1.3e-17  Score=155.07  Aligned_cols=157  Identities=15%  Similarity=0.084  Sum_probs=124.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567          291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  370 (532)
Q Consensus       291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP  370 (532)
                      .|++.|+..|.+.|+.++.++.++..+.+|++||+++.+|+..+.|++   ..|.+|.+.++++.+.+++++..+..   
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~---   77 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLER---   77 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHH---
Confidence            689999999999999999999999899999999999999999988865   26999999999999999987643100   


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567          371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  450 (532)
Q Consensus       371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee  450 (532)
                                     ..         .+++                        +            + .++.....++.
T Consensus        78 ---------------~~---------~~~~------------------------~------------~-~~~~~~~~~~~   96 (161)
T PRK12528         78 ---------------AY---------LEAL------------------------A------------Q-LPERVAPSEEE   96 (161)
T ss_pred             ---------------hh---------HHHh------------------------h------------c-cccccCCCHHH
Confidence                           00         0000                        0            0 00001112333


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       451 ~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      .....+....|..+|..||+++|+||.|+|.    +|+|.+|||+.||+|.++|+..+.+|+++||..
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    999999999999999999999999999999864

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=2.3e-17  Score=154.44  Aligned_cols=159  Identities=17%  Similarity=0.152  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  369 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl  369 (532)
                      ...+..++..|.+.|+.+|+++.++..+.+|++||+++.+|+..++|++.  ..|.+|++..+++.+.+++++..+....
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~~   82 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQD   82 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            46789999999999999999999999999999999999999999999864  3599999999999999998875421000


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567          370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  449 (532)
Q Consensus       370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe  449 (532)
                                                                            .+......         .+   ..++
T Consensus        83 ------------------------------------------------------~~~~~~~~---------~~---~~~~   96 (164)
T PRK12547         83 ------------------------------------------------------SDGVFTAR---------VA---VHPA   96 (164)
T ss_pred             ------------------------------------------------------cccccccc---------CC---CCch
Confidence                                                                  00000000         00   0111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      .  ........+..+|..||+++|+||.++|.    +++|++|||+.||+|.++|++.+.||+++||..+.-.
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    8999999999999999999999999999999988643

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=1.9e-17  Score=159.14  Aligned_cols=181  Identities=18%  Similarity=0.143  Sum_probs=132.3

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCC-HhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567          294 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  372 (532)
Q Consensus       294 e~LI~~nlrLV~sIAkrY~~~g~~-~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~  372 (532)
                      +..+..|.+.|+.+|+++.++..+ .+|++||+++.+|+++++|++.  .+|.+|++..+++.+.++++++.+.......
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  4799999999999999999876532110000


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567          373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  452 (532)
Q Consensus       373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~  452 (532)
                      .                      ..+.+           ...      ..+..   .. ++....+... ....+|+..+
T Consensus        86 ~----------------------~~~~~-----------~~~------~~~~~---~~-~~~~~~~~~~-~~~~~~e~~~  121 (195)
T PRK12532         86 L----------------------DDELL-----------DEA------FESHF---SQ-NGHWTPEGQP-QHWNTPEKSL  121 (195)
T ss_pred             c----------------------ccccc-----------chh------hhhhh---cc-ccccccccCc-cccCCHHHHH
Confidence            0                      00000           000      00000   00 0000000000 1123567777


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ...+....+..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|+..++||+++||+++....+
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            77777778999999999999999999998    999999999999999999999999999999999976543

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

Probab=99.77  E-value=1.9e-17  Score=158.89  Aligned_cols=178  Identities=12%  Similarity=0.132  Sum_probs=132.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567          294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  373 (532)
Q Consensus       294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~  373 (532)
                      .+.+..|.+.|+.+|+++.++..+.+|++||+++.+|+..++|++.  .+|.+|++..+++.+.++++++.+....+. +
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            3577889999999999999999999999999999999999999975  479999999999999999987653211100 0


Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 009567          374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  453 (532)
Q Consensus       374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~  453 (532)
                                        .     ++.                   ..-.++... ...+.......++ ....|+..+.
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 009567          454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      ..+....+..+|..||+++|+||.++|.    +++|++|||+.||+|.++|++++.||+++||+++...
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.

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.77  E-value=2.7e-17  Score=153.24  Aligned_cols=161  Identities=19%  Similarity=0.179  Sum_probs=129.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  369 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl  369 (532)
                      +.+++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|++  .|+.  +..|.+|++..+++.+.+++++..+..+.
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  34799999999999999999875521110


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567          370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  449 (532)
Q Consensus       370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe  449 (532)
                      .                                                      +.      .....+.  + ....|+
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             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      +.....+....+..+|..||+++|.||.++|     +|+|++|||+.||+|..+|+..+.||+++||+.+...
T Consensus        95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~  162 (166)
T PRK09639         95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM  162 (166)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            6666666677899999999999999999999     5899999999999999999999999999999988643

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=2.6e-17  Score=153.09  Aligned_cols=157  Identities=14%  Similarity=0.118  Sum_probs=124.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      ...+++.++..|.+.|+.++.++.++..+.+|++||+++.+|+..++|++.   .|.||++..+++.+.+++++..+...
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   59999999999999999987653100


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  448 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p  448 (532)
                      +                                                     ..+       +     ...+.....+
T Consensus        80 ~-----------------------------------------------------~~~-------~-----~~~~~~~~~~   94 (161)
T PRK12541         80 T-----------------------------------------------------TIE-------E-----FHLPNVPSTE   94 (161)
T ss_pred             c-----------------------------------------------------chh-------h-----hhccCCCCcH
Confidence            0                                                     000       0     0000000112


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      ++.....+. ..+..+|..||+++|.||.|+|.    +++|.+|||+.||+|..+|++...||+++||+.
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            222222222 34567899999999999999998    899999999999999999999999999999975

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=2.7e-17  Score=159.41  Aligned_cols=180  Identities=14%  Similarity=0.157  Sum_probs=130.5

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH
Q 009567          295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  374 (532)
Q Consensus       295 ~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~  374 (532)
                      .++..|.+.++.+|+++.++..+.+|++||.|+.+|+.+++|++.  ..|.+|++..+++.+.++++++.+...++..  
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~--   87 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSAL--   87 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence            458889999999999999999999999999999999999999975  3699999999999999999876532111000  


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch-hhhcccCCCCChhHHHH
Q 009567          375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF-QEITADTGVEIPDISVQ  453 (532)
Q Consensus       375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l-~d~i~d~~~~~pee~~~  453 (532)
                                            ..++.                  ....++...... ...+ .+..++ ....+++...
T Consensus        88 ----------------------~~~~~------------------~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~  125 (201)
T PRK12545         88 ----------------------DAELD------------------GEALLDRELFKD-NGHWAAHAKPR-PWPKPETILQ  125 (201)
T ss_pred             ----------------------ccccc------------------hhhhhhhhhhcc-cccccccccCc-CCCCHHHHHH
Confidence                                  00000                  000000000000 0000 000011 1124555555


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ..+....+..+|..||+++|+||.|+|+    +++|++|||+.||+|.++|+..+.||+++||+++...++
T Consensus       126 ~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~  192 (201)
T PRK12545        126 QQQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL  192 (201)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5556667899999999999999999998    999999999999999999999999999999999975543

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=3.1e-17  Score=157.38  Aligned_cols=177  Identities=16%  Similarity=0.109  Sum_probs=131.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567          294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  373 (532)
Q Consensus       294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~  373 (532)
                      +..|..|.+.++.+|.++.++..+.+|++||+|+.+|+..++|++.  .+|.+|++..+++.+.++++++.+...... .
T Consensus        10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~-~   86 (189)
T PRK12530         10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNESE-L   86 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCccc-c
Confidence            3457778999999999999998999999999999999999999875  369999999999999999987653211000 0


Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHH
Q 009567          374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  453 (532)
Q Consensus       374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~  453 (532)
                                        .     ++.                   .+....    +.......+.........|+..+.
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    000000000000111235666666


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      ..+....|..+|+.||+++|+||.|+|.    +++|++|||+.||+|.++|+.+++||+++||+++....
T Consensus       121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~  186 (189)
T PRK12530        121 KEEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTSNLHVLLYRARLQLQACLSKNW  186 (189)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6777788999999999999999999998    89999999999999999999999999999999986543

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=3.1e-17  Score=160.01  Aligned_cols=181  Identities=18%  Similarity=0.216  Sum_probs=134.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567          293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  372 (532)
Q Consensus       293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~  372 (532)
                      -..++..|.+.|+.+|+++.++....+|++||+++.+|+.+.+|++.  .+|.+|++..+++.+.+++++..+....+..
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            36788999999999999999999999999999999999999999864  4699999999999999999876542111100


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567          373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  452 (532)
Q Consensus       373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~  452 (532)
                      .                  .  ....+         ..+..+.              + ................|+..+
T Consensus        98 ~------------------~--~~~~~---------~~~~~~~--------------~-~~~~~~~~~~~~~~~~~e~~~  133 (206)
T PRK12544         98 L------------------R--DEEEE---------EDFEELF--------------D-ESGHWQKDERPQAWGNPEESL  133 (206)
T ss_pred             c------------------c--ccchh---------hHHHHhh--------------c-ccccccccccccccCCHHHHH
Confidence            0                  0  00000         0000000              0 000000000011123567667


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      ...+....+..+|..||+++|+||.++|.    +++|++|||+.||+|..+|+..+.||+++||+.+....
T Consensus       134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~  200 (206)
T PRK12544        134 EQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKW  200 (206)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            77777778899999999999999999998    89999999999999999999999999999999987543

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.76  E-value=4.6e-17  Score=169.48  Aligned_cols=187  Identities=18%  Similarity=0.200  Sum_probs=135.9

Q ss_pred             HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHH
Q 009567          281 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  359 (532)
Q Consensus       281 ~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~  359 (532)
                      +|+..++.| ..+++.|+..|.+.|+.+|.++.++..+.+|++||.++.+|+.+++|++.  ..|.+|++...+|.+.++
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            455555555 49999999999999999999999999999999999999999999999853  469999999999999999


Q ss_pred             HHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhh
Q 009567          360 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI  439 (532)
Q Consensus       360 ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~  439 (532)
                      ++++.+... +..                  .+ .+.                         .........+....+.+.
T Consensus        86 ~Rk~~~~~~-~~~------------------~~-~~~-------------------------~~~~~~~~~~~~~~~~~~  120 (339)
T PRK08241         86 LEGRARRPL-PTD------------------LG-APA-------------------------ADPVDELVERPEVPWLEP  120 (339)
T ss_pred             HHhhccccC-ccc------------------cC-CCc-------------------------CcccccccccccccccCC
Confidence            987643100 000                  00 000                         000000000000001111


Q ss_pred             cccC----CCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567          440 TADT----GVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  514 (532)
Q Consensus       440 i~d~----~~~~pee~~~~~~-l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkK  514 (532)
                      +.+.    ...+|++.+...+ ....|..+|..||+++|+||.|+|.    +++|++|||++||+|..+|++++.||+++
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 3456889999999999999999998    99999999999999999999999999999


Q ss_pred             HHHH
Q 009567          515 LKQS  518 (532)
Q Consensus       515 LR~~  518 (532)
                      ||+.
T Consensus       197 Lr~~  200 (339)
T PRK08241        197 LAER  200 (339)
T ss_pred             Hhhc
Confidence            9993

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.75  E-value=1.4e-17  Score=153.13  Aligned_cols=152  Identities=18%  Similarity=0.206  Sum_probs=122.3

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567          298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  377 (532)
Q Consensus       298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l  377 (532)
                      ..|.+.|+.++.++.++..+.+|++||+++.+|+.+++|++   .+|.+|++..+++.+.+++++..+....+       
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   37999999999999999987654211000       


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567          378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  457 (532)
Q Consensus       378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l  457 (532)
                                         .+.                                    +.+... .....|++.+...+.
T Consensus        72 -------------------~~~------------------------------------~~~~~~-~~~~~~~~~~~~~~~   95 (154)
T TIGR02950        72 -------------------DDA------------------------------------IGDLEQ-HPVESPEHHLLIKIE   95 (154)
T ss_pred             -------------------Hhh------------------------------------hhhccc-cccCChhHHHHHHHH
Confidence                               000                                    000000 011245555555566


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      ...|..+|..||+++++||.++|+    +|+|++|||+.||+|..+|++...||+++||+.+
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            678999999999999999999988    8999999999999999999999999999999875

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.

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=6.2e-17  Score=156.59  Aligned_cols=170  Identities=17%  Similarity=0.110  Sum_probs=129.6

Q ss_pred             HHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHH
Q 009567          282 LKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  360 (532)
Q Consensus       282 L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~i  360 (532)
                      |+..+..| ..+++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+..++|++.  ..|.+|++..+++.+.+++
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            44444444 59999999999999999975 67888899999999999999999999864  3699999999999999999


Q ss_pred             HhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhc
Q 009567          361 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT  440 (532)
Q Consensus       361 r~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i  440 (532)
                      ++..+..+.                                                     ..+ .. .    ...+  
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            875421110                                                     000 00 0    0000  


Q ss_pred             ccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          441 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       441 ~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                        .. ..++..... .....+..+|+.||+++|+||.++|.    +++|++|||+.||+|.++|++.+.||+++||+.+.
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    89999999999999999999999999999999987


Q ss_pred             cCc
Q 009567          521 GKA  523 (532)
Q Consensus       521 ~~~  523 (532)
                      ...
T Consensus       183 ~~~  185 (196)
T PRK12535        183 TGQ  185 (196)
T ss_pred             ccc
Confidence            654

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

Probab=99.75  E-value=5.6e-17  Score=167.45  Aligned_cols=182  Identities=17%  Similarity=0.187  Sum_probs=134.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      +..|++.|+..|.+.++.+|.++.++..+.+|++||.++.+|+.+++|++.  ..|.+|++..++|.+.++++++.+...
T Consensus         3 d~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~   80 (324)
T TIGR02960         3 DGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPR   80 (324)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcC
Confidence            458999999999999999999999999999999999999999999999864  469999999999999999987553110


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcc-------
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA-------  441 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~-------  441 (532)
                      ....                  ..  +                        ........ ..+......+.+.       
T Consensus        81 ~~~~------------------~~--~------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  115 (324)
T TIGR02960        81 PVGL------------------GA--P------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDLD  115 (324)
T ss_pred             cccc------------------CC--C------------------------CCcccccc-cccccccccCCCCccccccc
Confidence            0000                  00  0                        00000000 0000000000000       


Q ss_pred             cCCCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          442 DTGVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       442 d~~~~~pee~~~~~~-l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      .....+|++.+...+ +...+..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|++++.||+++||+++.
T Consensus       116 ~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~  191 (324)
T TIGR02960       116 DPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----LGWRAAETAELLGTSTASVNSALQRARATLDEVGP  191 (324)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence            011235665555444 4556889999999999999999998    89999999999999999999999999999999987


Q ss_pred             c
Q 009567          521 G  521 (532)
Q Consensus       521 ~  521 (532)
                      .
T Consensus       192 ~  192 (324)
T TIGR02960       192 S  192 (324)
T ss_pred             c
Confidence            4

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.

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.75  E-value=6.5e-17  Score=150.41  Aligned_cols=159  Identities=14%  Similarity=0.214  Sum_probs=124.9

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH
Q 009567          295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  374 (532)
Q Consensus       295 ~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~  374 (532)
                      .++..|.+.++.+|.++.++..+.+|++||+++.+|+....|++.   .|.+|++..+++.+.++++++.+....     
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            367788999999999999999999999999999999998877763   488999999999999999875421000     


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHH
Q 009567          375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  454 (532)
Q Consensus       375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~  454 (532)
                                                                      +      ..+.... .. .+. ..+|+..+..
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 009567          455 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       455 ~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      .+..+.+..+|..|||++|+||.++|.    +++|.+|||+.||+|.++|+....||+++||+.+...
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            566678899999999999999999998    8999999999999999999999999999999988654

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=6.6e-17  Score=154.54  Aligned_cols=160  Identities=18%  Similarity=0.220  Sum_probs=126.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567          291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  370 (532)
Q Consensus       291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP  370 (532)
                      .++..++..|.+.|+.+|.++.++..+.+|++||.++.+|+..++|++..  .|.+|++..+++.+.++++++.+.... 
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            56788999999999999999999999999999999999999999998753  699999999999999998765421000 


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567          371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  450 (532)
Q Consensus       371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee  450 (532)
                                                                           .+.        ...+... .   .++.
T Consensus        82 -----------------------------------------------------~~~--------~~~~~~~-~---~~~~   96 (182)
T PRK12540         82 -----------------------------------------------------ADG--------SYAKTLK-S---QPGQ   96 (182)
T ss_pred             -----------------------------------------------------ccc--------ccccccc-C---CCch
Confidence                                                                 000        0000000 0   1111


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       451 ~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ..  ......|..+|+.||+++|+||.++|.    +++|.+|||+.||+|..+|++.++||+++||+.+.....
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  112346889999999999999999998    999999999999999999999999999999999986553

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.74  E-value=9e-17  Score=149.21  Aligned_cols=155  Identities=12%  Similarity=0.090  Sum_probs=123.8

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567          298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  377 (532)
Q Consensus       298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l  377 (532)
                      ..|.+.++.++.++.++..+.+|++||.++.+|+..+.|++   .+|.||++..+++.+.++++++.+...         
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~---------   69 (159)
T PRK12527          2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQA---------   69 (159)
T ss_pred             hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence            56888899999999998889999999999999999999875   279999999999999999886531000         


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567          378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  457 (532)
Q Consensus       378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l  457 (532)
                                                                  .+++. . .+.        ......+|++.+...+.
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        00011246666666667


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      ...|..+|..||+++++||.|+|+    +++|.+|||+.||+|.++|+..+.||+++||+.+...
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    9999999999999999999999999999999998754

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.74  E-value=1.4e-16  Score=152.15  Aligned_cols=154  Identities=21%  Similarity=0.194  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567          293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  372 (532)
Q Consensus       293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~  372 (532)
                      ++.|+..|.+.|+.+|.++.++..+.+|++||.++.+|+.+..|++.  .+|.+|++..+++.+.++++++.+...++  
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  47999999999999999998765211000  


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567          373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  452 (532)
Q Consensus       373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~  452 (532)
                                                                               .+      +...+    .+++..
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 009567          453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ...+....+..+|..||+++|+||.++|.    ++++.+|||+.||+|..+|+....||+++||+.+..
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    999999999999999999999999999999998864

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.73  E-value=1.4e-16  Score=150.33  Aligned_cols=164  Identities=15%  Similarity=0.071  Sum_probs=126.6

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      +..|++.++..|.+.++.++.++.++..+.+|++||.++.+|+. ..|++-.  .|.+|++..+++.+.+++++..+...
T Consensus         8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~   84 (172)
T PRK09651          8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKA   84 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            35899999999999999999999999999999999999999998 3565432  58999999999999999876431000


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  448 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p  448 (532)
                                            .     .+.+                        +            . +.+....+|
T Consensus        85 ----------------------~-----~~~~------------------------~------------~-~~~~~~~~~  100 (172)
T PRK09651         85 ----------------------Y-----LEML------------------------A------------L-MPEGGAPSP  100 (172)
T ss_pred             ----------------------h-----hhHH------------------------h------------h-ccccCCCCh
Confidence                                  0     0000                        0            0 000011133


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      +......+....|..+|..||+++|+||.++|+    +++|++|||+.||+|.++|+....||+++|+...-..|
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            444444445567899999999999999999998    99999999999999999999999999999998765443

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=1.6e-16  Score=152.47  Aligned_cols=162  Identities=19%  Similarity=0.154  Sum_probs=125.7

Q ss_pred             HhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcc
Q 009567          286 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  365 (532)
Q Consensus       286 l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r  365 (532)
                      +..+..+++.++..|.+.|+.+|.++.++..+.+|++||.|+.+|+.++.|++.  ..|.+|++..+++.+.+..++..+
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            345679999999999999999999999999999999999999999999999864  369999999998876554432210


Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCC
Q 009567          366 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV  445 (532)
Q Consensus       366 ~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~  445 (532)
                      .                                                      ....+       ..    ...+...
T Consensus        96 ~------------------------------------------------------~~~~~-------~~----~~~~~~~  110 (188)
T PRK12517         96 D------------------------------------------------------LVDIE-------DD----SIEDDAS  110 (188)
T ss_pred             C------------------------------------------------------ccCcc-------cc----cccCccc
Confidence            0                                                      00000       00    0011111


Q ss_pred             CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          446 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       446 ~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      ..++..    ...+.|..+|..||+++|.||.++|+    ++++++|||+.||||..+|+.++.||+++||..+...
T Consensus       111 ~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  179 (188)
T PRK12517        111 HSSEEE----MEQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP  179 (188)
T ss_pred             cChhHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            123322    22356889999999999999999998    9999999999999999999999999999999998643

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.72  E-value=2e-16  Score=149.15  Aligned_cols=149  Identities=21%  Similarity=0.217  Sum_probs=120.9

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHH
Q 009567          298 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  377 (532)
Q Consensus       298 ~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l  377 (532)
                      ..|.+.++.++.++.++..+.+|++||+++.+|+++++|++.  .+|.+|++..+++.+.+++++..+...++       
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  57999999999999999998765311000       


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHH
Q 009567          378 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  457 (532)
Q Consensus       378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l  457 (532)
                                                                     +.            ... .  .++++.....+.
T Consensus        73 -----------------------------------------------~~------------~~~-~--~~~~~~~~~~e~   90 (170)
T TIGR02959        73 -----------------------------------------------ES------------LLA-A--DSAREETFVKEL   90 (170)
T ss_pred             -----------------------------------------------hh------------hcc-c--CCccHHHHHHHH
Confidence                                                           00            000 0  011222333445


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ...|..+|..||+++|.||.++|.    +++|.+|||+.||+|..+|++.+.||+++||..+..
T Consensus        91 ~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  150 (170)
T TIGR02959        91 SQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET  150 (170)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999999998    999999999999999999999999999999998863

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).

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=2.5e-16  Score=151.46  Aligned_cols=156  Identities=19%  Similarity=0.206  Sum_probs=121.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567          291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  370 (532)
Q Consensus       291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP  370 (532)
                      .+++.|+. |.+.|+.+|+.+.++..+.+|++||.++.+|+.+..|+..  ..|.+|++..+++.+.+++++..+...  
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            55666666 7799999999999999999999999999999999999864  469999999999999999877542100  


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567          371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  450 (532)
Q Consensus       371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee  450 (532)
                                                                          ..+.        ...+...+    .+..
T Consensus        83 ----------------------------------------------------~~~~--------~~~~~~~~----~~~~   98 (188)
T PRK12546         83 ----------------------------------------------------DPEG--------VHAASLAV----KPAH   98 (188)
T ss_pred             ----------------------------------------------------Cccc--------cccccccc----CCcc
Confidence                                                                0000        00000000    0100


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       451 ~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                        ........+..+|..||+++|+||.|+|.    +++|.+|||+.||||..+|+..+.||+++||+.+..
T Consensus        99 --~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~  163 (188)
T PRK12546         99 --DGRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL  163 (188)
T ss_pred             --hhHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence              01122346889999999999999999998    899999999999999999999999999999998865

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.70  E-value=4.1e-16  Score=149.18  Aligned_cols=157  Identities=13%  Similarity=0.167  Sum_probs=122.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567          293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  372 (532)
Q Consensus       293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~  372 (532)
                      ++..+..+++.|+.+|.++.++..+.+|++||.|+.+|+....|++.  .+|.+|++..+++.+.++++++.+.....  
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             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567          373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  452 (532)
Q Consensus       373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~  452 (532)
                                               +++                        .            +. .+.....+.   
T Consensus        82 -------------------------~~~------------------------~------------~~-~~~~~~~~~---   96 (182)
T PRK12511         82 -------------------------DEL------------------------A------------VL-ADASLPAAQ---   96 (182)
T ss_pred             -------------------------cch------------------------h------------hc-cccCCCcch---
Confidence                                     000                        0            00 000000111   


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      ........|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|+....||+++||..+...
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            11123456889999999999999999998    8999999999999999999999999999999988644

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.70  E-value=9.8e-16  Score=143.95  Aligned_cols=160  Identities=14%  Similarity=0.117  Sum_probs=126.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  369 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl  369 (532)
                      ..++..++..|.+.++.+|.++.++..+.+|++||.++.+|+..+.++.   ..|.+|.+..+++.+.+++++...    
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   369999999999999988875320    


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChh
Q 009567          370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  449 (532)
Q Consensus       370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pe  449 (532)
                              .+      ...         +                        +.+            + .+.....+|+
T Consensus        81 --------~~------~~~---------~------------------------~~~------------~-~~~~~~~~~~  100 (168)
T PRK12525         81 --------ER------AYL---------Q------------------------SLA------------E-APEAVQPSPE  100 (168)
T ss_pred             --------HH------HHH---------H------------------------HHh------------c-ccccccCChH
Confidence                    00      000         0                        000            0 0001112455


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          450 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       450 e~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      +..........|..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|+....+|+++||..+.
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            55555566678999999999999999999998    99999999999999999999999999999998763

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.69  E-value=8.4e-16  Score=142.32  Aligned_cols=156  Identities=17%  Similarity=0.183  Sum_probs=113.1

Q ss_pred             CCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcC
Q 009567          313 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGN  392 (532)
Q Consensus       313 ~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~g  392 (532)
                      ++..+.+|++||+|+.+|+..+. ++  +..|.+|++..+++.+.++++++.+..+...                     
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            34456899999999999999886 33  4579999999999999999987652110000                     


Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCC--CCChhHHHHHHHHHHHHHHHHhcCCH
Q 009567          393 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG--VEIPDISVQKQLMRQHVRNLLTLLNP  470 (532)
Q Consensus       393 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~--~~~pee~~~~~~l~~~L~~~L~~L~~  470 (532)
                                                 ...++.... ++++....+.+.+..  ..+|++.+...+....|..+|..||+
T Consensus        58 ---------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~  109 (161)
T PRK09047         58 ---------------------------LFSSFSDDD-DDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA  109 (161)
T ss_pred             ---------------------------ccccccccc-ccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence                                       000000000 001111112222211  23577777777778889999999999


Q ss_pred             HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       471 rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ++|+||.|+|+    +++|++|||+.||+|..+|+.+..||+++||+.+...++
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    999999999999999999999999999999999986654

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.67  E-value=1.8e-15  Score=154.85  Aligned_cols=161  Identities=16%  Similarity=0.095  Sum_probs=123.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567          291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  370 (532)
Q Consensus       291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP  370 (532)
                      .....++..|.+.++.+|+++.++..+.+|++||.++. |.....|+   ...|.+|++..++|.+.+++++..+.... 
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~-   78 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRET-   78 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence            34678999999999999999999999999999999999 66667775   34799999999999999999865421000 


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567          371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  450 (532)
Q Consensus       371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee  450 (532)
                                          .                            ....+..+            ..+.. ..|++
T Consensus        79 --------------------~----------------------------~~~~~~e~------------~~~~~-~~~~~   97 (293)
T PRK09636         79 --------------------Y----------------------------VGPWLPEP------------VVEEL-DDPLE   97 (293)
T ss_pred             --------------------c----------------------------cCCcCCcC------------CCCCC-CChHH
Confidence                                0                            00000000            00111 12333


Q ss_pred             HH-HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          451 SV-QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       451 ~~-~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      .. ........+..+|+.|||++|.||.|+|.    +++|++|||+.||+|..+|+++.+||+++||+.+..
T Consensus        98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~  165 (293)
T PRK09636         98 AVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRARKHVRAARPR  165 (293)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence            33 34455567899999999999999999998    899999999999999999999999999999997653

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.62  E-value=1.1e-14  Score=144.48  Aligned_cols=158  Identities=18%  Similarity=0.178  Sum_probs=122.1

Q ss_pred             HHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHH
Q 009567          282 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  361 (532)
Q Consensus       282 L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir  361 (532)
                      |...+..+..+++.++..| +.++.++.++.++..+.+||+||.++.+|+.   |+..  ..|.+|++..++|.+.++++
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            4444555668888888888 7899999999999999999999999999876   5543  25999999999999999987


Q ss_pred             hhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcc
Q 009567          362 QHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA  441 (532)
Q Consensus       362 ~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~  441 (532)
                      ++.+.-.                                                       +.    ++  ..      
T Consensus        83 k~k~~~~-------------------------------------------------------~~----~~--~~------   95 (228)
T PRK06704         83 SKSVHEK-------------------------------------------------------IR----DQ--IT------   95 (228)
T ss_pred             ccccccc-------------------------------------------------------cc----cc--cc------
Confidence            6542000                                                       00    00  00      


Q ss_pred             cCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          442 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       442 d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                         ...+....  ....+.+..+|+.||+++|.||.|+|.    +++|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus        96 ---~~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~  166 (228)
T PRK06704         96 ---FEEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE  166 (228)
T ss_pred             ---cCChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence               00111111  123356888999999999999999998    899999999999999999999999999999998865

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

Probab=99.62  E-value=1.3e-14  Score=147.97  Aligned_cols=156  Identities=21%  Similarity=0.141  Sum_probs=118.7

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHH
Q 009567          295 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  374 (532)
Q Consensus       295 ~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~  374 (532)
                      +++..|.+.++.+|+++.++..+.+|++||+++.+++.  .|+.  ...|.+|.+.++++.+.+++++..+.-..     
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~-----   71 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREV-----   71 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence            36889999999999999999999999999999997765  4543  23699999999999999999765310000     


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHHHH
Q 009567          375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  454 (532)
Q Consensus       375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~  454 (532)
                                          .                        ....+..+            ..+. ...|++....
T Consensus        72 --------------------~------------------------~~~~~~e~------------~~~~-~~~~~~~~~~   94 (281)
T TIGR02957        72 --------------------Y------------------------VGPWLPEP------------LLTT-SADPAESVEL   94 (281)
T ss_pred             --------------------c------------------------CCCCCCcc------------cCCC-CCChHHHHHH
Confidence                                0                        00000000            0000 1234444433


Q ss_pred             -HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          455 -QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       455 -~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                       +.+...+..+|+.|||+||.||.|+|.    .++|++|||+.||+|..+|+++.+||+++||+...
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             345567888999999999999999998    89999999999999999999999999999999764

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=99.62  E-value=1.5e-14  Score=148.45  Aligned_cols=162  Identities=17%  Similarity=0.086  Sum_probs=123.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccc
Q 009567          291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  370 (532)
Q Consensus       291 ~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP  370 (532)
                      ..+..++..|.+.++.+|+++.++..+.||++||.++.+|++...+ .   ..|.+|++...++.+.+++++..+.-.. 
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   3599999999999999999864310000 


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhH
Q 009567          371 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  450 (532)
Q Consensus       371 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee  450 (532)
                                                                        ....+..  .. +    +..++  ..+|++
T Consensus        80 --------------------------------------------------~~~~~~~--~~-~----~~~~~--~~~~~~  100 (290)
T PRK09635         80 --------------------------------------------------PQDIAAW--HD-G----DASVS--SVDPAD  100 (290)
T ss_pred             --------------------------------------------------ccccccc--Cc-c----ccCCC--CCCcHH
Confidence                                                              0000000  00 0    00001  113333


Q ss_pred             -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          451 -SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       451 -~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                       .....+....+..+|+.|||++|.||.|+|.    .++|++|||+.||+|..+|+++.+||+++||....
T Consensus       101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~  167 (290)
T PRK09635        101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAHRARRKINESRI  167 (290)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCC
Confidence             3344555678899999999999999999998    89999999999999999999999999999998643

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.49  E-value=4.7e-13  Score=122.13  Aligned_cols=136  Identities=12%  Similarity=0.139  Sum_probs=99.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhh-----hCCcCCCchhhHHHHHHHHHHHHHHHhhcccc
Q 009567          293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  367 (532)
Q Consensus       293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiek-----FDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~I  367 (532)
                      ++.++..|.++++.+|++|.+.    +| +||.++.+|..+.+     |++.  ..|.||.+..+++.+.++++++.+..
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     5432  47999999999999999998654210


Q ss_pred             ccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCC
Q 009567          368 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  447 (532)
Q Consensus       368 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~  447 (532)
                      +.                 .        ...++                               .+         ... .
T Consensus        74 ~~-----------------~--------~~~~~-------------------------------~~---------~~~-~   87 (142)
T TIGR03209        74 KI-----------------I--------YNSEI-------------------------------TD---------IKL-S   87 (142)
T ss_pred             hh-----------------h--------hhhhh-------------------------------hc---------ccc-c
Confidence            00                 0        00000                               00         000 1


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR  505 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVR  505 (532)
                      +.+.....+....+..+|+.||+++|+||.|+|.    +++|++|||+.||+|.++|+
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            1122233344556889999999999999999998    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=99.47  E-value=4.2e-13  Score=132.92  Aligned_cols=137  Identities=17%  Similarity=0.123  Sum_probs=110.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccch
Q 009567          292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  371 (532)
Q Consensus       292 Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~  371 (532)
                      ++..|+..|.+.|+.+|.++.++..+.+|++||+++.+|+...+|++.  ..|.+|++.++++.....            
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~------------   67 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA------------   67 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc------------
Confidence            578899999999999999999999999999999999999999999874  458999887665321000            


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567          372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  451 (532)
Q Consensus       372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~  451 (532)
                                                                             .. ...         ..  ..+.. 
T Consensus        68 -------------------------------------------------------~~-~~~---------~~--~~~~~-   79 (261)
T PRK09191         68 -------------------------------------------------------GA-NDP---------EP--GSPFE-   79 (261)
T ss_pred             -------------------------------------------------------cc-cCC---------CC--CCCch-
Confidence                                                                   00 000         00  01111 


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       452 ~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                             ..+..+|..||+++|+||.++|.    +++|++|||+.||+|.++|+....+|+++||..+..
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                   15888999999999999999998    999999999999999999999999999999987653

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.46  E-value=4.4e-12  Score=126.71  Aligned_cols=90  Identities=20%  Similarity=0.328  Sum_probs=78.8

Q ss_pred             HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCC--CHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          279 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       279 ~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~--~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      .+.++..++.| ..|++.|+..|.++|+++|.++.++..  +.+|++|||++++|+++++|++++|..|.+|+..+|++.
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            34455556655 489999999999999999999998765  489999999999999999999999888999999999999


Q ss_pred             HHHHHHhhccccc
Q 009567          356 IRKAIFQHSRTIR  368 (532)
Q Consensus       356 I~~~ir~~~r~IR  368 (532)
                      +.++++++.+...
T Consensus        85 ~iDylRk~~~~~~   97 (237)
T PRK08311         85 LIDYFRKESKHNL   97 (237)
T ss_pred             HHHHHHHhhcccc
Confidence            9999998776433

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.35  E-value=6.4e-11  Score=113.71  Aligned_cols=174  Identities=20%  Similarity=0.309  Sum_probs=118.3

Q ss_pred             HHHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCC---CCCHhh--HHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHH
Q 009567          280 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  353 (532)
Q Consensus       280 ~~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~---g~~~eD--LiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr  353 (532)
                      .+|+..++.|+ .|.+.|+..|++-++.+|+++.+.   +.+.+|  |++|.++.++..-...+++....|..|+...++
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            34566666665 999999999999999999987643   344554  467777777663333233333468888888888


Q ss_pred             HHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 009567          354 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD  433 (532)
Q Consensus       354 ~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~  433 (532)
                      +.+.++.+.+.+..|                      +|..                         ...+|+...     
T Consensus        85 r~lid~~R~~~a~KR----------------------g~~~-------------------------~~~~l~~~~-----  112 (185)
T PF07638_consen   85 RKLIDHARRRQAQKR----------------------GGDQ-------------------------VRVELDERA-----  112 (185)
T ss_pred             HHHHHHHHHHHHHhc----------------------CCCC-------------------------cccchhhhh-----
Confidence            888888776542111                      1100                         011122111     


Q ss_pred             cchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567          434 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  513 (532)
Q Consensus       434 ~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk  513 (532)
                             .+...+.|+..+   ++.+.+..+.. |+|+++++|.++|.    .|+|.+|||+.||||..+|+.....|..
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                   001112444433   23444555555 99999999999987    8999999999999999999999999999


Q ss_pred             HHHHHhh
Q 009567          514 RLKQSLG  520 (532)
Q Consensus       514 KLR~~l~  520 (532)
                      +|+..+.
T Consensus       178 ~l~~~l~  184 (185)
T PF07638_consen  178 WLRRELR  184 (185)
T ss_pred             HHHHHhc
Confidence            9998764

>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=2.1e-11  Score=92.60  Aligned_cols=50  Identities=36%  Similarity=0.628  Sum_probs=46.3

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +|+.|||+|++||.++|+    +++|++|||+.||+|+++|+++..+|++|||+
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 ....

>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=99.23  E-value=2.9e-11  Score=96.64  Aligned_cols=70  Identities=23%  Similarity=0.432  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcc
Q 009567          296 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  365 (532)
Q Consensus       296 LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r  365 (532)
                      |++.|.++|+.++++|.+++.+.+|++||++++||+++++||+++|..|.+|++..+++.+.++++++.|
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            6889999999999999999999999999999999999999999999899999999999999999998764

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 ....

>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=99.09  E-value=2.7e-10  Score=94.05  Aligned_cols=77  Identities=30%  Similarity=0.491  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHH
Q 009567          375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  451 (532)
Q Consensus       375 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~  451 (532)
                      +++++|.+++..|.+++||.||.+|||+.|||++++|..++...+.++||+.+++.+++.++.+++.|+...+|++.
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            36789999999999999999999999999999999999999999999999999998888999999999988888764

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=98.92  E-value=3.7e-09  Score=81.27  Aligned_cols=54  Identities=30%  Similarity=0.440  Sum_probs=46.4

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                      ++.|..+|..|||++|.||.++|.    +++|++|||+.+|+|.++|++...+|+++|
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            357889999999999999999998    999999999999999999999999999987

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=98.65  E-value=1.2e-07  Score=90.28  Aligned_cols=71  Identities=18%  Similarity=0.285  Sum_probs=62.5

Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      +.+.....+....|..++..||+++|+||.++|+    +++|++|||+.||+|.++|+.+..||+++|+..+...
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    9999999999999999999999999999999988754

>PRK00118 putative DNA-binding protein; Validated

Probab=98.44  E-value=9.7e-07  Score=77.56  Aligned_cols=61  Identities=21%  Similarity=0.146  Sum_probs=55.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       460 ~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      .+.-....||+++++|+.++|.    +++|.+|||+.+|+|+.+|+.+..+|+++||+++..-++
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            4445668999999999999998    999999999999999999999999999999999887654

>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=98.28  E-value=2.5e-06  Score=63.45  Aligned_cols=53  Identities=38%  Similarity=0.589  Sum_probs=49.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       460 ~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .+..++..|++.++.++.++|.    +++|..+||+.+|+|..+|+++..++..+||
T Consensus         3 ~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           3 RLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            5778899999999999999997    8999999999999999999999999988874

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=98.20  E-value=3.4e-06  Score=77.64  Aligned_cols=57  Identities=19%  Similarity=0.269  Sum_probs=49.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY  527 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~y  527 (532)
                      ..||++|++||.+++     +|+|++|||+.||+|+.+|++++++|+++|+.......+-.+
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            459999999999975     799999999999999999999999999999986555444433

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=98.18  E-value=4.3e-06  Score=77.32  Aligned_cols=51  Identities=24%  Similarity=0.399  Sum_probs=47.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ..|+|+|++||.+++     +++|++|||+.||+|+.+|+.++++|+++||+....
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            469999999999975     799999999999999999999999999999997654

>PRK04217 hypothetical protein; Provisional

Probab=98.06  E-value=8.3e-06  Score=72.41  Aligned_cols=55  Identities=20%  Similarity=0.136  Sum_probs=50.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ..|++.|++|+.++|.    +++|++|||+.+|||+.+|++++.+|+++|++.+.....
T Consensus        41 ~~Lt~eereai~l~~~----eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~   95 (110)
T PRK04217         41 IFMTYEEFEALRLVDY----EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE   95 (110)
T ss_pred             ccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            5799999999999997    899999999999999999999999999999999876544

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.02  E-value=1.6e-06  Score=62.14  Aligned_cols=34  Identities=41%  Similarity=0.464  Sum_probs=30.0

Q ss_pred             ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH
Q 009567          217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR  250 (532)
Q Consensus       217 ~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~  250 (532)
                      +|+++.||++|+++|+||++||++|+++|+.+..
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            3799999999999999999999999999998543

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 ....

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=97.96  E-value=3.6e-05  Score=70.59  Aligned_cols=63  Identities=19%  Similarity=0.295  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      ...+.|..+|+.|++.+|.||.++|+  .+..+|..+||..||+|+.+|.++..+|+.+|+..+.
T Consensus        71 ~~~~~I~~~l~~Ld~~er~II~~rY~--~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~lG  133 (134)
T TIGR01636        71 RNRDAIENCLNEADEQTRVIIQELYM--KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEELG  133 (134)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc--cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhC
Confidence            34567899999999999999999996  2234699999999999999999999999999998753

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.

>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=97.93  E-value=4.6e-05  Score=66.58  Aligned_cols=57  Identities=28%  Similarity=0.367  Sum_probs=44.8

Q ss_pred             HHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          461 VRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       461 L~~~L-~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      |.... .-|+++|++++.++|.    +++|+.|||+.+||||..|...++||.++|...=..
T Consensus        10 L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k   67 (101)
T PF04297_consen   10 LFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK   67 (101)
T ss_dssp             HHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            44444 4599999999999998    999999999999999999999999999999775443

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.

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=97.87  E-value=0.0038  Score=70.95  Aligned_cols=34  Identities=32%  Similarity=0.493  Sum_probs=31.4

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHH
Q 009567          216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI  249 (532)
Q Consensus       216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~  249 (532)
                      .+||+++||++|+..||||+|+|++++++|..+.
T Consensus       102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~  135 (619)
T PRK05658        102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE  135 (619)
T ss_pred             CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999998643

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.85  E-value=3.5e-05  Score=58.30  Aligned_cols=46  Identities=26%  Similarity=0.400  Sum_probs=41.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|+.|+.+.+     .++|.+|||+.+|+|+.+|+++..+++++|.
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            468999999998754     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=97.74  E-value=6.9e-05  Score=58.52  Aligned_cols=47  Identities=23%  Similarity=0.317  Sum_probs=41.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ..|+++|.+|+.+..     .|+|.+|||+.+|||..+|+.+..++++||.-
T Consensus         2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~   48 (58)
T PF00196_consen    2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV   48 (58)
T ss_dssp             GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred             CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence            579999999999987     79999999999999999999999999999853

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=97.66  E-value=0.00012  Score=55.50  Aligned_cols=45  Identities=29%  Similarity=0.487  Sum_probs=40.3

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      |+++|++|+.+.+     .++|.+|||+.+|+|+.+|+.+..+++++|+.
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            6899999998855     68999999999999999999999999888754

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=97.54  E-value=0.00045  Score=60.27  Aligned_cols=55  Identities=22%  Similarity=0.439  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          457 MRQHVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       457 l~~~L~~~L~~L~-~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                      .+..+..+++.|+ +.+|.||.++|.    .+++..+|++.||+|+.++-.+..+|++.|
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            3456888888886 899999999998    789999999999999999999999999986

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.

>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=0.00031  Score=54.41  Aligned_cols=48  Identities=27%  Similarity=0.428  Sum_probs=42.3

Q ss_pred             CCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       468 L~~rER~VL~LRyGL~--~-~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                      |+++|++||..-|-.+  + ...-|+.|||+.||||+.++..++.+|.+||
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            7899999999876443  3 4688999999999999999999999999987

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

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.53  E-value=0.00021  Score=58.90  Aligned_cols=47  Identities=19%  Similarity=0.213  Sum_probs=41.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          460 HVRNLLTLLNPKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       460 ~L~~~L~~L~~rER~VL~LR-yGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .+.+-|..||++.+.++.|. |.    +++|++|||+.||+|..+|+.++++
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            45667899999999999995 44    8999999999999999999998775

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.

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.50  E-value=0.00017  Score=62.24  Aligned_cols=50  Identities=22%  Similarity=0.240  Sum_probs=43.5

Q ss_pred             HHHHHHH-hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHH
Q 009567          459 QHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLE  508 (532)
Q Consensus       459 ~~L~~~L-~~L~~rER~VL~LRyGL~~---~e~~Tl~EIAe~LgISrerVRqie  508 (532)
                      +.+..+| ..|+|+|+.+|..|||+.+   ..++|++|||+.+|||+.+|.+..
T Consensus        23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s   76 (94)
T TIGR01321        23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS   76 (94)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence            3566677 5599999999999999987   689999999999999999997653

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=97.40  E-value=0.00034  Score=66.83  Aligned_cols=47  Identities=23%  Similarity=0.352  Sum_probs=43.8

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ..|+++|++|+.+.-     +|+|.+|||+.||+|..||+....++++||.-
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     89999999999999999999999999999954

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.36  E-value=0.00033  Score=68.52  Aligned_cols=46  Identities=11%  Similarity=0.237  Sum_probs=43.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .|++||++||.+.-     +|+|.+|||+.||+|..||+.+..+.++||.-
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            49999999999987     89999999999999999999999999999963

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.32  E-value=0.00039  Score=67.31  Aligned_cols=46  Identities=22%  Similarity=0.291  Sum_probs=43.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|++||++|+.+.-     +|+|.+|||+.||+|..||+.+..+.++||-
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            469999999999987     7999999999999999999999999999994

>PRK13870 transcriptional regulator TraR; Provisional

Probab=97.30  E-value=0.00041  Score=69.43  Aligned_cols=46  Identities=26%  Similarity=0.364  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .|++||++||.+-=     +|+|..|||.+||||..||..++++|++||-.
T Consensus       173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga  218 (234)
T PRK13870        173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDV  218 (234)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            59999999999986     89999999999999999999999999999943

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.30  E-value=0.00044  Score=67.91  Aligned_cols=46  Identities=20%  Similarity=0.342  Sum_probs=43.5

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|++||++||.+.-     +|+|.+|||+.|+||..||+.+..+.++||.
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            469999999999987     7999999999999999999999999999994

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.28  E-value=0.00046  Score=68.06  Aligned_cols=50  Identities=8%  Similarity=-0.050  Sum_probs=46.5

Q ss_pred             HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          462 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       462 ~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .++...|+|+|++|+.+.-     +|+|.+|||+.|++|..||+....+.++||.
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            5567899999999999986     7999999999999999999999999999994

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.27  E-value=0.00049  Score=69.56  Aligned_cols=48  Identities=21%  Similarity=0.261  Sum_probs=44.5

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +..|+++|++|+.+..     +|+|.+|||++||||..||+....++++||.-
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            4579999999999976     89999999999999999999999999999964

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.

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.25  E-value=0.00049  Score=68.55  Aligned_cols=48  Identities=19%  Similarity=0.267  Sum_probs=44.5

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ...|+++|++||.+..     +|+|..|||++||||..+|+.++.++++||+.
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            3579999999999975     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.

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=97.24  E-value=0.00055  Score=68.71  Aligned_cols=45  Identities=16%  Similarity=0.258  Sum_probs=43.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .|++||++||.+..     +|+|..|||.+||||..||+.++.++++||-
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            69999999999996     8999999999999999999999999999995

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=97.20  E-value=0.00063  Score=67.24  Aligned_cols=48  Identities=17%  Similarity=0.127  Sum_probs=44.5

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +..|+++|++|+.+..     +|+|.+|||+.|++|..||+.+..++++||.-
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     79999999999999999999999999999954

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=97.16  E-value=0.00068  Score=66.70  Aligned_cols=46  Identities=30%  Similarity=0.371  Sum_probs=43.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|++||++|+++.-     +|+|.+|||+.|++|..||+.+..+.++||.
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            479999999999876     7999999999999999999999999999994

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=97.09  E-value=0.002  Score=62.23  Aligned_cols=60  Identities=17%  Similarity=0.231  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      .....+...+.+|+||||+|+..--     .|+..++||..||||.-||..+..+.++||+..--
T Consensus       131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~Sl  190 (202)
T COG4566         131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSL  190 (202)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccH
Confidence            3446788999999999999999887     79999999999999999999999999999986543

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=97.09  E-value=0.0014  Score=57.88  Aligned_cols=53  Identities=19%  Similarity=0.164  Sum_probs=48.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      .|+..|-+.|+|.+.    +++|.+|.|+.||||+.|+..++..|.+|+-..|....
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            578889999999998    99999999999999999999999999999999886544

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=97.05  E-value=0.0019  Score=50.43  Aligned_cols=48  Identities=33%  Similarity=0.432  Sum_probs=43.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      ..|+++|.+|+.+.-     .|+|..|||..+|+|..+|+....++.+||.-.
T Consensus         3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~   50 (65)
T COG2771           3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVK   50 (65)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            468999999998876     689999999999999999999999999998653

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=96.97  E-value=0.001  Score=49.37  Aligned_cols=41  Identities=24%  Similarity=0.339  Sum_probs=24.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      ..|++.||..|...+-    +|+|..+||+.||+|++||...++|
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            4689999999998875    8999999999999999999988776

>PRK09483 response regulator; Provisional

Probab=96.96  E-value=0.0014  Score=62.25  Aligned_cols=46  Identities=22%  Similarity=0.300  Sum_probs=42.5

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|++|+.+..     +|+|.+|||+.|++|..||+.+..+.++||-
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            469999999998765     7999999999999999999999999999983

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.74  E-value=0.0031  Score=58.51  Aligned_cols=46  Identities=22%  Similarity=0.358  Sum_probs=42.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|++|+.+. .    +++|.+|||+.+++|..||+....++++||.
T Consensus       148 ~~lt~~e~~vl~l~-~----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~  193 (211)
T PRK15369        148 PLLTPRERQILKLI-T----EGYTNRDIAEQLSISIKTVETHRLNMMRKLD  193 (211)
T ss_pred             cCCCHHHHHHHHHH-H----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            45999999999984 4    8899999999999999999999999999995

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.70  E-value=0.011  Score=53.73  Aligned_cols=62  Identities=21%  Similarity=0.244  Sum_probs=53.5

Q ss_pred             HHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          457 MRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       457 l~~~L~~~L-~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      ....+..++ ..|++.+|+||..+|. . .++++.-+|+..+|+|+.+...+.++|+.++-..+.
T Consensus        68 ~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~  130 (132)
T TIGR01637        68 EARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG  130 (132)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence            345677777 9999999999999997 2 137899999999999999999999999999987664

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=96.62  E-value=0.0045  Score=60.98  Aligned_cols=53  Identities=23%  Similarity=0.350  Sum_probs=46.1

Q ss_pred             cCCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          467 LLNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~--~-~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      .|+++|++||+.-|-++  + ....+++|||+.||||+.++.+++.+|.+||=..+
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            69999999999877543  3 47789999999999999999999999999996643

>PRK01381 Trp operon repressor; Provisional

Probab=96.59  E-value=0.0025  Score=55.51  Aligned_cols=48  Identities=27%  Similarity=0.312  Sum_probs=40.8

Q ss_pred             HHHHHHHHhc-CCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHH
Q 009567          458 RQHVRNLLTL-LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVR  505 (532)
Q Consensus       458 ~~~L~~~L~~-L~~rER~VL~LRyGL~~---~e~~Tl~EIAe~LgISrerVR  505 (532)
                      .+.+..+|.. |+|+|+..|..||++..   ..++|++||++.+|||..+|.
T Consensus        22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT   73 (99)
T PRK01381         22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT   73 (99)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence            3456666755 99999999999999876   457999999999999998885

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.55  E-value=0.0043  Score=58.31  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=42.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|++|+.+..     ++++.++||+.+++|..||+.+..++++||.
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            459999999999866     7899999999999999999999999999994

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=96.53  E-value=0.002  Score=58.06  Aligned_cols=48  Identities=25%  Similarity=0.359  Sum_probs=44.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      -|+++|-.||.||-     +|+|.+|||++||-|+..|+-++++|+.++.+.-
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            48899999999998     7999999999999999999999999999998753

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.49  E-value=0.0077  Score=55.55  Aligned_cols=54  Identities=13%  Similarity=0.189  Sum_probs=47.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       460 ~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      .+...+..|+++|++|+.+.+     .+++.++||+.+|+|..+|+....++++||+..
T Consensus       134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~  187 (202)
T PRK09390        134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAG  187 (202)
T ss_pred             HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence            355667889999999999754     689999999999999999999999999999653

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.26  E-value=0.018  Score=50.15  Aligned_cols=48  Identities=25%  Similarity=0.328  Sum_probs=43.7

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .-|+.+|+..+.++|.    +++|+.|||+.++|||..|...++|.-+.|-.
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            5589999999999998    89999999999999999999999998776644

>PRK15320 transcriptional activator SprB; Provisional

Probab=96.21  E-value=0.0089  Score=58.25  Aligned_cols=50  Identities=22%  Similarity=0.308  Sum_probs=44.8

Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       463 ~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ++--.|+++|.+|+.+--     +|+|.+|||+.|++|..+|+...++.+.||.-
T Consensus       160 ~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA  209 (251)
T PRK15320        160 NLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM  209 (251)
T ss_pred             cCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence            334689999999999887     79999999999999999999999999999843

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=96.13  E-value=0.016  Score=50.02  Aligned_cols=52  Identities=19%  Similarity=0.148  Sum_probs=47.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  522 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~  522 (532)
                      .|+..|-+.|+|...    ++++.+|-|..||||+.|+-..+..|++|+-..+...
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            367778899999988    8999999999999999999999999999999988654

>PRK10403 transcriptional regulator NarP; Provisional

Probab=96.00  E-value=0.013  Score=54.87  Aligned_cols=46  Identities=15%  Similarity=0.230  Sum_probs=42.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|.+|+.+..     +++|.+|||+.+|+|..||+.+..++++||.
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            459999999998875     7899999999999999999999999999984

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.68  E-value=0.016  Score=54.00  Aligned_cols=46  Identities=20%  Similarity=0.255  Sum_probs=42.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|++|+.+..     +++|.++||+.+++|..+|+.+..+.++||.
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            469999999999976     6899999999999999999999999999985

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=95.66  E-value=0.023  Score=53.36  Aligned_cols=47  Identities=21%  Similarity=0.320  Sum_probs=42.8

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      +..|+++|++|+.+..     .+.|.+|||+.+++|..+|+.+..+.++||.
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            3569999999999887     6889999999999999999999999999983

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.66  E-value=0.023  Score=53.26  Aligned_cols=45  Identities=24%  Similarity=0.242  Sum_probs=40.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .|+++|.+|+.+..     +++|.+|||+.+++|..+|+....++++||.
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            48999999998754     6799999999999999999999999999984

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

Probab=95.52  E-value=0.35  Score=50.87  Aligned_cols=49  Identities=24%  Similarity=0.323  Sum_probs=46.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      -.|++.+|-.+.||..    -|+|..|||..|=|+..++-|.+.||.++++..
T Consensus       119 Pal~~~~riALtLR~v----~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a  167 (415)
T COG4941         119 PALPPEQRIALTLRLV----GGLSTAEIARAFLVPEAAMAQRIVRAKARIREA  167 (415)
T ss_pred             CCCChhhHHHHHHHHH----cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence            6699999999999998    799999999999999999999999999999974

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.37  E-value=0.026  Score=66.14  Aligned_cols=46  Identities=11%  Similarity=0.172  Sum_probs=43.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|++|+.+..     +|+|.+|||+.|+||..||+.+.++.++||.
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            459999999999977     8999999999999999999999999999995

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=95.18  E-value=0.026  Score=39.27  Aligned_cols=27  Identities=30%  Similarity=0.643  Sum_probs=20.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ++|.+|||+.+|+|+++|+    |++++|++
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            4799999999999999996    66777765

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 ....

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.08  E-value=0.042  Score=62.39  Aligned_cols=55  Identities=13%  Similarity=0.070  Sum_probs=45.9

Q ss_pred             HhcCCHHHHHHHHHHhccc---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          465 LTLLNPKERCIVRLRFGIE---DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~---~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      ...|+++|+++|..-|..+   -..+-|..|||+.||||+.++.+++.+|.+||=..+
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            4689999999999988621   123449999999999999999999999999986543

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=95.06  E-value=0.058  Score=41.46  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=43.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  519 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l  519 (532)
                      .|+..++-++.+.|.   ..+.|++.+|..+|||+++|.++.+..+.-|...+
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            578888888888775   37899999999999999999999999888776654

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=94.97  E-value=0.053  Score=46.45  Aligned_cols=38  Identities=13%  Similarity=0.239  Sum_probs=31.6

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  508 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie  508 (532)
                      ++.|++| .+|+.+.-     .++|..|||+.+|||+.||..+.
T Consensus        34 ~~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~   71 (88)
T TIGR02531        34 IQSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK   71 (88)
T ss_pred             HHhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence            3468999 78887754     67999999999999999998843

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.

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=94.86  E-value=0.026  Score=42.25  Aligned_cols=33  Identities=27%  Similarity=0.326  Sum_probs=22.9

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      +||.++.     +++|..+||+.||||+.+|+++.++-
T Consensus         9 ~ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~   41 (50)
T PF13384_consen    9 QIIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY   41 (50)
T ss_dssp             -HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred             HHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence            3555555     68999999999999999999987663

>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=94.73  E-value=0.14  Score=41.42  Aligned_cols=56  Identities=18%  Similarity=0.286  Sum_probs=44.7

Q ss_pred             HHHHHhhcHHHHHHHHHHHHHHHHHHHHHh----hC--CCCCHhhHHHHHHHHHHHhhhhhC
Q 009567          282 LKSELHSGNSSREKLINANLRLVVHVAKQY----QG--RGISLHDLLQEGSMGLMKSVEKFK  337 (532)
Q Consensus       282 L~~~l~~g~~Are~LI~~nlrLV~sIAkrY----~~--~g~~~eDLiQEG~iGLikAiekFD  337 (532)
                      +..+.+|+..|.++++..|.|++.+.+.+-    .+  ++.--+|+-|+-...|++++-+|+
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            444555667999999999999999998772    22  133349999999999999999996

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

>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=94.71  E-value=0.091  Score=39.13  Aligned_cols=41  Identities=17%  Similarity=0.255  Sum_probs=29.6

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      |++.++.||.+-+-   +.+.|..|||+.+|+|..+|+++.++-
T Consensus         1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L   41 (48)
T PF13412_consen    1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKL   41 (48)
T ss_dssp             --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            57788888876553   366999999999999999998766543

...

>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=94.31  E-value=0.068  Score=43.11  Aligned_cols=45  Identities=18%  Similarity=0.417  Sum_probs=29.3

Q ss_pred             HhcCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 009567          465 LTLLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLS-KERVRQLES  509 (532)
Q Consensus       465 L~~L~~rER~VL~L--RyGL~~~e~~Tl~EIAe~LgIS-rerVRqie~  509 (532)
                      +..|+++|++||..  .|.-..|-+-|.+|||+.||++ ..+|.+.+.
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            35799999999987  3333456788999999999997 999976554

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.

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=94.24  E-value=0.15  Score=46.71  Aligned_cols=54  Identities=17%  Similarity=0.334  Sum_probs=45.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  513 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk  513 (532)
                      +..|...++.|.+.++.||.+||+  ...++|..+||..|++|..+++.+...-..
T Consensus        72 k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~  125 (130)
T PF05263_consen   72 KEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKN  125 (130)
T ss_pred             HHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHH
Confidence            456788889999999999999998  334699999999999999999876654433

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=93.89  E-value=0.12  Score=42.30  Aligned_cols=38  Identities=32%  Similarity=0.613  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHH
Q 009567          249 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL  286 (532)
Q Consensus       249 ~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l  286 (532)
                      .++.+++.+|+..+||+||.+|.|+..|++.+.+...+
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            35667889999999999999999999999988775544

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 ....

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=93.61  E-value=0.098  Score=54.85  Aligned_cols=36  Identities=22%  Similarity=0.344  Sum_probs=32.5

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567          474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  513 (532)
Q Consensus       474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk  513 (532)
                      +|-.|+|.    +++|.+|||+.|||||.+|.+++.+|++
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            46678887    9999999999999999999999999876

>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=93.49  E-value=0.099  Score=38.81  Aligned_cols=32  Identities=25%  Similarity=0.296  Sum_probs=23.6

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567          472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  508 (532)
Q Consensus       472 ER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie  508 (532)
                      ..+|+.|+-     +|+|..+||+.+|||+.+|..++
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            355666665     67999999999999999998775

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 ....

>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=93.47  E-value=0.17  Score=33.39  Aligned_cols=36  Identities=19%  Similarity=0.335  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL  507 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqi  507 (532)
                      +++.++..+...|-    .+.|..+||+.+|+|+.+|..+
T Consensus         6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence            45555655655554    5779999999999999999875

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

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=93.19  E-value=0.57  Score=42.54  Aligned_cols=55  Identities=18%  Similarity=0.123  Sum_probs=49.2

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      |..-.|.+-++|.++|.    .++|...||..+++|...||+...+|-.-+..++.-.+
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            45588999999999999    89999999999999999999999999999988765433

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

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

Probab=93.16  E-value=1.2  Score=44.25  Aligned_cols=35  Identities=31%  Similarity=0.574  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  284 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~  284 (532)
                      ++.+....|...+|++||.+|.|+..|++.+.+..
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~  122 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE  122 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34456778888899999999999999999877743

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.

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=92.88  E-value=1.5  Score=46.84  Aligned_cols=130  Identities=18%  Similarity=0.278  Sum_probs=73.1

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHH-HHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG-SMG  328 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG-~iG  328 (532)
                      ++.+...+|...+|++||..|.|+..|++.+.+...+...                   ..    .+++++.+.++ -..
T Consensus       217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~  273 (367)
T PRK09210        217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSH  273 (367)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcch
Confidence            4456677888889999999999999999988775433211                   00    11111111110 011


Q ss_pred             HHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCH
Q 009567          329 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV  408 (532)
Q Consensus       329 LikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~  408 (532)
                      |...+.  |+.............++..+.+++.      .+|..-...+..      .+.-..|.+-|.+|||+.+|+|.
T Consensus       274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~l------rygl~~~~~~tl~EIa~~lgvs~  339 (367)
T PRK09210        274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLRL------RFGLDDGRTRTLEEVGKVFGVTR  339 (367)
T ss_pred             hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHHH------HhccCCCCCccHHHHHHHHCCCH
Confidence            111111  1111223444455566666666663      344433222211      11112346789999999999999


Q ss_pred             HHHHHHHH
Q 009567          409 EKLERLIF  416 (532)
Q Consensus       409 e~v~~ll~  416 (532)
                      ++|+.+..
T Consensus       340 erVrQi~~  347 (367)
T PRK09210        340 ERIRQIEA  347 (367)
T ss_pred             HHHHHHHH
Confidence            99998854

>PF13730 HTH_36: Helix-turn-helix domain

Probab=92.57  E-value=0.42  Score=36.42  Aligned_cols=47  Identities=19%  Similarity=0.289  Sum_probs=35.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCC---CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPK---SLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~---Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .|++.++.|+....-+.++.+.   |.+.||+.+|+|+.+|+    ++++.|.+
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~~   51 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELEE   51 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            5888888888775555433332   89999999999999996    56666654

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=92.55  E-value=2.2  Score=45.01  Aligned_cols=130  Identities=18%  Similarity=0.218  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHH-HHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG  328 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQE-G~iG  328 (532)
                      ++.++..+|...+|++||..|.|+..|++.+.+......                   +    ..-.++++.+.+ +...
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~-------------------~----~~~~SLd~~~~~~~~~~  230 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEH-------------------S----RDPVSLDMPVGSDEEAP  230 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------c----CCCceecCCCCCCCCch
Confidence            455677888889999999999999999998776432210                   0    011111111111 0011


Q ss_pred             HHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCH
Q 009567          329 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV  408 (532)
Q Consensus       329 LikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~  408 (532)
                      |...+..  +........+...-.+..+..++.      .+|.+-...+..      .+.-.++.+-|.+|||+.+|+|.
T Consensus       231 l~d~l~d--~~~~~pe~~~~~~~~~~~l~~~L~------~L~eREr~Vl~~------rygl~~~~~~Tl~eIa~~lgvS~  296 (324)
T PRK07921        231 LGDFIED--SEATSAENAVIAGLLHTDIRSVLA------TLDEREQQVIRL------RFGLDDGQPRTLDQIGKLFGLSR  296 (324)
T ss_pred             HHHHhcC--CCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHHH------HHhcCCCCCcCHHHHHHHHCCCH
Confidence            2222221  111112333333344444555542      234332222211      11112345679999999999999


Q ss_pred             HHHHHHHH
Q 009567          409 EKLERLIF  416 (532)
Q Consensus       409 e~v~~ll~  416 (532)
                      ++|+.+..
T Consensus       297 eRVrQIe~  304 (324)
T PRK07921        297 ERVRQIER  304 (324)
T ss_pred             HHHHHHHH
Confidence            99998854

>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=92.43  E-value=0.37  Score=35.50  Aligned_cols=40  Identities=33%  Similarity=0.422  Sum_probs=27.4

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      |++-.+.||...-.   +...|+.+||+.+|+|..+|.+.+.+
T Consensus         1 lD~~D~~Il~~Lq~---d~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    1 LDELDRKILRLLQE---DGRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence            34556677766543   25789999999999999999877654

...

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=92.39  E-value=0.36  Score=43.26  Aligned_cols=50  Identities=20%  Similarity=0.299  Sum_probs=42.7

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .+..|++.+..-|....-    ..=+++|+++.||||-.|||..+.+.+++|.-
T Consensus        30 ~~~~L~~E~~~Fi~~Fi~----~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   30 WFARLSPEQLEFIKLFIK----NRGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hhhcCCHHHHHHHHHHHH----hcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            367899998888877654    34499999999999999999999999999965

>PHA00675 hypothetical protein

Probab=92.23  E-value=0.27  Score=40.92  Aligned_cols=40  Identities=18%  Similarity=0.089  Sum_probs=31.5

Q ss_pred             hcCCHHHHHHHHHHh-cccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRF-GIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       466 ~~L~~rER~VL~LRy-GL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      ..|++.+-+.|+.++ -    .+.|+.+||..||||+++|.+|..
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            356666666666655 4    678999999999999999999865

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=91.97  E-value=0.31  Score=47.99  Aligned_cols=48  Identities=15%  Similarity=0.070  Sum_probs=36.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  514 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkK  514 (532)
                      .|+++|.+++.....=..++++|.+|||+.||+|..||+.+..++...
T Consensus       158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~  205 (239)
T PRK10430        158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNC  205 (239)
T ss_pred             CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhC
Confidence            488999877654331112389999999999999999999998887543

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=91.96  E-value=2.7  Score=47.06  Aligned_cols=130  Identities=17%  Similarity=0.282  Sum_probs=71.4

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHH-HHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG  328 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQE-G~iG  328 (532)
                      ++.+.+.+|...+|++||.+|.|+..|++.+.+....+.                       ...-+++++.+.+ +...
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~-----------------------~~~~~SLD~~i~~d~~~~  415 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKY-----------------------NREPISLDKTIGKEGDSQ  415 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh-----------------------cCCCcccccccccCCccc
Confidence            455677888899999999999999999987776443211                       1112222222211 1111


Q ss_pred             HHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCH
Q 009567          329 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV  408 (532)
Q Consensus       329 LikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~  408 (532)
                      +...+.  |+........+..+..+..+..++.      .||.+-...+..      .+.-..+..-|..|||..+|||.
T Consensus       416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~------~L~eREr~VI~l------RyGL~~~e~~TL~EIa~~lGVSr  481 (509)
T PRK05901        416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLE------TLSEREAGVIRM------RFGLTDGQPKTLDEIGQVYGVTR  481 (509)
T ss_pred             HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHh------hCCHHHHHHHHH------HhhccCCCCCCHHHHHHHHCCCH
Confidence            211111  1111122333344445555555553      234332222221      11112246789999999999999


Q ss_pred             HHHHHHHH
Q 009567          409 EKLERLIF  416 (532)
Q Consensus       409 e~v~~ll~  416 (532)
                      ++|+.+..
T Consensus       482 ERVRQIe~  489 (509)
T PRK05901        482 ERIRQIES  489 (509)
T ss_pred             HHHHHHHH
Confidence            99998854

>PF13518 HTH_28: Helix-turn-helix domain

Probab=91.82  E-value=0.37  Score=35.95  Aligned_cols=27  Identities=26%  Similarity=0.382  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      ++.|+.+||..+|||+.+|+++..+-.
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~~y~   37 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIKRYR   37 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            456999999999999999998876644

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

Probab=91.46  E-value=5.9  Score=40.31  Aligned_cols=147  Identities=20%  Similarity=0.207  Sum_probs=81.1

Q ss_pred             HHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhhcHHHHHHHHH
Q 009567          219 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  298 (532)
Q Consensus       219 ~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~g~~Are~LI~  298 (532)
                      .+..||++-.  +.--+.--.+++.+      +..+..+|+..+|++||..|.|+..|++.+++...+..+.        
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            4567888877  11122333444444      4457788999999999999999999999887754433322        


Q ss_pred             HHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHH
Q 009567          299 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  378 (532)
Q Consensus       299 ~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~  378 (532)
                        .....++--.....+.+  +            +   +...+..+..+-.|-..+.+..++.      .+|..-...+ 
T Consensus       152 --~~~~~sld~~~~~~~d~--~------------~---~~~~~~~~~~~~~~~~~~~l~~ai~------~L~EREk~Vl-  205 (247)
T COG1191         152 --GSQLLSLDEDVLKDDDD--D------------V---DDQIENPDDGVEKEELLEILKEAIE------PLPEREKLVL-  205 (247)
T ss_pred             --cccccchhhhhcccccc--c------------h---hhccccchhHHHHHHHHHHHHHHHH------ccCHHHHHHH-
Confidence              11222222211111111  0            0   1112233444555555566665553      2232111111 


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          379 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF  416 (532)
Q Consensus       379 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~  416 (532)
                               .-...-+-|..|||+.+|||..+|..+..
T Consensus       206 ---------~l~y~eelt~kEI~~~LgISes~VSql~k  234 (247)
T COG1191         206 ---------VLRYKEELTQKEIAEVLGISESRVSRLHK  234 (247)
T ss_pred             ---------HHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence                     01112256789999999999999987754

>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=91.43  E-value=0.39  Score=37.90  Aligned_cols=26  Identities=19%  Similarity=0.331  Sum_probs=24.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      +|++..|||+.||+++.+|.....+-
T Consensus        12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   12 QGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            89999999999999999999988763

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>smart00351 PAX Paired Box domain

Probab=90.78  E-value=0.62  Score=42.17  Aligned_cols=42  Identities=14%  Similarity=0.051  Sum_probs=32.6

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  513 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk  513 (532)
                      ++..+|.=|...|-    ++.|..+||+.||||+.+|..+.++...
T Consensus        18 ~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~~   59 (125)
T smart00351       18 LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYYE   59 (125)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45555555555554    6889999999999999999999888643

>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=90.70  E-value=0.47  Score=37.82  Aligned_cols=26  Identities=23%  Similarity=0.468  Sum_probs=23.1

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          485 GKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       485 ~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      +..+++.+||+.||||..+||....+
T Consensus        20 ~g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   20 NGKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence            36899999999999999999987654

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 [].

>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=90.67  E-value=0.32  Score=37.57  Aligned_cols=40  Identities=20%  Similarity=0.305  Sum_probs=26.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|+..|+.=|.-+|-    .|.+..+||..|||++++|+.|...
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            456666555555554    6779999999999999999998865

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.

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=90.56  E-value=6.5  Score=42.94  Aligned_cols=37  Identities=22%  Similarity=0.399  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567          379 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI  415 (532)
Q Consensus       379 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll  415 (532)
                      .+.+.+..+..++|++||.+|.|..+|+++..++..+
T Consensus       112 ~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l  148 (415)
T PRK07598        112 RLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL  148 (415)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence            3455667888999999999999988887766666554

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=90.50  E-value=0.92  Score=41.42  Aligned_cols=53  Identities=21%  Similarity=0.290  Sum_probs=42.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ..+..++-.|++.+-+|+....  ..+.++|..|||+.+|+++++|.    ||+++|=.
T Consensus        16 ~dvl~c~~GLs~~Dv~v~~~LL--~~~~~~tvdelae~lnr~rStv~----rsl~~L~~   68 (126)
T COG3355          16 EDVLKCVYGLSELDVEVYKALL--EENGPLTVDELAEILNRSRSTVY----RSLQNLLE   68 (126)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHH--hhcCCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence            3567788899999999987654  12379999999999999999994    77777744

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=90.33  E-value=0.59  Score=39.83  Aligned_cols=45  Identities=29%  Similarity=0.322  Sum_probs=33.7

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 009567          464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF--GLSKERVRQLESRA  511 (532)
Q Consensus       464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L--gISrerVRqie~rA  511 (532)
                      .+..||+..+++..+|.-   ....|+.|+|+.|  .||++.|..+..+.
T Consensus        34 ~~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl   80 (85)
T PF02650_consen   34 GLDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL   80 (85)
T ss_dssp             -GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence            358999999999999974   4789999999999  99999998765543

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=90.32  E-value=0.32  Score=56.52  Aligned_cols=45  Identities=18%  Similarity=0.100  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      -|+.||++|+.+.|     .|+|.+|||+.+.||-.||+....+...||.
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            39999999999999     7999999999999999999999999999984

>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=90.29  E-value=0.51  Score=35.91  Aligned_cols=38  Identities=21%  Similarity=0.438  Sum_probs=26.8

Q ss_pred             HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       471 rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      |++.||.+.+  ..+.+.|.+|||+.||||+.+|+..+..
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  2335699999999999999999865543

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 ....

>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=90.27  E-value=0.6  Score=36.08  Aligned_cols=43  Identities=23%  Similarity=0.287  Sum_probs=32.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|++.+..||..-+.-+ +.+.|..|||+.+|+++.+|.++.++
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            47888888888766522 23489999999999999999765544

...

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=89.51  E-value=0.48  Score=49.87  Aligned_cols=35  Identities=23%  Similarity=0.290  Sum_probs=30.7

Q ss_pred             HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567          475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  513 (532)
Q Consensus       475 VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk  513 (532)
                      +-.++|-    +++|..|||+.||||+.+|+..+.+|.+
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            4557776    9999999999999999999988888865

>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=89.28  E-value=0.92  Score=33.74  Aligned_cols=37  Identities=27%  Similarity=0.390  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      |.-..|+.+-..    .+++..||++.+|+|+.+|++....
T Consensus         2 ~~R~~Il~~L~~----~~~~~~el~~~l~~s~~~vs~hL~~   38 (47)
T PF01022_consen    2 PTRLRILKLLSE----GPLTVSELAEELGLSQSTVSHHLKK   38 (47)
T ss_dssp             HHHHHHHHHHTT----SSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHh----CCCchhhHHHhccccchHHHHHHHH
Confidence            444556655543    6899999999999999999876543

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 ....

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=89.25  E-value=18  Score=37.79  Aligned_cols=178  Identities=13%  Similarity=0.148  Sum_probs=92.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhH
Q 009567          294 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  373 (532)
Q Consensus       294 e~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~  373 (532)
                      ++-+...+..+..++.+.   ++  .+-+.|....+++.+.....-+|.....++.-.|.-+++    .           
T Consensus       119 er~l~~a~~~I~~~~~~L---~L--p~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR----~-----------  178 (310)
T PRK00423        119 ERNLAFALSELDRIASQL---GL--PRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR----R-----------  178 (310)
T ss_pred             hHHHHHHHHHHHHHHHHc---CC--CHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH----H-----------
Confidence            344444556666666655   23  356777777777777666777887776666655544432    1           


Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh-hhcccCCCCChhHHH
Q 009567          374 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ-EITADTGVEIPDISV  452 (532)
Q Consensus       374 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~-d~i~d~~~~~pee~~  452 (532)
                                       .+-+-|..||+..++++..++..........+.++.+..  +...+. .+...-..  +....
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                             223456788888888888888665443333233322221  111111 11111111  11111


Q ss_pred             HHHHHHHHHHHHHh-cC----CHHH--HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          453 QKQLMRQHVRNLLT-LL----NPKE--RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       453 ~~~~l~~~L~~~L~-~L----~~rE--R~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                      ..  ....+..+.+ .|    +|.-  --+|.+-.-+ .|.+.|++|||...|||..+|++..+.-.+.|
T Consensus       238 ~~--A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~-~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l  304 (310)
T PRK00423        238 KK--AIEILQKAKEKGLTSGKGPTGLAAAAIYIASLL-LGERRTQREVAEVAGVTEVTVRNRYKELAEKL  304 (310)
T ss_pred             HH--HHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHH-hCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence            11  1112222221 11    1211  1112221111 24889999999999999999997776666554

>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=88.91  E-value=0.69  Score=36.62  Aligned_cols=46  Identities=22%  Similarity=0.407  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       468 L~~rER~VL~LRyGL~-~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      |++....-|...|.|. ++.+-+..+||+.||||+.+|.    .++++|.+
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt----~ml~~L~~   48 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVT----EMLKRLAE   48 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHH----HHHHHHHH
Confidence            5555556666666554 5688999999999999999996    45556644

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 ....

>PHA02591 hypothetical protein; Provisional

Probab=88.68  E-value=0.87  Score=38.04  Aligned_cols=24  Identities=21%  Similarity=0.436  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .|+|.++||+.||+|.++||++..
T Consensus        58 qGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         58 KGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHh
Confidence            689999999999999999999865

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=88.66  E-value=0.64  Score=44.04  Aligned_cols=50  Identities=14%  Similarity=0.050  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS-----KERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgIS-----rerVRqie~rALkKLR~  517 (532)
                      .|+++|.+|+.+..- +.|.++|.+||++.++.+     ..+|+.+..+.++||..
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            599999999988763 345679999999999986     78999999999999964

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=88.51  E-value=3.4  Score=41.85  Aligned_cols=34  Identities=26%  Similarity=0.423  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567          251 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  284 (532)
Q Consensus       251 le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~  284 (532)
                      +......|...+|++||..|.|+..|++.+.+..
T Consensus       112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~  145 (257)
T PRK05911        112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSG  145 (257)
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence            3345566778889999999999999999877743

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=88.21  E-value=1.3  Score=44.68  Aligned_cols=35  Identities=29%  Similarity=0.497  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  284 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~  284 (532)
                      ++.+...+|...+|++||..|.|+..|++.+.+..
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~  148 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE  148 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence            44566778888999999999999999999877643

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=87.74  E-value=0.79  Score=43.95  Aligned_cols=50  Identities=18%  Similarity=0.120  Sum_probs=44.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR~  517 (532)
                      .|+++|++|+.+... +.|++.|.++|++.+.     ++..+|+....+.++||..
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

>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=87.71  E-value=1.8  Score=33.80  Aligned_cols=37  Identities=27%  Similarity=0.373  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      |.-+.||.+-.   .+.++|..|||+.+|++..+|++.+.
T Consensus        10 p~R~~Il~~L~---~~~~~t~~ela~~l~~~~~t~s~hL~   46 (61)
T PF12840_consen   10 PTRLRILRLLA---SNGPMTVSELAEELGISQSTVSYHLK   46 (61)
T ss_dssp             HHHHHHHHHHH---HCSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHh---cCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            66666776651   13899999999999999999976543

...

>cd00131 PAX Paired Box domain

Probab=87.46  E-value=1.5  Score=39.98  Aligned_cols=41  Identities=12%  Similarity=0.017  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      |+...|.-|...|-    +++|..+||+.||||+.+|..+.++-.
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            44444444444454    789999999999999999998888754

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=87.45  E-value=1.9  Score=41.21  Aligned_cols=65  Identities=12%  Similarity=0.136  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHHHHHhhCCCCC---HhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHH
Q 009567          296 LINANLRLVVHVAKQYQGRGIS---LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  360 (532)
Q Consensus       296 LI~~nlrLV~sIAkrY~~~g~~---~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~i  360 (532)
                      +=.+-+..+..++++|.-+|..   -+|+|.+|.-..++.++.|||++...+-.|.+..+-++..+-|
T Consensus        42 ig~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI  109 (179)
T PHA02547         42 IGLAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRI  109 (179)
T ss_pred             HHHHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHH
Confidence            3344555666666666555555   4999999999999999999999987776676665555544444

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=87.23  E-value=9.1  Score=41.21  Aligned_cols=34  Identities=32%  Similarity=0.584  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  283 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~  283 (532)
                      ++.+....|...+|++||..|.|+..|++.+.+.
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            4556677888889999999999999999977764

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=87.18  E-value=2.3  Score=41.92  Aligned_cols=32  Identities=38%  Similarity=0.579  Sum_probs=26.3

Q ss_pred             HHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567          253 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  284 (532)
Q Consensus       253 ~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~  284 (532)
                      +....|...+|++||..|.|+..|++.+.+..
T Consensus       101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~  132 (231)
T TIGR02885       101 YMKEELSKELGREPTINELAEALGVSPEEIVM  132 (231)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence            45567777889999999999999999877643

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.

>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=86.97  E-value=1.1  Score=35.18  Aligned_cols=41  Identities=20%  Similarity=0.332  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      |++.|..||..-.  ..+.++|..+|++.+|+++.+|...+++
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            4666777766555  2458999999999999999999754443

>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=86.91  E-value=1.4  Score=36.93  Aligned_cols=42  Identities=24%  Similarity=0.400  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLSKERVRQLE  508 (532)
Q Consensus       467 ~L~~rER~VL~LRyG--L~~~e~~Tl~EIAe~LgISrerVRqie  508 (532)
                      .|++++++||...--  ...|++-.-++||+.+|+|..+||+..
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            388999999876432  346799999999999999999999764

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

>PRK05949 RNA polymerase sigma factor; Validated

Probab=86.88  E-value=9.7  Score=40.15  Aligned_cols=35  Identities=26%  Similarity=0.461  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  284 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~  284 (532)
                      ++.+....+...+|++||..|.|+..|++.+.+..
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            44556677778899999999999999999877644

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=86.79  E-value=8.7  Score=39.10  Aligned_cols=35  Identities=29%  Similarity=0.554  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  284 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~  284 (532)
                      ++.+...+|...+|++||..|.|+..|++.+.+..
T Consensus       128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~  162 (264)
T PRK07122        128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVE  162 (264)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34456677888899999999999999999877754

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=86.53  E-value=13  Score=37.67  Aligned_cols=35  Identities=29%  Similarity=0.532  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  284 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~  284 (532)
                      ++.+....|+..+|++||..+.|...|++.+.+..
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~  153 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS  153 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence            45566777888899999999999999998776643

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=86.45  E-value=1.6  Score=37.66  Aligned_cols=41  Identities=27%  Similarity=0.252  Sum_probs=31.6

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      |++.++.||....-   +...|..+||+.+|+|+.+|+....+-
T Consensus         1 ld~~D~~il~~L~~---~~~~~~~~la~~l~~s~~tv~~~l~~L   41 (108)
T smart00344        1 LDEIDRKILEELQK---DARISLAELAKKVGLSPSTVHNRVKRL   41 (108)
T ss_pred             CCHHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            46778888876543   247899999999999999998655443

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=86.43  E-value=1.2  Score=42.04  Aligned_cols=49  Identities=18%  Similarity=0.233  Sum_probs=41.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR  516 (532)
                      .|+++|.+|+.+..- +-|...|.++|++.+.     +|..+|+.+..+.++||.
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            599999999987652 3346679999999986     999999999999999985

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=86.33  E-value=17  Score=37.51  Aligned_cols=84  Identities=23%  Similarity=0.326  Sum_probs=45.9

Q ss_pred             CCCHHHHHHHhC--CCHHHHHHHHHhcCC--CcccCCCCCCCCCcchhh-hcccCCCCChhHHH--HHHHHHHHHHHHHh
Q 009567          394 SPDKEDLARRVG--ITVEKLERLIFITRM--PLSMQQPVWADQDTTFQE-ITADTGVEIPDISV--QKQLMRQHVRNLLT  466 (532)
Q Consensus       394 ~Pt~eEIA~~lg--is~e~v~~ll~~~~~--~iSLD~~v~~d~~~~l~d-~i~d~~~~~pee~~--~~~~l~~~L~~~L~  466 (532)
                      .+++++||+.++  ||.++|+..+.....  -+--+.    ++.-...+ .+.... +.+...+  ...++.+.-.++|+
T Consensus       137 ~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~----~g~y~~t~~~l~~~~-~~~~~avr~~h~q~l~lA~~al~  211 (271)
T TIGR02147       137 ADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE----DGFYKQTDKAVSTGD-EVIPLAVRQYQKQMIDLAKEALD  211 (271)
T ss_pred             CCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC----CCcEEeecceeecCC-ccchHHHHHHHHHHHHHHHHHHH
Confidence            567889999999  999999988764321  111111    11000011 111111 1222211  12233444567788


Q ss_pred             cCCHHHHHHHHHHhcc
Q 009567          467 LLNPKERCIVRLRFGI  482 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL  482 (532)
                      ..|+.+|.+=.+-+|+
T Consensus       212 ~~p~~eR~~S~lT~~i  227 (271)
T TIGR02147       212 ALPPSERDVSTVTFGI  227 (271)
T ss_pred             hCCccccccceeeEec
Confidence            9999999977776664

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.

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=85.84  E-value=1.9  Score=32.33  Aligned_cols=34  Identities=26%  Similarity=0.408  Sum_probs=26.8

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       473 R~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      ..|+.+..     +..|.++||+.+|||..+|+.+..+.
T Consensus        18 ~~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   18 QYILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            34555554     34699999999999999999988764

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

Probab=85.72  E-value=14  Score=38.21  Aligned_cols=35  Identities=26%  Similarity=0.496  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  284 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~  284 (532)
                      ++.+.+..+...+|++||..+.|...|++.+.+..
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~  196 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE  196 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            44556667778899999999999999999877753

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).

>PRK12423 LexA repressor; Provisional

Probab=85.62  E-value=1.5  Score=42.84  Aligned_cols=47  Identities=30%  Similarity=0.513  Sum_probs=35.6

Q ss_pred             cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyG--L~~~e~~Tl~EIAe~Lg-ISrerVRqie~rALkKLR~  517 (532)
                      .|++++++|+..---  ..+|-+-|..|||+.|| +|+.+|+    ++|++|++
T Consensus         3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~----~~l~~L~~   52 (202)
T PRK12423          3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVAR----KHVQALAE   52 (202)
T ss_pred             cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence            489999999886432  22344679999999999 5999998    46667766

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=85.26  E-value=11  Score=37.98  Aligned_cols=35  Identities=29%  Similarity=0.346  Sum_probs=28.2

Q ss_pred             HHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHH
Q 009567          252 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL  286 (532)
Q Consensus       252 e~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l  286 (532)
                      .+...++...+|++||.+|.|+..|++.+.+...+
T Consensus       123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~  157 (254)
T TIGR02850       123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL  157 (254)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34566777888999999999999999988775443

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.

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=85.25  E-value=0.66  Score=43.77  Aligned_cols=50  Identities=16%  Similarity=0.114  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEV-----GNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EI-----Ae~LgISrerVRqie~rALkKLR~  517 (532)
                      .|+++|.+|+.+... +-|+++|.++|     |..++++..+|+....+.++||..
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (226)
T TIGR02154       154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP  208 (226)
T ss_pred             EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence            599999999988764 33467888888     778999999999999999999963

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.

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=85.12  E-value=1.2  Score=42.06  Aligned_cols=49  Identities=16%  Similarity=0.180  Sum_probs=41.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR  516 (532)
                      .|+++|.+|+.+..- +.|..+|.++|++.+.     ++..+|+.+..+.++||.
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 3346699999999996     999999999999999985

>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=84.64  E-value=1.3  Score=38.01  Aligned_cols=41  Identities=22%  Similarity=0.327  Sum_probs=30.3

Q ss_pred             hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQ  506 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~---~e~~Tl~EIAe~LgISrerVRq  506 (532)
                      .-++|.|+.-|..|+-+-.   .+++|+.||++.+|+|..+|.+
T Consensus        25 dL~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR   68 (87)
T PF01371_consen   25 DLCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR   68 (87)
T ss_dssp             HHSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH
Confidence            3467777776666554322   1689999999999999999963

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 ....

>PF12728 HTH_17: Helix-turn-helix domain

Probab=84.36  E-value=1.1  Score=33.63  Aligned_cols=24  Identities=17%  Similarity=0.376  Sum_probs=21.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          488 KSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       488 ~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      +|.+|+|+.||||+.+|+++..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g   25 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQG   25 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            689999999999999999987643

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=84.32  E-value=1.4  Score=41.97  Aligned_cols=50  Identities=14%  Similarity=0.087  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEV--GNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EI--Ae~LgISrerVRqie~rALkKLR~  517 (532)
                      .|+++|.+||.+..- +.|..+|.++|  +..++++..+|+.+..+.++||..
T Consensus       156 ~Lt~~E~~il~~l~~-~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~  207 (227)
T TIGR03787       156 DLTVTEFWMVHALAK-HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA  207 (227)
T ss_pred             cCCHHHHHHHHHHHh-CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence            499999999988762 22355699999  888999999999999999999963

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.

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=84.29  E-value=4.1  Score=35.03  Aligned_cols=49  Identities=18%  Similarity=0.244  Sum_probs=37.0

Q ss_pred             HhcCCHHHHHHHHHH----hccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          465 LTLLNPKERCIVRLR----FGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       465 L~~L~~rER~VL~LR----yGL~-~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ...+++++..+|...    ||.. ...+.|..|||+.+|+++++|+    |++++|.+
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            467899999987743    3322 2378999999999999999996    66666654

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=84.28  E-value=1.9  Score=35.80  Aligned_cols=45  Identities=29%  Similarity=0.341  Sum_probs=29.9

Q ss_pred             HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH-----HHHHHHHHHhhcCc
Q 009567          475 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES-----RALYRLKQSLGGKA  523 (532)
Q Consensus       475 VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~-----rALkKLR~~l~~~~  523 (532)
                      |..++--    .++|..|+|+.+|+|+.+|+++++     -.+.+|...+..-+
T Consensus        23 i~~~~~~----~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG   72 (80)
T PF13744_consen   23 IRELREE----RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG   72 (80)
T ss_dssp             HHHHHHC----CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred             HHHHHHH----cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence            4444444    789999999999999999999985     24666666555443

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=84.21  E-value=2.3  Score=34.38  Aligned_cols=41  Identities=22%  Similarity=0.384  Sum_probs=27.1

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       472 ER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +..||.+... .++++.|..|||+.+||++.+|++    .|.+|.+
T Consensus         8 ~~~IL~~L~~-~g~~~~ta~eLa~~lgl~~~~v~r----~L~~L~~   48 (68)
T smart00550        8 EEKILEFLEN-SGDETSTALQLAKNLGLPKKEVNR----VLYSLEK   48 (68)
T ss_pred             HHHHHHHHHH-CCCCCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence            3444444332 122369999999999999999875    4555544

Helix-turn-helix-containing domain. Also known as Zab.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=84.08  E-value=13  Score=37.16  Aligned_cols=35  Identities=23%  Similarity=0.363  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHH
Q 009567          251 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  285 (532)
Q Consensus       251 le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~  285 (532)
                      +++....+...+|++|+..++|+..|++.+.+...
T Consensus       111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~  145 (251)
T PRK07670        111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT  145 (251)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHH
Confidence            34455667778899999999999999998777543

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=83.88  E-value=12  Score=39.34  Aligned_cols=34  Identities=26%  Similarity=0.522  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHH
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  283 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~  283 (532)
                      ++.+....+...+|++||..|.|++.|++.+.+.
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~  202 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR  202 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            4556777888889999999999999999876664

>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=83.87  E-value=1.4  Score=33.38  Aligned_cols=32  Identities=38%  Similarity=0.516  Sum_probs=23.3

Q ss_pred             HHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          478 LRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       478 LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      +.+.-..+.++|+.|||+.+|+++.+|..+..
T Consensus         9 L~~l~~~~~~~t~~eia~~~gl~~stv~r~L~   40 (52)
T PF09339_consen    9 LEALAESGGPLTLSEIARALGLPKSTVHRLLQ   40 (52)
T ss_dssp             HHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            33433455778999999999999999976543

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.

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=83.85  E-value=3.4  Score=35.12  Aligned_cols=40  Identities=20%  Similarity=0.256  Sum_probs=28.0

Q ss_pred             CCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHHHhhc-Cchhhhhh
Q 009567          486 KPKSLSEVGNIFG-LSKERVRQLESRALYRLKQSLGG-KASYGYAD  529 (532)
Q Consensus       486 e~~Tl~EIAe~Lg-ISrerVRqie~rALkKLR~~l~~-~~l~~yld  529 (532)
                      -++|+.+||+.|| .+.++|.....    ++.+.+.. ..++..++
T Consensus        43 ~~~s~~~Ig~~fg~r~hStV~~a~~----ri~~~~~~d~~~~~~v~   84 (90)
T cd06571          43 TGLSLPEIGRAFGGRDHSTVLHAVR----KIEELLEEDPELKEDVE   84 (90)
T ss_pred             hCCCHHHHHHHhCCCCHhHHHHHHH----HHHHHHHhCHHHHHHHH
Confidence            4799999999999 99999975554    44444433 34444443

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>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=83.80  E-value=1.1  Score=35.76  Aligned_cols=44  Identities=25%  Similarity=0.349  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .|++.|..|+..-.   ...+.|..|||+.+|+++.+|+    +++++|.+
T Consensus         5 gLs~~E~~vy~~Ll---~~~~~t~~eIa~~l~i~~~~v~----~~L~~L~~   48 (68)
T PF01978_consen    5 GLSENEAKVYLALL---KNGPATAEEIAEELGISRSTVY----RALKSLEE   48 (68)
T ss_dssp             CHHHHHHHHHHHHH---HHCHEEHHHHHHHHTSSHHHHH----HHHHHHHH
T ss_pred             CcCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            46777888776543   1268999999999999999996    55555544

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.

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=83.69  E-value=1.1  Score=33.64  Aligned_cols=22  Identities=18%  Similarity=0.356  Sum_probs=19.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q 009567          489 SLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       489 Tl~EIAe~LgISrerVRqie~r  510 (532)
                      |++|||+..|||..+|+..++.
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            7899999999999999987764

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 ....

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=83.56  E-value=2.1  Score=39.74  Aligned_cols=27  Identities=26%  Similarity=0.208  Sum_probs=24.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      +|+|.+|||++||||.++|..+.++-.
T Consensus        20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415          20 EGLSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence            799999999999999999999888754

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=83.51  E-value=5.7  Score=36.95  Aligned_cols=64  Identities=19%  Similarity=0.326  Sum_probs=36.8

Q ss_pred             HHHHHhcCCHHHHHHHHHH----hcccCCCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHHHhhcCch
Q 009567          461 VRNLLTLLNPKERCIVRLR----FGIEDGKPKSLSEVGNIFGLSKERVRQLES--RALYRLKQSLGGKAS  524 (532)
Q Consensus       461 L~~~L~~L~~rER~VL~LR----yGL~~~e~~Tl~EIAe~LgISrerVRqie~--rALkKLR~~l~~~~l  524 (532)
                      +..+=..|++.|+....+.    |...+|+.+|+.|||+.+||++.++-++.+  +++-.....+....+
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            4445578999988843332    222245789999999999999999999884  444444444443333

>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=83.38  E-value=2.2  Score=32.64  Aligned_cols=41  Identities=24%  Similarity=0.416  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      |+..|-.||..-+-   ..+.|..|||+.+|+++.+|.++.++-
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            45666666666553   257999999999999999997665543

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 ....

>TIGR00498 lexA SOS regulatory protein LexA

Probab=83.07  E-value=2  Score=41.58  Aligned_cols=48  Identities=21%  Similarity=0.337  Sum_probs=36.3

Q ss_pred             hcCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCC-HHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLS-KERVRQLESRALYRLKQ  517 (532)
Q Consensus       466 ~~L~~rER~VL~LRyG--L~~~e~~Tl~EIAe~LgIS-rerVRqie~rALkKLR~  517 (532)
                      ..|+++|++||.+-.-  ..++.+.|.+|||+.+|++ +.+|+.    .+++|.+
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~----~l~~L~~   52 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEE----HLKALER   52 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence            3589999999987652  2245678999999999998 999974    4455544

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.

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=82.97  E-value=1.2  Score=43.47  Aligned_cols=39  Identities=18%  Similarity=0.232  Sum_probs=28.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .|+++  +|+.+.-  .+..++|.+|||+.||||+.||+.+..
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  5665543  122479999999999999999998875

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=82.90  E-value=2.1  Score=32.31  Aligned_cols=30  Identities=37%  Similarity=0.493  Sum_probs=24.0

Q ss_pred             CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          484 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       484 ~~e~~-Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .|... |..|||+.+|+|+.+|+    +++++|.+
T Consensus        16 ~~~~l~s~~~la~~~~vs~~tv~----~~l~~L~~   46 (60)
T smart00345       16 PGDKLPSERELAAQLGVSRTTVR----EALSRLEA   46 (60)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            34556 99999999999999997    56666655

>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=82.87  E-value=3.9  Score=32.94  Aligned_cols=40  Identities=28%  Similarity=0.472  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCC-HHHHHHHHHh
Q 009567          378 SKVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIFI  417 (532)
Q Consensus       378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis-~e~v~~ll~~  417 (532)
                      .++-.....+..+.|..||..|||+.+|++ ...|...+..
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            344455566777899999999999999997 8888877654

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.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=82.67  E-value=2.7  Score=39.09  Aligned_cols=41  Identities=15%  Similarity=0.261  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|++.++.||..---   +...|+.|||+.+|+|+.+|+.+..+
T Consensus         6 ~lD~~D~~Il~~Lq~---d~R~s~~eiA~~lglS~~tV~~Ri~r   46 (153)
T PRK11179          6 QIDNLDRGILEALME---NARTPYAELAKQFGVSPGTIHVRVEK   46 (153)
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            377888888877543   25789999999999999999865543

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=82.32  E-value=14  Score=33.06  Aligned_cols=28  Identities=32%  Similarity=0.432  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .+.|+.|||+.||||..+|.    ++|++|.-
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    56666643

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 [].

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=82.31  E-value=3.3  Score=31.84  Aligned_cols=39  Identities=21%  Similarity=0.242  Sum_probs=25.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .|++.|+--|....-    .++++.|||..+|-|+..|+..++
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            467777766666665    689999999999999999987754

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=82.18  E-value=29  Score=35.82  Aligned_cols=26  Identities=19%  Similarity=0.332  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhc
Q 009567          393 HSPDKEDLARRVGITVEKLERLIFIT  418 (532)
Q Consensus       393 r~Pt~eEIA~~lgis~e~v~~ll~~~  418 (532)
                      ..-|.+|||+.+|+|.++|..+....
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~A  269 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEARA  269 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            45689999999999999999886543

>TIGR01764 excise DNA binding domain, excisionase family

Probab=82.13  E-value=1.6  Score=31.62  Aligned_cols=24  Identities=25%  Similarity=0.407  Sum_probs=21.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          488 KSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       488 ~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      +|.+|+|+.||||+.+|+++.+..
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).

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=81.85  E-value=1.7  Score=31.25  Aligned_cols=25  Identities=16%  Similarity=0.300  Sum_probs=22.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          488 KSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       488 ~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      +|..|+|+.+|||+.+|+++.....
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~   25 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGK   25 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence            5889999999999999999988764

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.

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=81.80  E-value=2.5  Score=41.01  Aligned_cols=34  Identities=26%  Similarity=0.293  Sum_probs=27.5

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          472 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       472 ER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      ++.|..++-     .++|..+||+.||||+.+|.++.+.
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            345666644     6899999999999999999988763

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=81.79  E-value=2.8  Score=34.55  Aligned_cols=51  Identities=20%  Similarity=0.251  Sum_probs=34.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhc-ccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLE  508 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyG-L~~~e~~Tl~EIAe~LgISrerVRqie  508 (532)
                      ...|......|++.|+.|..+..- .+.-..+|..|||+..|||..+|.+..
T Consensus         4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~   55 (77)
T PF01418_consen    4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFC   55 (77)
T ss_dssp             HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHH
T ss_pred             HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHH
Confidence            456777789999999998865432 011257999999999999999996543

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>CHL00148 orf27 Ycf27; Reviewed

Probab=81.75  E-value=2  Score=41.16  Aligned_cols=50  Identities=18%  Similarity=0.115  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-------GLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L-------gISrerVRqie~rALkKLR~  517 (532)
                      .|+++|.+|+.+... +.|+++|.+||++.+       +++..+|+.+..+.++||..
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            499999999987652 344789999999999       48999999999999999964

>PRK00215 LexA repressor; Validated

Probab=81.64  E-value=2.7  Score=40.82  Aligned_cols=44  Identities=25%  Similarity=0.320  Sum_probs=33.7

Q ss_pred             cCCHHHHHHHHHHh--cccCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRF--GIEDGKPKSLSEVGNIFGL-SKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRy--GL~~~e~~Tl~EIAe~LgI-SrerVRqie~r  510 (532)
                      .|+++|++||.+-.  ....+.+.|+.|||+.+|+ ++.+|..++.+
T Consensus         1 ~lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~   47 (205)
T PRK00215          1 MLTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA   47 (205)
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            37889999987543  2234578899999999999 99999755443

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=81.40  E-value=3.6  Score=35.12  Aligned_cols=44  Identities=18%  Similarity=0.209  Sum_probs=36.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      ..|+|.-|..|..+..   .++++..++|+.||||+.+++++..|=.
T Consensus         7 A~Lt~~gR~~lv~~vv---~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr   50 (85)
T PF13011_consen    7 ARLTPRGRLRLVRRVV---EQGWPVAHAAAEFGVSRRTAYKWLARYR   50 (85)
T ss_pred             CCCCHHHHHHHHHHHH---HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3689999988888774   1589999999999999999999887744

>PRK11564 stationary phase inducible protein CsiE; Provisional

Probab=80.68  E-value=4  Score=44.18  Aligned_cols=51  Identities=16%  Similarity=0.203  Sum_probs=42.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .+++.||..+.+.+.|...++.|+.++|+.|+||++||.+-+++..+.|.+
T Consensus        10 ~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~   60 (426)
T PRK11564         10 VLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR   60 (426)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            478889888888777777789999999999999999999877766666655

>PF13551 HTH_29: Winged helix-turn helix

Probab=80.37  E-value=3.2  Score=35.59  Aligned_cols=26  Identities=19%  Similarity=0.349  Sum_probs=23.1

Q ss_pred             CCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 009567          486 KPK-SLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       486 e~~-Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      ++. |..+||+.+|+|+.+|.++.++-
T Consensus        10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~   36 (112)
T PF13551_consen   10 EGVSTIAEIARRLGISRRTVYRWLKRY   36 (112)
T ss_pred             cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            677 69999999999999999988773

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	532
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		3e-45
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		3e-45
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		4e-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		6e-43
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		3e-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		2e-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		6e-11
4g94_A	62	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		8e-11
1rp3_A	239	Cocrystal Structure Of The Flagellar SigmaANTI-Sigm		6e-07
1rio_H	73	Structure Of Bacteriophage Lambda Ci-Ntd In Complex		8e-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 = 3e-45,   Method: Compositional matrix adjust.
 Identities = 106/320 (33%), Positives = 188/320 (58%), Gaps = 23/320 (7%)
Query: 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 273
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 274 AIGLS------------CRDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISL 318
            +G +             ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S 
Sbjct: 59  ILGTARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSF 118
Query: 319 HDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 378
            DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +RTIR+P ++   ++
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETIN 178
Query: 379 KVLEAKRLYIQEGNHSPDKEDLARRVGIT--VEKLERLIFITRMPLSMQQPVWADQDTTF 436
           K+    R   QE    P  E++A  +G     +++E  + I + P+S++ P+  ++D+ +
Sbjct: 179 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFY 238
Query: 437 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 496
            +   D  +  P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  
Sbjct: 239 GDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAY 298
Query: 497 FGLSKERVRQLESRALYRLK 516
           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 (454), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 84/242 (34%), Positives = 155/242 (64%), Gaps = 4/242 (1%)
Query: 279 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 334
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 335 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 394
           KF+ + G +F++YA WW+RQ I ++I   +RTIR+P ++   ++K+    R  +QE    
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 395 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 454
           P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+D+   +   DT +E+P  S   
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT 537
Query: 455 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 514
           + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +
Sbjct: 538 ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 597
Query: 515 LK 516
           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 = 4e-45,   Method: Compositional matrix adjust.
 Identities = 84/242 (34%), Positives = 155/242 (64%), Gaps = 4/242 (1%)
Query: 279 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 334
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 335 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 394
           KF+ + G +F++YA WW+RQ I ++I   +RTIR+P ++   ++K+    R  +QE    
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 395 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 454
           P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+D+   +   DT +E+P  S   
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT 537
Query: 455 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 514
           + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +
Sbjct: 538 ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRK 597
Query: 515 LK 516
           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 (443), Expect = 6e-44,   Method: Compositional matrix adjust.
 Identities = 106/335 (31%), Positives = 188/335 (56%), Gaps = 38/335 (11%)
Query: 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 273
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 93  SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 149
Query: 274 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 303
            +G +                            ++LK  LH    G ++R+ LI ANLRL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 304 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 363
           VV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 364 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI--TVEKLERLIFITRMP 421
           +RTIR+P ++   ++K+    R   QE    P  E++A  +G     +++E  + I + P
Sbjct: 270 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 329
Query: 422 LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFG 481
           +S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+ L+ +E  +++LR G
Sbjct: 330 VSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKG 389
Query: 482 IEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           + 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: 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 348
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 406
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 407 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 466
             +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
            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: 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 348
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 406
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 407 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 466
             +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
            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 = 6e-43,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 348
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 349 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 406
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 407 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 466
             +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 379
Query: 467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
            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 =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 60/150 (40%), Positives = 97/150 (64%), Gaps = 5/150 (3%)
Query: 280 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 336
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 92  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 151
Query: 337 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 396
           + +   +F++YA WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P 
Sbjct: 152 EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPS 211
Query: 397 KEDLARRVGIT--VEKLERLIFITRMPLSM 424
            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: 217 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 273
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 6   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 62
Query: 274 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 303
            +G +                            ++LK  LH    G ++R+ LI ANLRL
Sbjct: 63  ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 122
Query: 304 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 363
           VV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   
Sbjct: 123 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 182
Query: 364 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGIT--VEKLERLIFITRMP 421
           +RTIR+P ++   ++K+    R   QE    P  E++A  +G     +++E  + I + P
Sbjct: 183 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 242
Query: 422 LSM 424
           +S+
Sbjct: 243 VSL 245

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 97.8 bits (242), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 45/89 (50%), Positives = 65/89 (73%), Gaps = 3/89 (3%)
Query: 280 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 336
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 91  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 337 KPQAGCRFASYAYWWVRQTIRKAIFQHSR 365
           + + 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: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
           ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 352 VRQTIRKAIFQHSR 365
           +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 = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 117/229 (51%), Gaps = 18/229 (7%)
Query: 292 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 351
           +R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF      +F++YA   
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 352 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 411
           +   I++   +   T+++  ++  + +K+ +AK    +    +P   ++A  +GI+ E +
Sbjct: 89  IIGEIQR-FLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 412 ERLIFITRMPLSMQQPVW---ADQDTTFQEIT-ADTGVEIPDISVQKQLMRQHVRNLLTL 467
                  R+P S+ + V+    D  T   +I  AD       I+++K +           
Sbjct: 148 VLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASWFDKIALKKAIEE--------- 198
Query: 468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           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: 454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 513
           + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +AL 
Sbjct: 5   RMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALR 64
Query: 514 RLKQ 517
           +L+ 
Sbjct: 65  KLRH 68

>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 73

Iteration: 1
 Score = 65.9 bits (159), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 51/73 (69%)
Query: 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           M++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 517 QSLGGKASYGYAD 529
                K    + D
Sbjct: 61  HPSRSKRLKDFMD 73

>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 62

Iteration: 1
 Score = 65.1 bits (157), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 48/61 (78%)
Query: 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           M++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 517 Q 517
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 = 65/253 (25%), Positives = 120/253 (47%), Gaps = 41/253 (16%)
Query: 287 HSGNSSREKLINANLRLVVHVA---KQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 343
           +S    RE+LI   L LV  +A   K++    + + DL+  G +GL+K+V+    +   R
Sbjct: 8   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67
Query: 344 FASYAYWWVRQTIRKAIFQHSRTI------------RLPENIYTLLSKVLEAKRLYIQEG 391
               A  +++  I+ AI+ + R++            R+ E +  L  K+           
Sbjct: 68  ----AEAYIKLRIKGAIYDYLRSLDFGSRQVREKERRIKEVVEKLKEKL----------- 112
Query: 392 NHSPDKEDLARRVGITVEKLERLIFITRMP--LSMQQPVWADQDTTFQE-ITADTGVEIP 448
              P  E++A+ +GI+ E+L + +        LS+++ V+ D    + E I + T VE  
Sbjct: 113 GREPTDEEVAKELGISTEELFKTLDKINFSYILSLEE-VFRDFARDYSELIPSSTNVE-- 169
Query: 449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 508
              V K+ + + V+  ++ L  +E+ +++L F  E+   K   EV  I   S  RV QL+
Sbjct: 170 -EEVIKRELTEKVKEAVSKLPEREKLVIQLIF-YEELPAK---EVAKILETSVSRVSQLK 224
Query: 509 SRALYRLKQSLGG 521
           ++AL RL++ L  
Sbjct: 225 AKALERLREMLSN 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 = 8e-07,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 40/52 (76%)
Query: 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           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: 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           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: 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 2   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 61
Query: 511 ALYRLKQ 517
           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 = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 3   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62
Query: 511 ALYRLKQ 517
           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 = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 40/53 (75%)
Query: 465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           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 = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 38/55 (69%)
Query: 463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           ++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	532
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	1e-64
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	1e-63
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	1e-62
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	4e-57
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	8e-46
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	4e-38
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	3e-22
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	6e-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	2e-14
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	3e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-13
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	7e-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 =  215 bits (549), Expect = 1e-64
 Identities = 101/339 (29%), Positives = 180/339 (53%), Gaps = 32/339 (9%)

Query: 211 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQ---------------------DLI 249
                 +DP+R +L       LLT +EE EL  +++                     +++
Sbjct: 72  IPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVV 131

Query: 250 RLEKEKSKL--QSQFGREPTLIEWAKAIGLSCRDLKSEL-------HSGNSSREKLINAN 300
           R +   S         +E    +  + I    + L  E          G ++R+ LI AN
Sbjct: 132 RAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEAN 191

Query: 301 LRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 360
           LRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI
Sbjct: 192 LRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAI 251

Query: 361 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR--VGITVEKLERLIFIT 418
              +RTIR+P ++   ++K+    R   QE    P  E++A     G   +++E  + I 
Sbjct: 252 ADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIA 311

Query: 419 RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRL 478
           + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+ L+ +E  +++L
Sbjct: 312 QEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKL 371

Query: 479 RFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           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 =  213 bits (543), Expect = 1e-63
 Identities = 92/294 (31%), Positives = 163/294 (55%), Gaps = 6/294 (2%)

Query: 226 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 285
           G +   +        L       I   KEK   ++    +  L    K +    +     
Sbjct: 136 GLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKEL----KRYLHI 191

Query: 286 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 345
              G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F+
Sbjct: 192 AREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 251

Query: 346 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR-- 403
           +YA WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A    
Sbjct: 252 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMG 311

Query: 404 VGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRN 463
            G   +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +  
Sbjct: 312 PGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEK 371

Query: 464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
            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 =  215 bits (548), Expect = 1e-62
 Identities = 115/504 (22%), Positives = 226/504 (44%), Gaps = 37/504 (7%)

Query: 37  PLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM 96
            LL    E   ++   D  N    +     +    L +    +E +     DL       
Sbjct: 109 ELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDP 168

Query: 97  KRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTD 156
              ED + + T        E+  D E  D      +           + +P+L   +F +
Sbjct: 169 NAEEDLAPTATHVGSELSQEDLDDDEDED-----EEDGDDDSADDDNSIDPELAREKFAE 223

Query: 157 ISLTSSLGYPLEEVKQFSQPRFLERRSK----------KRKVSKPQVTNHETYNSRKASV 206
           +     +     + K  S     E   K            K     V +      R  + 
Sbjct: 224 LRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQ 283

Query: 207 KKKLSE------GFDRNDPLRLFL-------WGPETRKLLTADEEFELIAQIQDLIRLEK 253
           ++ + +         + + + LF        W      +     E  L    +++ R  +
Sbjct: 284 ERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEK-LHDVSEEVHRALQ 342

Query: 254 EKSKLQSQFGREPT-LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQ 312
           +  +++ + G     + +  + + +     +        ++++++ ANLRLV+ +AK+Y 
Sbjct: 343 KLQQIEEETGLTIEQVKDINRRMSIGEAKARR-------AKKEMVEANLRLVISIAKKYT 395

Query: 313 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 372
            RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I   +RTIR+P +
Sbjct: 396 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 455

Query: 373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 432
           +   ++K+    R  +QE    P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+
Sbjct: 456 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDE 515

Query: 433 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSE 492
           D+   +   DT +E+P  S   + +R    ++L  L  +E  ++R+RFGI+     +L E
Sbjct: 516 DSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEE 575

Query: 493 VGNIFGLSKERVRQLESRALYRLK 516
           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 =  189 bits (483), Expect = 4e-57
 Identities = 59/238 (24%), Positives = 117/238 (49%), Gaps = 11/238 (4%)

Query: 280 RDLKSELHSGNSS-REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 338
           ++L      G+   R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF  
Sbjct: 16  KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDL 75

Query: 339 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 398
               +F++YA   +   I++ +     T+++  ++  + +K+ +AK    +    +P   
Sbjct: 76  SYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVT 134

Query: 399 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 458
           ++A  +GI+ E +       R+P S+ + V+ +          D    I D        +
Sbjct: 135 EIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPIT--LLDQ---IADADEASWFDK 189

Query: 459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
             ++  +  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 =  159 bits (405), Expect = 8e-46
 Identities = 53/238 (22%), Positives = 108/238 (45%), Gaps = 15/238 (6%)

Query: 287 HSGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 343
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 8   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67

Query: 344 FASYAYWWVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLAR 402
             +Y    ++     AI+ + R++      +     ++ E      ++    P  E++A+
Sbjct: 68  AEAYIKLRIKG----AIYDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAK 123

Query: 403 RVGITVEKLERLIFITRMPLSMQ-QPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHV 461
            +GI+ E+L + +        +  + V+ D    + E+   +     +  V K+ + + V
Sbjct: 124 ELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSS--TNVEEEVIKRELTEKV 181

Query: 462 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 519
           +  ++ 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 =  139 bits (352), Expect = 4e-38
 Identities = 71/242 (29%), Positives = 122/242 (50%), Gaps = 36/242 (14%)

Query: 217 NDPLRLFLWGPETRK--LLTADEEFELIAQI------------------QDLIRLEKEKS 256
           +DP+R +L   E  +  LLT +EE +L  ++                  + +  + + K 
Sbjct: 6   SDPVRQYLH--EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKI 63

Query: 257 KLQSQFGREPTLIEWAKAIGLS------------CRDLKSELHSGNSSREKLINANLRLV 304
              ++  + P L E      +              +        G ++R+ LI ANLRLV
Sbjct: 64  LGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLV 123

Query: 305 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 364
           V +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +
Sbjct: 124 VSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQA 183

Query: 365 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR--VGITVEKLERLIFITRMPL 422
           RTIR+P ++   ++K+    R   QE    P  E++A     G   +++E  + I + P+
Sbjct: 184 RTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV 243

Query: 423 SM 424
           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 = 97.3 bits (242), Expect = 3e-22
 Identities = 40/123 (32%), Positives = 69/123 (56%), Gaps = 10/123 (8%)

Query: 250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK-------LINANLR 302
           +L     ++     +   L +  +  GL+   +K      +    K       ++ ANLR
Sbjct: 220 KLHDVSEEVHRALQK---LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLR 276

Query: 303 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 362
           LV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I  
Sbjct: 277 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 336

Query: 363 HSR 365
            +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 = 74.7 bits (184), Expect = 6e-17
 Identities = 28/66 (42%), Positives = 48/66 (72%)

Query: 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510
              + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +
Sbjct: 2   EAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVK 61

Query: 511 ALYRLK 516
           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 = 73.6 bits (181), Expect = 2e-16
 Identities = 23/66 (34%), Positives = 42/66 (63%)

Query: 451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 510
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 3   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62

Query: 511 ALYRLK 516
           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 = 67.3 bits (165), Expect = 2e-14
 Identities = 21/54 (38%), Positives = 38/54 (70%)

Query: 463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           ++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 = 66.6 bits (163), Expect = 3e-14
 Identities = 22/59 (37%), Positives = 42/59 (71%)

Query: 459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           + +   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 = 71.0 bits (173), Expect = 4e-13
 Identities = 95/565 (16%), Positives = 175/565 (30%), Gaps = 152/565 (26%)

Query: 1   MHNEQSAPAVASVPTSSVARHFPTSVL---LQEQRDEYRPLLH-MFKEDKTSQATSDSRN 56
           ++N+            +V+R  P   L   L E R     L+  +    KT  A     +
Sbjct: 119 LYND-----NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLS 173

Query: 57  IETEAFF--------VEEKNSGD--LDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVS- 105
            + +           ++  NS +  L+ L Q L +Q    P+  + S      +    S 
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEML-QKLLYQID--PNWTSRSDHSSNIKLRIHSI 230

Query: 106 ---LTMQSLSNDTEES------V-DAEPFDAVALARKALSASKEAASLAENPKLNGAEFT 155
              L     S   E        V +A+ ++A  L+ K L  ++    + +   L+ A  T
Sbjct: 231 QAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK-QVTD--FLSAATTT 287

Query: 156 DISLT-SSLGYPLEEVKQ-FSQPRFLERRSKK--RKVSK--PQVTNHETYNSRKASVKKK 209
            ISL   S+    +EVK      ++L+ R +   R+V    P+           + + + 
Sbjct: 288 HISLDHHSMTLTPDEVKSLLL--KYLDCRPQDLPREVLTTNPRRL---------SIIAES 336

Query: 210 LSEGFDRNDPLRLFLWGPETRKL---LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 266
           + +G    D  +       T  +   L   E  E       L       + + +      
Sbjct: 337 IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS-AHIPTI----- 390

Query: 267 TL-IEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG 325
            L + W   I      + ++LH     +  L+           KQ +   IS+  +  E 
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLH-----KYSLVE----------KQPKESTISIPSIYLEL 435

Query: 326 SMGLMKS-------VEKFK-PQAGCRFA-------SYAYWWVRQTIRKAIFQHSRTIRLP 370
            + L          V+ +  P+              Y Y          I  H + I  P
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH--------IGHHLKNIEHP 487

Query: 371 ENIYTLLSKV------LEAK-RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLS 423
           E   TL   V      LE K R      N S    +        ++  +   +I      
Sbjct: 488 ER-MTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTL----QQLKFYKP--YIC----- 535

Query: 424 MQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIE 483
                  D D  ++ +       +  I      + +   NL+     K   ++R+    E
Sbjct: 536 -------DNDPKYERL-------VNAI---LDFLPKIEENLI---CSKYTDLLRIALMAE 575

Query: 484 DGKPKSLSEVGNIFGLSKERVRQLE 508
           D              + +E  +Q++
Sbjct: 576 DE------------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 = 54.1 bits (130), Expect = 7e-09
 Identities = 27/205 (13%), Positives = 69/205 (33%), Gaps = 49/205 (23%)

Query: 315 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 374
           G    DL+QEG +GL+K+++ +       F+S+A+  +R+ +  AI + +    +  N  
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDET-KSSFSSFAFLCIRREMISAIRKANTQKHMVLNEA 59

Query: 375 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 434
              + +LE    +  EG++  + +                                    
Sbjct: 60  LKTNAILEDSAYFDDEGHNINNYK------------------------------------ 83

Query: 435 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVG 494
                   +     +  + K+ + +  +      +  E+ ++        G   S  E+ 
Sbjct: 84  -------SSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLI---RG--YSYREIA 131

Query: 495 NIFGLSKERVRQLESRALYRLKQSL 519
            I   + + +     R   + ++ +
Sbjct: 132 TILSKNLKSIDNTIQRIRKKSEEWI 156

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	532
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	99.88
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	99.68
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.63
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.54
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.5
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.34
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	98.97
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	98.86
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.82
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.76
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.68
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.64
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.54
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.5
3c57_A	95	Two component transcriptional regulatory protein;	98.48
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.47
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.35
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.19
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	98.01
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.93
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.89
2q0o_A	236	Probable transcriptional activator protein TRAR; h	97.49
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	97.46
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	97.32
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	97.21
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.93
1yio_A	208	Response regulatory protein; transcription regulat	96.55
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.38
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.32
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.15
3c3w_A	225	Two component transcriptional regulatory protein;	96.05
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	95.36
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	94.9
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	94.05
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	93.55
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	93.49
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	93.29
2gwr_A	238	DNA-binding response regulator MTRA; two-component	93.26
2oqr_A	230	Sensory transduction protein REGX3; response regul	92.94
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	92.69
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	92.6
1ys7_A	233	Transcriptional regulatory protein PRRA; response	92.21
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	91.38
1u78_A	141	TC3 transposase, transposable element TC3 transpos	91.26
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	91.04
2hqr_A	223	Putative transcriptional regulator; phosporylation	91.04
3r0j_A	250	Possible two component system response transcript	90.89
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	90.8
3q9s_A	249	DNA-binding response regulator; DNA binding protei	90.62
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	89.88
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	89.43
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	88.99
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	88.76
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	88.59
3r0a_A	123	Putative transcriptional regulator; structural gen	88.43
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	87.79
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	87.41
3nqo_A	189	MARR-family transcriptional regulator; structural	87.39
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	87.16
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	86.83
1y0u_A	96	Arsenical resistance operon repressor, putative; s	86.57
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	86.15
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	86.0
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	85.99
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	85.79
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	85.74
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	85.72
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	85.61
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	85.21
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	85.11
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	85.07
3frw_A	107	Putative Trp repressor protein; structural genomic	85.02
2w25_A	150	Probable transcriptional regulatory protein; trans	84.88
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	84.66
1sfx_A	109	Conserved hypothetical protein AF2008; structural	84.65
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	84.62
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	84.61
2gxg_A	146	146AA long hypothetical transcriptional regulator;	84.42
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	84.36
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	84.11
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	83.95
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	83.65
2k27_A	159	Paired box protein PAX-8; paired domain, solution	82.95
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	82.79
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	82.53
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	82.52
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	82.46
2nnn_A	140	Probable transcriptional regulator; structural gen	82.29
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	82.22
3jth_A	98	Transcription activator HLYU; transcription factor	81.93
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	81.89
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	81.77
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	81.75
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	81.69
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	81.58
3sqn_A	485	Conserved domain protein; structural genomics, PSI	81.56
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	81.48
1ku9_A	152	Hypothetical protein MJ223; putative transcription	81.45
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	81.43
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	81.43
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	81.35
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	81.25
3mn2_A	108	Probable ARAC family transcriptional regulator; st	81.24
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	80.85
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	80.7
3iwf_A	107	Transcription regulator RPIR family; transcription	80.69
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	80.6
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	80.53

>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=3.1e-55  Score=467.94  Aligned_cols=315  Identities=31%  Similarity=0.569  Sum_probs=284.6

Q ss_pred             CCChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHhhhCCCCcHHHHHH---
Q 009567          215 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAK---  273 (532)
Q Consensus       215 ~~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~------------------~l~~~~g~~pt~~ewA~---  273 (532)
                      ...|+++.||++|+++|+||++||++|+++|+.++.++....                  ......|+.|+..+|+.   
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             ---------HccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCch
Q 009567          274 ---------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF  344 (532)
Q Consensus       274 ---------aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rF  344 (532)
                               +.|++...|...+++|..|++.||.+|+++|++||++|.++|.+++|||||||||||+|+++|||++|++|
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                     23566788889999899999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCCc
Q 009567          345 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPL  422 (532)
Q Consensus       345 STYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~~i  422 (532)
                      +|||+||||+.|.+++++++|++|+|.|+...+++++++.+.+.+.+||.|+.++||..+|  +++++|..++......+
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             ccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHH
Q 009567          423 SMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE  502 (532)
Q Consensus       423 SLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISre  502 (532)
                      |+|.+++++++..+.+.+++....+|++.+....+...|..+|..||++||.||.+||||+|++++|++|||+.||||++
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            99999987776678888887666678888888888899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH-HHhhcCchhhhhh
Q 009567          503 RVRQLESRALYRLK-QSLGGKASYGYAD  529 (532)
Q Consensus       503 rVRqie~rALkKLR-~~l~~~~l~~yld  529 (532)
                      ||||++++|++||| ..+....+++|++
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=1.8e-55  Score=469.60  Aligned_cols=311  Identities=33%  Similarity=0.589  Sum_probs=276.6

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh---------------------hhCCCCcHHH----
Q 009567          216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS---------------------QFGREPTLIE----  270 (532)
Q Consensus       216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~---------------------~~g~~pt~~e----  270 (532)
                      ..|+++.||++|+++|+||++||++|+++|+.+..+..   .|..                     ..|+.|+..+    
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            46899999999999999999999999999998653322   2222                     2234555443    


Q ss_pred             -----HHH---HccCCHHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCC
Q 009567          271 -----WAK---AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGC  342 (532)
Q Consensus       271 -----wA~---aag~~~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~  342 (532)
                           |+.   ++++++..|...+++|..|++.||.+|+++|++||++|.++|.+++|||||||+|||+|+++|||++|+
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   346778889999998899999999999999999999999999999999999999999999999999999


Q ss_pred             chhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--CCHHHHHHHHHhcCC
Q 009567          343 RFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRM  420 (532)
Q Consensus       343 rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~  420 (532)
                      +|+|||+||||+.|.+++++++|+||+|.|+...+++++++.+.+.+.+||.|+.++||..+|  +++++|..++.....
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             CcccCCCCCCCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC
Q 009567          421 PLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS  500 (532)
Q Consensus       421 ~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgIS  500 (532)
                      ++|+|.+++++++..+.+++++....+|++.+....+...|..+|..||++||.||.+||||+||+++|++|||+.||||
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            99999999877777888888887666888888888888999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH-HHhhcCchhhhhh
Q 009567          501 KERVRQLESRALYRLK-QSLGGKASYGYAD  529 (532)
Q Consensus       501 rerVRqie~rALkKLR-~~l~~~~l~~yld  529 (532)
                      ++||||++.+|++||| ..+....|++|++
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 8888888998874

>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=3.7e-42  Score=382.46  Aligned_cols=251  Identities=34%  Similarity=0.671  Sum_probs=237.1

Q ss_pred             HHHHHHHHhhcH-HH---HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHH
Q 009567          279 CRDLKSELHSGN-SS---REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  354 (532)
Q Consensus       279 ~~~L~~~l~~g~-~A---re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~  354 (532)
                      ...|...++.|+ .|   ++.||..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+||++||||+
T Consensus       358 ~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn  437 (613)
T 3iyd_F          358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ  437 (613)
T ss_dssp             HHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHH
Confidence            456777777776 66   99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc
Q 009567          355 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT  434 (532)
Q Consensus       355 aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~  434 (532)
                      .|.++++++.+.+|+|.|+...+++++++...+.+++||.||.+|||+.+|++++++..++.....++|++.+++++++.
T Consensus       438 ~i~~~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~~~~~~~  517 (613)
T 3iyd_F          438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS  517 (613)
T ss_dssp             HHHHHTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCCSSSSSC
T ss_pred             HHHHHHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCCCCCCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999888777


Q ss_pred             chhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 009567          435 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  514 (532)
Q Consensus       435 ~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkK  514 (532)
                      .+.+.+.+....+|++.+...++...|..+|..||+++|.||.||||+++++++|++|||+.||||++||++++++|+++
T Consensus       518 ~l~d~i~d~~~~~p~~~~~~~e~~~~l~~aL~~Lp~~er~Vl~Lr~~~~~~e~~s~~EIA~~lgis~~tVk~~~~rAl~k  597 (613)
T 3iyd_F          518 HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK  597 (613)
T ss_dssp             CGGGSCCCSSSCCHHHHHHHHTTSSSHHHHTTSSCHHHHHHHHHHHTSSSCCCCSTTGGGTTTSSCSSHHHHHHHHHHTT
T ss_pred             cHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            88888888777789998888888888999999999999999999999998899999999999999999999999999999


Q ss_pred             HHHHhhcCchhhhhh
Q 009567          515 LKQSLGGKASYGYAD  529 (532)
Q Consensus       515 LR~~l~~~~l~~yld  529 (532)
                      ||+++....++.|+|
T Consensus       598 LR~~~~~~~l~~~l~  612 (613)
T 3iyd_F          598 LRHPSRSEVLRSFLD  612 (613)
T ss_dssp             TTSCSSSCSSTTCC-
T ss_pred             hhCcchhhHHHHHhc
Confidence            999999999999986

>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=1.6e-36  Score=301.73  Aligned_cols=209  Identities=33%  Similarity=0.577  Sum_probs=132.1

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHHH--h-----------------------hhCCCCcHH
Q 009567          216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR-LEKEKSKLQ--S-----------------------QFGREPTLI  269 (532)
Q Consensus       216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~-le~~~~~l~--~-----------------------~~g~~pt~~  269 (532)
                      ..|+++.||++|+++||||++||++|+++|+.++. .+.+.....  .                       ..+.+|+..
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            47999999999999999999999999999999764 333322110  0                       024689999


Q ss_pred             HHHHHccCCH----HHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchh
Q 009567          270 EWAKAIGLSC----RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA  345 (532)
Q Consensus       270 ewA~aag~~~----~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFS  345 (532)
                      +||.+.|++.    ..|...+++|..|++.||..|.++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+
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            9999999853    456677888899999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCCcc
Q 009567          346 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLS  423 (532)
Q Consensus       346 TYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~~iS  423 (532)
                      ||++||||++|.++++++.+.+++|.++...++++.++.+.+...+++.||.+|||+.||  +|+++|...+...+.++|
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  999999999988887777


Q ss_pred             c
Q 009567          424 M  424 (532)
Q Consensus       424 L  424 (532)
                      |
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=8.3e-32  Score=260.34  Aligned_cols=222  Identities=22%  Similarity=0.304  Sum_probs=192.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhh---CCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  366 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~---~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~  366 (532)
                      ..|++.|+..|.++|+.+|++|.   +++.+.+||+|||+++||+++++||+.+|.+|.||+++||++.|.++++++.  
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--CCcccCCCCCCCCCcchhhhcccCC
Q 009567          367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTG  444 (532)
Q Consensus       367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~iSLD~~v~~d~~~~l~d~i~d~~  444 (532)
                       +.|.+.....++++++...+....|+.|+.+++|..+|++++++..++....  ...|++.+..++++.. .+. ++. 
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             5788888889999999999999999999999999999999999988775432  2345554432222112 233 332 


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          445 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       445 ~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ..+|++.+...+....|..+|..||+++|.||.++|+    +++|++|||+.||||.++|++++++|+++||+.+..
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    899999999999999999999999999999998764

>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=2e-31  Score=257.52  Aligned_cols=215  Identities=27%  Similarity=0.445  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhcccccc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  369 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRl  369 (532)
                      ..|++.|+..|.++|+++|++|.++..+.+||+|||++++|+++++|||.+|.+|.||+++|+++.+.++++++. .+++
T Consensus        27 ~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~~d~~r~~~-~~~~  105 (243)
T 1l0o_C           27 QEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKV  105 (243)
T ss_dssp             -------------------------------------------------------------------------CC-CCTT
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-CccC
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999987 7899


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC--cchhhhcccCCCCC
Q 009567          370 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQEITADTGVEI  447 (532)
Q Consensus       370 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~--~~l~d~i~d~~~~~  447 (532)
                      |.++.....+++++...+.+..++.|+.++++..+|++.+.+...+.......|++.++.++++  .++.+.++      
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~------  179 (243)
T 1l0o_C          106 SRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIA------  179 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC-----------------------------
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCcccchhhccC------
Confidence            9999999999999999999999999999999999999999998887776667888877544322  22333322      


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                       ++.+...+....|..+|..||+++|+||.++|+    +++|++|||+.||||.++|++++.+|+++||
T Consensus       180 -~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr  243 (243)
T 1l0o_C          180 -DADEASWFDKIALKKAIEELDERERLIVYLRYY----KDQTQSEVASRLGISQVQMSRLEKKILQHIK  243 (243)
T ss_dssp             ---------------------------------------------------------------------
T ss_pred             -cchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence             223334455667899999999999999999998    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=99.88  E-value=2.4e-22  Score=188.73  Aligned_cols=180  Identities=16%  Similarity=0.180  Sum_probs=136.6

Q ss_pred             HHHHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHH
Q 009567          279 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  357 (532)
Q Consensus       279 ~~~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~  357 (532)
                      +.+|...++.| ..|++.|+..|.+.|+.+|++|.+ ..+.+|++||+++++|+++++|++..  .|.+|++.++++.+.
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            45566666655 599999999999999999999999 89999999999999999999999874  599999999999999


Q ss_pred             HHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 009567          358 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  437 (532)
Q Consensus       358 ~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~  437 (532)
                      +++++..+..+..                            ++.           ....     ..++.+      ..  
T Consensus        87 d~~R~~~~~~~~~----------------------------~~~-----------~~~~-----~~~~~~------~~--  114 (194)
T 1or7_A           87 NYLVAQGRRPPSS----------------------------DVD-----------AIEA-----ENFESG------GA--  114 (194)
T ss_dssp             HHHHHHTTCCTHH----------------------------HHH-----------HHHH-----HSCCSS------CC--
T ss_pred             HHHHHHhccCccc----------------------------ccc-----------cccc-----cccccc------cc--
Confidence            9998866432110                            000           0000     000000      00  


Q ss_pred             hhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          438 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       438 d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                        +.+.  .+|++.+...+....|..+|..||+++|+||.++|+    +++|++|||+.||+|..+|++++.||+++||+
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  123322333445567889999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhhc
Q 009567          518 SLGG  521 (532)
Q Consensus       518 ~l~~  521 (532)
                      .+..
T Consensus       187 ~l~~  190 (194)
T 1or7_A          187 KVQP  190 (194)
T ss_dssp             HHCC
T ss_pred             HHHH
Confidence            8754

>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=2.7e-21  Score=175.62  Aligned_cols=155  Identities=15%  Similarity=0.189  Sum_probs=108.3

Q ss_pred             CCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCC
Q 009567          315 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS  394 (532)
Q Consensus       315 g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~  394 (532)
                      |.+++|++|||++++|+++++||+.+ .+|.||+++++++.+.++++++.+..+.|..                      
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 7899999999999999999987643322210                      


Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh----hhcccCCCCChhHHHHHHHHHHHHHHHHh-cCC
Q 009567          395 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ----EITADTGVEIPDISVQKQLMRQHVRNLLT-LLN  469 (532)
Q Consensus       395 Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~----d~i~d~~~~~pee~~~~~~l~~~L~~~L~-~L~  469 (532)
                                               ..++.+.+..++....+.    +.+.+ ...+|++.+...+....|..+|. .||
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                                     011111111111111111    11111 22367777888888889999999 999


Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      +++|+||. +|.    +|+|++|||+.||||.++|+++..||+++||+.+...+
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    89999999999999999999999999999999987643

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

Probab=99.68  E-value=8e-19  Score=161.65  Aligned_cols=143  Identities=11%  Similarity=0.084  Sum_probs=118.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccccchh
Q 009567          293 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  372 (532)
Q Consensus       293 re~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IRlP~~  372 (532)
                      ++.|+..|.+.|+.+|.++.++..+.+|++||+++.+|+++++|++.  ..|.+|++..+++.+.+++++...       
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~-------   73 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRD--VDPRLGLYRMFQGIWASANADGEA-------   73 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCS--SCTTHHHHHHHHHHHHHHTTTTSC-------
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCC--CcHHHHHHHHHHHHHHHHhhccCc-------
Confidence            56788999999999999999998999999999999999999999976  369999999999999988764210       


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCChhHHH
Q 009567          373 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  452 (532)
Q Consensus       373 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~pee~~  452 (532)
                                            +                             +.+.  +          ..         
T Consensus        74 ----------------------~-----------------------------~~~~--e----------~~---------   81 (157)
T 2lfw_A           74 ----------------------Q-----------------------------TSQS--D----------AE---------   81 (157)
T ss_dssp             ----------------------C-----------------------------CCCC--S----------CS---------
T ss_pred             ----------------------c-----------------------------cCCc--c----------hH---------
Confidence                                  0                             0000  0          00         


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          453 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       453 ~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                         +....|..+|..||+++|+||.|+|.    +++|++|||+.||||..+|++.+.||+++||+.+....
T Consensus        82 ---~~~~~l~~~l~~Lp~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~  145 (157)
T 2lfw_A           82 ---GTEAVARARLARMTPLSRQALLLTAM----EGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRALE  145 (157)
T ss_dssp             ---SSSSTTTTTTTTSCTTHHHHHTTTSS----SCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSCCC
T ss_pred             ---HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence               01124667889999999999999998    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=99.63  E-value=3.5e-16  Score=161.75  Aligned_cols=85  Identities=41%  Similarity=0.902  Sum_probs=77.0

Q ss_pred             HHHHHHHhhc-H---HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          280 RDLKSELHSG-N---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       280 ~~L~~~l~~g-~---~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      ..|...++.| .   .|++.||..|+++|+++|++|.+++.+++||+||||+|||+++++|+|.+|++|+||++|||+|.
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            3455555555 4   69999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhc
Q 009567          356 IRKAIFQHS  364 (532)
Q Consensus       356 I~~~ir~~~  364 (532)
                      |.++++++.
T Consensus       330 ~~~~lr~~~  338 (339)
T 1sig_A          330 ITRSIADQA  338 (339)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHhc
Confidence            999998865

>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=2.5e-14  Score=123.17  Aligned_cols=80  Identities=29%  Similarity=0.490  Sum_probs=74.5

Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhh
Q 009567          451 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADL  530 (532)
Q Consensus       451 ~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yldl  530 (532)
                      .+...++...|..+|+.|||++|+||.+|||++|++++|++|||+.||||+++|++++.+|+++||..+....++.|+..
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            35566778899999999999999999999999988999999999999999999999999999999999999999999853

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

Probab=99.50  E-value=1.1e-14  Score=146.85  Aligned_cols=142  Identities=13%  Similarity=0.040  Sum_probs=118.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhccccc
Q 009567          289 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  368 (532)
Q Consensus       289 g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~r~IR  368 (532)
                      +..+++.|+..|.+.++.+|.+|.++..+.+|++||.|+.+|+..++|++.  ..|.+|++..++|.+.+++++..    
T Consensus        19 ~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~~----   92 (286)
T 3n0r_A           19 SEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQLE----   92 (286)
T ss_dssp             -CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC-------
T ss_pred             CcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhccccc----
Confidence            347899999999999999999999999999999999999999999999975  46999999999988877654210    


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhhcccCCCCCh
Q 009567          369 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  448 (532)
Q Consensus       369 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~l~d~i~d~~~~~p  448 (532)
                                                                               .+  ....         ..    
T Consensus        93 ---------------------------------------------------------~~--~~~~---------~~----  100 (286)
T 3n0r_A           93 ---------------------------------------------------------VG--HDQG---------LH----  100 (286)
T ss_dssp             ----------------------------------------------------------C--CCCC---------CC----
T ss_pred             ---------------------------------------------------------cC--CCcc---------cc----
Confidence                                                                     00  0000         00    


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          449 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       449 ee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                              ....|..+|..||+++|+||.|+|.    +++|++|||+.+|+|..+|+....+|+++|+..+.
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    99999999999999999999999999999988654

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

Probab=99.34  E-value=1.3e-12  Score=109.18  Aligned_cols=72  Identities=38%  Similarity=0.713  Sum_probs=67.1

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhh
Q 009567          459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADL  530 (532)
Q Consensus       459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yldl  530 (532)
                      ..|..+|..||+++|+||.++|+|++++++|++|||+.||+|+++|++++.+|+++||..+....++.|+..
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            357889999999999999999999988999999999999999999999999999999999988888888764

>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=8.3e-13  Score=106.47  Aligned_cols=68  Identities=32%  Similarity=0.627  Sum_probs=55.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH-HHhhcCchhhhh
Q 009567          461 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK-QSLGGKASYGYA  528 (532)
Q Consensus       461 L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR-~~l~~~~l~~yl  528 (532)
                      |..+|+.||++||+||.++|+|+|++++|++|||+.||+|.++|+++..+|+++|| ..+....++.|+
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            45678899999999999999999889999999999999999999999999999999 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=103.56  Aligned_cols=75  Identities=16%  Similarity=0.211  Sum_probs=69.8

Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 009567          445 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  523 (532)
Q Consensus       445 ~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~  523 (532)
                      ..+|++.+...+....|..+|..||+++|+||.++|.    +++|++|||+.||||..+|++++.+|+++||+.+...+
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=1.5e-12  Score=103.52  Aligned_cols=66  Identities=33%  Similarity=0.614  Sum_probs=61.3

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567          464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  529 (532)
Q Consensus       464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld  529 (532)
                      +|..|||+||+||.++|||++.+++|++|||+.||+|.++|++++.+|++|||..+....+..|++
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            367899999999999999888899999999999999999999999999999999998888888764

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

Probab=98.97  E-value=8.6e-10  Score=86.96  Aligned_cols=64  Identities=16%  Similarity=0.067  Sum_probs=53.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       457 l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ....+..+|..||++++.||.++|.    +++|++|||+.+|+|+.+|+++.++|+++||..+....+
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            3457888999999999999999997    899999999999999999999999999999998876543

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

Probab=98.86  E-value=4.8e-09  Score=90.31  Aligned_cols=82  Identities=17%  Similarity=0.157  Sum_probs=69.1

Q ss_pred             HHHHHHhhc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHH
Q 009567          281 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  359 (532)
Q Consensus       281 ~L~~~l~~g-~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~  359 (532)
                      .|...+..| ..|++.|+..|.+.++.+|.++ ++..+.+|++||+++.+|+.+.+|++.  ..|.+|++..+++.+.++
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            344444444 5999999999999999999999 888899999999999999999999974  369999999999999999


Q ss_pred             HHhhcc
Q 009567          360 IFQHSR  365 (532)
Q Consensus       360 ir~~~r  365 (532)
                      ++++.+
T Consensus        90 ~R~~~~   95 (112)
T 2o7g_A           90 IRHVRS   95 (112)
T ss_dssp             TC----
T ss_pred             HHHhhc
Confidence            987654

>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=98.82  E-value=1.7e-08  Score=88.42  Aligned_cols=69  Identities=22%  Similarity=0.202  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          452 VQKQLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       452 ~~~~~l~~~L~~~L-~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ++.......+..++ ..||+++|+||.++|.    +++|++|||+.||+|..+|+.+..||+++||..+...++
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            34445566788899 9999999999999987    899999999999999999999999999999999876554

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

Probab=98.76  E-value=9.1e-09  Score=84.56  Aligned_cols=75  Identities=15%  Similarity=0.135  Sum_probs=67.0

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhc
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  364 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~  364 (532)
                      ++..+++.|+..|.+.++.+|.++.++..+.+|++||+++.+|+.+++|++.  ..|.+|++..+++.+.++++++.
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            3458999999999999999999999998999999999999999999999975  47999999999999999987654

>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=98.68  E-value=2.9e-08  Score=87.07  Aligned_cols=63  Identities=21%  Similarity=0.212  Sum_probs=57.5

Q ss_pred             HHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          458 RQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       458 ~~~L~~~L-~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ...+..++ ..|||++++||.++|.    +|+|.+|||+.+|+|+.+|+.+..+|+++||..+...++
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            44677788 8999999999999988    899999999999999999999999999999999876554

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

Probab=98.64  E-value=2.5e-11  Score=120.44  Aligned_cols=154  Identities=10%  Similarity=0.037  Sum_probs=109.6

Q ss_pred             HHHHHHhhcH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHH----HHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHH
Q 009567          281 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLL----QEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  355 (532)
Q Consensus       281 ~L~~~l~~g~-~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLi----QEG~iGLikAiekFDp~kG~rFSTYA~~wIr~a  355 (532)
                      .|...++.++ .+.+.+...+.++++.+............|+.    ||.++.+|+.+..|++..  .|.+|++..+++.
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 78999999999999999988777777778886    999999999999998653  5888876554433


Q ss_pred             HHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 009567          356 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  435 (532)
Q Consensus       356 I~~~ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~~d~~~~  435 (532)
                      +.++.+..                                                           .+...+...... 
T Consensus       164 ~~d~~r~~-----------------------------------------------------------~~~~~~~~~~~~-  183 (258)
T 3clo_A          164 SADQRPEQ-----------------------------------------------------------GIYATITQMERG-  183 (258)
T ss_dssp             CSCCCCCS-----------------------------------------------------------SCCCEEEETTTT-
T ss_pred             Hcchhhhh-----------------------------------------------------------HHHHHHHhhccc-
Confidence            32221000                                                           000000000000 


Q ss_pred             hhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          436 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       436 l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                        +...     .+           .+..++..||+++|+||.+++     +|+|.+|||+.||+|..+|+.+..||++||
T Consensus       184 --~~~~-----~~-----------~~~~~~~~L~~~erevl~L~~-----~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL  240 (258)
T 3clo_A          184 --EVET-----LS-----------LSEEHRNILSEREKEILRCIR-----KGLSSKEIAATLYISVNTVNRHRQNILEKL  240 (258)
T ss_dssp             --EEEE-----CC-----------CHHHHTTSSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             --cccc-----ch-----------hhHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence              0000     00           135567899999999999985     799999999999999999999999999999


Q ss_pred             HHHh
Q 009567          516 KQSL  519 (532)
Q Consensus       516 R~~l  519 (532)
                      |...
T Consensus       241 ~~~~  244 (258)
T 3clo_A          241 SVGN  244 (258)
T ss_dssp             TCSS
T ss_pred             cCCC
Confidence            8743

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

Probab=98.54  E-value=3.8e-08  Score=82.38  Aligned_cols=58  Identities=21%  Similarity=0.181  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          456 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       456 ~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      .....+..++..|+++|++||.++ .    +|+|.+|||+.||||..+|+.+..++++||+..
T Consensus        18 ~~~~~l~~~l~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   75 (91)
T 2rnj_A           18 SHMKKRAELYEMLTEREMEILLLI-A----KGYSNQEIASASHITIKTVKTHVSNILSKLEVQ   75 (91)
T ss_dssp             -------CTGGGCCSHHHHHHHHH-H----TTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            344567888999999999999995 4    799999999999999999999999999999764

>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=98.50  E-value=8.5e-08  Score=82.53  Aligned_cols=64  Identities=23%  Similarity=0.201  Sum_probs=55.0

Q ss_pred             HHHHHHHHH-hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          457 MRQHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       457 l~~~L~~~L-~~L~~rER~VL~LRyGL~~---~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ..+.+..++ ..|+++|+.+|.+|||+.+   +.++|++|||+.+|+|+.+|.++ +|+|++|...++.
T Consensus        24 ~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k~   91 (101)
T 1jhg_A           24 QNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELRQ   91 (101)
T ss_dssp             HTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHHH
T ss_pred             CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHHH
Confidence            344567777 6799999999999999975   45799999999999999999999 8999999876543

>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=98.48  E-value=1.8e-07  Score=79.17  Aligned_cols=60  Identities=20%  Similarity=0.230  Sum_probs=46.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       457 l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      ....|..++..|+++|++||.+++     +++|.+|||+.||||..+|+.+..++++||+..-..
T Consensus        17 ~~~~l~~~l~~Lt~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~   76 (95)
T 3c57_A           17 RGSHMQDPLSGLTDQERTLLGLLS-----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRT   76 (95)
T ss_dssp             ----------CCCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHH
Confidence            345678889999999999999974     899999999999999999999999999999875433

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

Probab=98.47  E-value=1.9e-07  Score=75.23  Aligned_cols=55  Identities=15%  Similarity=0.187  Sum_probs=50.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          459 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       459 ~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      ..+..++..||++|++||.++ .    +++|.+|||+.||+|..+|+++..++++||+..
T Consensus         8 ~~l~~~l~~L~~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~~   62 (79)
T 1x3u_A            8 NDIRARLQTLSERERQVLSAV-V----AGLPNKSIAYDLDISPRTVEVHRANVMAKMKAK   62 (79)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHH-T----TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHhCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            357788999999999999995 4    799999999999999999999999999999753

>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=98.35  E-value=3.1e-07  Score=75.55  Aligned_cols=56  Identities=16%  Similarity=0.221  Sum_probs=48.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          460 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       460 ~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      .+..++..|+++|++||.++ .    +++|.+|||+.||||..+|+.+..++++||+....
T Consensus        14 ~~~~~~~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   69 (82)
T 1je8_A           14 TTERDVNQLTPRERDILKLI-A----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSR   69 (82)
T ss_dssp             ---CCGGGSCHHHHHHHHHH-T----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSH
T ss_pred             HHHHHHccCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence            35677899999999999995 4    79999999999999999999999999999976443

>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=1.5e-06  Score=68.83  Aligned_cols=53  Identities=25%  Similarity=0.238  Sum_probs=45.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          461 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       461 L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      ....+..|+++|++||.+. .    +++|.+|||+.||+|..+|+++..++++||+..
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            3456788999999999995 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=98.01  E-value=8.2e-06  Score=68.44  Aligned_cols=49  Identities=20%  Similarity=0.225  Sum_probs=43.1

Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       463 ~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .....|+++|++||.+.+     +|+|.+|||+.||||..+|+....++++||.
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     7999999999999999999999999999984

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

Probab=97.93  E-value=7.9e-06  Score=62.50  Aligned_cols=43  Identities=14%  Similarity=0.227  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      |+|++|+.+ +.    +|+|.+|||+.||+|..+|+....++++||+.
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            579999999 55    89999999999999999999999999999965

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

Probab=97.89  E-value=1.6e-05  Score=68.03  Aligned_cols=47  Identities=21%  Similarity=0.275  Sum_probs=43.5

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ..|+++|++||.+.+     +++|.+|||+.||||..+|+....++++||.-
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     79999999999999999999999999999953

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=97.49  E-value=0.00015  Score=70.34  Aligned_cols=46  Identities=24%  Similarity=0.327  Sum_probs=42.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .|+++|++||.+.+     +|+|.+|||++||||..||+.+..++++||.-
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            59999999999965     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=97.46  E-value=0.00015  Score=70.19  Aligned_cols=45  Identities=27%  Similarity=0.383  Sum_probs=42.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .|+++|++||.+.+     +|+|.+|||++||||..+|+....++++||.
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     7999999999999999999999999999984

>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=97.32  E-value=0.00025  Score=69.11  Aligned_cols=46  Identities=20%  Similarity=0.307  Sum_probs=43.0

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|++|+.+..     +|+|.+|||+.||||..||+....++++||.
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            469999999999975     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=97.21  E-value=0.00037  Score=69.21  Aligned_cols=46  Identities=20%  Similarity=0.239  Sum_probs=43.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .|+++|++||.+..     +|+|.+|||++||||..||+....++++||.-
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            69999999999986     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=96.93  E-value=0.0012  Score=47.02  Aligned_cols=40  Identities=20%  Similarity=0.124  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|++.++..+...|.    +++|..|||+.||||+.+|+.+..+
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            478888866666565    7899999999999999999987654

>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=96.55  E-value=0.0049  Score=56.99  Aligned_cols=50  Identities=14%  Similarity=0.310  Sum_probs=44.6

Q ss_pred             HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          462 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       462 ~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ...+..|+++|++|+.+..     +++|.+|||+.+|+|..+|+.+..++++||.
T Consensus       137 ~~~~~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~  186 (208)
T 1yio_A          137 EQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLN  186 (208)
T ss_dssp             HHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhcCHHHHHHHHHHH-----cCCcHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence            4445689999999998865     6899999999999999999999999999985

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.38  E-value=0.012  Score=50.40  Aligned_cols=46  Identities=17%  Similarity=0.147  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .+++.-..|-.++|.    +|+|..|||+.||||+.+|.+++.+|...+-
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    9999999999999999999999999988764

>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=96.32  E-value=0.0064  Score=56.61  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=42.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|++|+.+..     +++|.+|||+.+++|..+|+.+..+.++||.
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            469999999999876     6899999999999999999999999999994

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

Probab=96.15  E-value=0.0049  Score=45.80  Aligned_cols=38  Identities=16%  Similarity=0.233  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       469 ~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      ++..+.|+.+ +.    .++|..|||+.||||+.+|+.+..+|
T Consensus        18 ~~~~~~i~~l-~~----~g~s~~eIA~~lgis~~TV~~~l~~a   55 (55)
T 2x48_A           18 DDLVSVAHEL-AK----MGYTVQQIANALGVSERKVRRYLESC   55 (55)
T ss_dssp             HHHHHHHHHH-HH----TTCCHHHHHHHHTSCHHHHHHHHTC-
T ss_pred             HHHHHHHHHH-HH----cCCCHHHHHHHHCcCHHHHHHHHHhC
Confidence            4455666666 44    78999999999999999999987654

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=96.05  E-value=0.0085  Score=56.68  Aligned_cols=46  Identities=22%  Similarity=0.260  Sum_probs=42.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ..|+++|++|+.+..     +++|.+|||+.+++|..||+....+.++||.
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            469999999998876     6899999999999999999999999999984

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=95.36  E-value=0.014  Score=54.94  Aligned_cols=47  Identities=17%  Similarity=0.197  Sum_probs=42.3

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      ...|+++|++|+.+..     +++|.+|||+.+++|..+|+.+..+.++||.
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            3469999999999854     6899999999999999999999999999883

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=94.90  E-value=0.068  Score=50.79  Aligned_cols=54  Identities=22%  Similarity=0.322  Sum_probs=48.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .......+..|++++++|+.+..     .+++.++||..||+|..+|+....++++||.
T Consensus       189 ~~~~~~~l~~L~~r~~~i~~~~~-----~g~~~~eia~~l~~s~~tv~~~l~~i~~kl~  242 (258)
T 3p7n_A          189 RERAAEMLKTLSPRQLEVTTLVA-----SGLRNKEVAARLGLSEKTVKMHRGLVMEKLN  242 (258)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhhcCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            44567889999999999999876     6899999999999999999999999999884

>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=94.05  E-value=0.01  Score=65.69  Aligned_cols=33  Identities=30%  Similarity=0.547  Sum_probs=12.9

Q ss_pred             CChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHH
Q 009567          216 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDL  248 (532)
Q Consensus       216 ~~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~  248 (532)
                      .+||+++||++|++.||||+++|++|+++|..+
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            579999999999999999999999999999874

>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=93.55  E-value=0.061  Score=50.04  Aligned_cols=50  Identities=20%  Similarity=0.121  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG---LSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg---ISrerVRqie~rALkKLR~  517 (532)
                      .|+++|++|+.+..- +.|+.+|.+|||+.++   +|..+|+.+..+.++||..
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            599999999987652 2335599999999999   9999999999999999963

>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=93.49  E-value=0.087  Score=42.52  Aligned_cols=44  Identities=20%  Similarity=0.466  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +.++.||.+..-...|++.|..|||+.+|||+.+|+++    |.+|.+
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            44577776655544456899999999999999998754    555644

>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=93.29  E-value=0.085  Score=37.58  Aligned_cols=33  Identities=21%  Similarity=0.296  Sum_probs=25.6

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       473 R~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      +.|+.+ +.    .+.|..+||+.+|||+.+|..+..+
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    5699999999999999999887643

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=93.26  E-value=0.085  Score=49.94  Aligned_cols=50  Identities=10%  Similarity=-0.049  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L-----gISrerVRqie~rALkKLR~  517 (532)
                      .|+++|.+||.+..- +-|..+|.+|||+.+     ++|..+|+....+.++||..
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            599999999987652 233559999999999     99999999999999999953

>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=0.078  Score=49.57  Aligned_cols=50  Identities=10%  Similarity=0.034  Sum_probs=43.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L-----gISrerVRqie~rALkKLR~  517 (532)
                      .|+++|.+||.+..- +.|+.+|.+|||+.+     ++|..+|+.+..+.++||..
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            599999999987652 334569999999999     99999999999999999853

>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=92.69  E-value=0.17  Score=41.32  Aligned_cols=43  Identities=23%  Similarity=0.494  Sum_probs=31.9

Q ss_pred             HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          471 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       471 rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .++.||.+......|+..|..|||+.||||+.+|+    +.|.+|.+
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~----~~L~~Le~   53 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTPKKEIN----RVLYSLAK   53 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            45666665554444578999999999999998886    55666654

>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=92.60  E-value=0.089  Score=48.87  Aligned_cols=50  Identities=12%  Similarity=0.056  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR~  517 (532)
                      .|+++|.+|+.+..- +.|..+|.+|||+.++     +|..+|+.+..+.++||..
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            599999999987652 2234599999999998     9999999999999999964

>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=92.21  E-value=0.088  Score=49.21  Aligned_cols=50  Identities=10%  Similarity=-0.023  Sum_probs=41.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR~  517 (532)
                      .|+++|.+|+.+..- +.|..+|.+|||+.++     +|..+|+.+..+.++||..
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 2234599999999998     9999999999999999964

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=91.38  E-value=0.18  Score=44.34  Aligned_cols=35  Identities=9%  Similarity=0.130  Sum_probs=28.5

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQ  506 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRq  506 (532)
                      ..|+.| .+|+.+..     +++|+.|||+.+|+|..||..
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            455666 67777765     679999999999999999975

>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=91.26  E-value=0.24  Score=42.86  Aligned_cols=40  Identities=20%  Similarity=0.124  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|++.++..|...+-    .|+|..+||+.||+|+.+|+.+..+
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            467777766666664    6899999999999999999988765

>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=91.04  E-value=0.041  Score=54.00  Aligned_cols=51  Identities=18%  Similarity=0.266  Sum_probs=0.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHHHH
Q 009567          461 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG--LSKERVRQLESRALYRLK  516 (532)
Q Consensus       461 L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg--ISrerVRqie~rALkKLR  516 (532)
                      +...+..|++..+. |...||    .+.|.+|||+.||  ||.++|+.++.+|++.|.
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            45566778887777 445666    7899999999999  999999999999988763

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=91.04  E-value=0.076  Score=49.50  Aligned_cols=50  Identities=4%  Similarity=-0.050  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~Lg-----ISrerVRqie~rALkKLR~  517 (532)
                      .|+++|++||.+..- +.|..+|.+|||+.++     +|..+|+.+..+.++||..
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            599999999988652 1123499999999999     9999999999999999974

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=90.89  E-value=0.35  Score=46.09  Aligned_cols=50  Identities=18%  Similarity=0.130  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L-----gISrerVRqie~rALkKLR~  517 (532)
                      .|+++|.+||.+..- +.|+..|.+||++.+     +++..+|+.+..+.++||..
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            599999999988753 446889999999999     78999999999999999964

>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=90.80  E-value=0.38  Score=40.51  Aligned_cols=42  Identities=12%  Similarity=-0.018  Sum_probs=31.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      .+++.++.-+...+.    .++|..+||+.||||+.+|+.+..+..
T Consensus        17 ~~s~~~r~~i~~~~~----~g~s~~~ia~~lgis~~Tv~~w~~~~~   58 (128)
T 1pdn_C           17 PLPNNIRLKIVEMAA----DGIRPCVISRQLRVSHGCVSKILNRYQ   58 (128)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            355555544444444    679999999999999999999887643

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=90.62  E-value=0.15  Score=49.00  Aligned_cols=50  Identities=24%  Similarity=0.246  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe-----~LgISrerVRqie~rALkKLR~  517 (532)
                      .|+++|++||.+..- +.|..+|.+|||+     .++++..+|+....+.++||..
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 3346699999999     5888999999999999999853

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=89.88  E-value=0.28  Score=46.53  Aligned_cols=35  Identities=20%  Similarity=0.196  Sum_probs=29.1

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       473 R~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      ..+..+ |.    .|+|..|||+.||||+.+|.+++..|.
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    789999999999999999999987764

>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=89.43  E-value=0.73  Score=37.61  Aligned_cols=48  Identities=23%  Similarity=0.277  Sum_probs=35.7

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ....|++.+..+|...+.  .+.+.|..|||+.+|+|+.+|++    .+++|.+
T Consensus        15 ~~~~l~~~~~~~l~~l~~--~~~~~t~~ela~~l~is~~tv~~----~l~~L~~   62 (109)
T 2d1h_A           15 CCYKITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVEN----SLKKLIE   62 (109)
T ss_dssp             HHHTCCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHH----HHHHHHH
T ss_pred             HhhcCCHHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            346789988888765441  12689999999999999999975    4555543

>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=88.99  E-value=0.6  Score=41.21  Aligned_cols=42  Identities=12%  Similarity=-0.002  Sum_probs=32.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      .+++.+|.-|...+-    .++|..+||+.||||+.+|+.+..+..
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            355555555555454    679999999999999999999987753

>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=88.76  E-value=0.44  Score=44.52  Aligned_cols=42  Identities=17%  Similarity=0.235  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHHHHhcc--cCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGI--EDGKPKSLSEVGNIFGLSKERVRQLE  508 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL--~~~e~~Tl~EIAe~LgISrerVRqie  508 (532)
                      .|+++|++|+.+-.-+  ..|.+.|.+|||+.||+|..+|+.++
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            5899999999875422  23478999999999999988876543

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=88.59  E-value=0.57  Score=36.41  Aligned_cols=44  Identities=25%  Similarity=0.406  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +++..+.||.+.-  .++.+.|..|||+.+|+|+.+|.    +.++.|++
T Consensus         8 m~~~~~~IL~~L~--~~~~~~s~~eLA~~lglsr~tv~----~~l~~L~~   51 (67)
T 2heo_A            8 GDNLEQKILQVLS--DDGGPVAIFQLVKKCQVPKKTLN----QVLYRLKK   51 (67)
T ss_dssp             -CHHHHHHHHHHH--HHCSCEEHHHHHHHHCSCHHHHH----HHHHHHHH
T ss_pred             ccHHHHHHHHHHH--HcCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            3444555665542  12367999999999999988886    55666665

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=88.43  E-value=0.91  Score=39.27  Aligned_cols=49  Identities=10%  Similarity=0.159  Sum_probs=38.1

Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          463 NLLTLLNPKERCIVRLRFGIEDGKP-KSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       463 ~~L~~L~~rER~VL~LRyGL~~~e~-~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ...-.|++.+..|+.....  .+.+ .|..|||+.+|+|+.+|.    |++++|.+
T Consensus        19 ~~~~gLt~~e~~il~~L~~--~~~~~~t~~eLa~~l~~s~sTV~----r~L~~L~~   68 (123)
T 3r0a_A           19 KCALNLTKADLNVMKSFLN--EPDRWIDTDALSKSLKLDVSTVQ----RSVKKLHE   68 (123)
T ss_dssp             HHHHTCCHHHHHHHHHHHH--STTCCEEHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHH--CCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            4456899999999887653  2234 899999999999999996    66666655

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=87.79  E-value=0.4  Score=39.36  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=21.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          487 PKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       487 ~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      +.|..|||+.||||+.+|++++.+
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            499999999999999999876654

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=87.41  E-value=0.97  Score=36.68  Aligned_cols=27  Identities=15%  Similarity=0.139  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      .+.|..+||+.||||+.+|+++..+..
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            468999999999999999999986543

>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=87.39  E-value=1.5  Score=40.26  Aligned_cols=53  Identities=11%  Similarity=0.256  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       457 l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      +...+...+..|++.+..||..-+... +.+.|..+||+.+|+++.+|..++.+
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            344556667789999999998776321 25899999999999999999755443

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=87.16  E-value=1.1  Score=39.61  Aligned_cols=45  Identities=16%  Similarity=0.310  Sum_probs=34.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ..|++.++.||.+...   +...|..|||+.+|+|+.+|+.+    +++|.+
T Consensus         5 ~~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~----l~~L~~   49 (151)
T 2dbb_A            5 RKLDRVDMQLVKILSE---NSRLTYRELADILNTTRQRIARR----IDKLKK   49 (151)
T ss_dssp             -CCCHHHHHHHHHHHH---CTTCCHHHHHHHTTSCHHHHHHH----HHHHHH
T ss_pred             hhCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            3488999999876432   25799999999999999999754    455544

>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=86.83  E-value=1.1  Score=39.55  Aligned_cols=40  Identities=20%  Similarity=0.137  Sum_probs=31.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .|++.++.||.+...   +...|..|||+.+|+|+.+|+.+.+
T Consensus         2 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~   41 (144)
T 2cfx_A            2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVR   41 (144)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            378888888876542   2579999999999999999975543

>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=86.57  E-value=3.2  Score=33.79  Aligned_cols=40  Identities=33%  Similarity=0.399  Sum_probs=29.9

Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       469 ~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ++....||.+. .    .+.|..|||+.+|+|+.+|++.    ++.|.+
T Consensus        30 ~~~r~~Il~~L-~----~~~~~~eLa~~l~is~~tv~~~----L~~L~~   69 (96)
T 1y0u_A           30 NPVRRKILRML-D----KGRSEEEIMQTLSLSKKQLDYH----LKVLEA   69 (96)
T ss_dssp             CHHHHHHHHHH-H----TTCCHHHHHHHHTCCHHHHHHH----HHHHHH
T ss_pred             CHHHHHHHHHH-c----CCCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            45666677655 3    5799999999999999999754    455544

>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=86.15  E-value=1.9  Score=36.84  Aligned_cols=49  Identities=16%  Similarity=0.247  Sum_probs=39.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          459 QHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       459 ~~L~~~L~~L~~rER~VL~LRyGL~~~---e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      ..|...+..|++.|+.|..+..-  ..   ..+|..|||+..|+|..+|.+..+
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            45667788999999999876552  11   369999999999999999986654

>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=86.00  E-value=1.5  Score=38.91  Aligned_cols=40  Identities=18%  Similarity=0.312  Sum_probs=31.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .|++.++.||.+...   +...|..|||+.+|+|+.+|+++.+
T Consensus         4 ~ld~~~~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~   43 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN---DGKAPLREISKITGLAESTIHERIR   43 (151)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHCSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            478888888876432   2479999999999999999976543

>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=85.99  E-value=1.3  Score=38.51  Aligned_cols=43  Identities=16%  Similarity=0.397  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      |++.++.||.....   +...|..|||+.+|+|+.+|++    .+++|.+
T Consensus         2 ld~~~~~il~~L~~---~~~~~~~ela~~lg~s~~tv~~----~l~~L~~   44 (141)
T 1i1g_A            2 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRK----RVKALEE   44 (141)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHH----HHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            67788888875431   2578999999999999999975    4555544

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=85.79  E-value=0.87  Score=45.73  Aligned_cols=36  Identities=14%  Similarity=0.284  Sum_probs=29.7

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 009567          474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  513 (532)
Q Consensus       474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALk  513 (532)
                      .|..++|.    +++|.+|||+.||||+.+||+.+..+.+
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            46667776    7899999999999999999977766543

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=85.74  E-value=1.4  Score=32.90  Aligned_cols=33  Identities=6%  Similarity=0.182  Sum_probs=26.5

Q ss_pred             CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          487 PKS----LSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       487 ~~T----l~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      +.|    ..+||..|||++++|+++... .+.++..+.
T Consensus        21 g~s~~~~~~~vA~~~gIs~~tl~~W~~~-~~~~~~~~~   57 (59)
T 2glo_A           21 DNDCKGNQRATARKYNIHRRQIQKWLQC-ESNLRSSVA   57 (59)
T ss_dssp             CTTTTTCHHHHHHHTTSCHHHHHHHHTT-HHHHHHHHT
T ss_pred             CCCcchHHHHHHHHHCcCHHHHHHHHHH-HHHHHHHHh
Confidence            467    999999999999999999764 556665543

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=85.72  E-value=1.3  Score=38.09  Aligned_cols=40  Identities=18%  Similarity=0.130  Sum_probs=31.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|++.+..||..-+.   +. .|..|||+.+|+|+.+|+++..+
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            467888888876553   23 99999999999999999754443

>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=85.61  E-value=1.6  Score=38.77  Aligned_cols=40  Identities=23%  Similarity=0.395  Sum_probs=31.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .|++.++.||.+...   +...|..|||+.+|+|+.+|+++.+
T Consensus         5 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~   44 (152)
T 2cg4_A            5 LIDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVE   44 (152)
T ss_dssp             CCCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            478888888876432   2578999999999999999976543

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=85.21  E-value=1.3  Score=38.38  Aligned_cols=45  Identities=11%  Similarity=0.105  Sum_probs=33.4

Q ss_pred             hcCCHHHHHHHHHHhcc-cCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL-~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      ..|++.+..+|...+.+ ..+.+.|..+||+.+|+|+.+|++++++
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            46888888887765543 2346899999999999999999754443

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=85.11  E-value=1.4  Score=39.55  Aligned_cols=41  Identities=12%  Similarity=0.042  Sum_probs=32.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|++.++.||.+...   +...|..|||+.+|+|+.+|++++.+
T Consensus         7 ~ld~~~~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   47 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE---NGRLTNVELSERVALSPSPCLRRLKQ   47 (162)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            488888888876542   24689999999999999999765443

>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=85.07  E-value=2.8  Score=34.91  Aligned_cols=50  Identities=22%  Similarity=0.237  Sum_probs=34.5

Q ss_pred             HHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          460 HVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       460 ~L~~~L~~L~-~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .+...+..|. +....||.+-..    .++|..|||+.+|+|+.+|+++    +++|++
T Consensus        15 ~~~~~~~~l~~~~r~~IL~~L~~----~~~~~~ela~~l~is~stvs~~----L~~L~~   65 (106)
T 1r1u_A           15 RVTEIFKALGDYNRIRIMELLSV----SEASVGHISHQLNLSQSNVSHQ----LKLLKS   65 (106)
T ss_dssp             HHHHHHHHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTCCHHHHHHH----HHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            3445555555 555566665442    5789999999999999999754    455554

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=85.02  E-value=2.3  Score=36.54  Aligned_cols=41  Identities=12%  Similarity=0.223  Sum_probs=29.6

Q ss_pred             hcCCHHHHHHHHHHhcccC--CCCCCHHHHHHHhCCCHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIED--GKPKSLSEVGNIFGLSKERVRQ  506 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~--~e~~Tl~EIAe~LgISrerVRq  506 (532)
                      .-+++.|+.-|-.|+-+-.  .+|+|+.||++.+|+|..+|.+
T Consensus        35 dL~T~~E~~alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsR   77 (107)
T 3frw_A           35 DVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISR   77 (107)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHH
Confidence            3467777766655543321  1579999999999999999964

>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=84.88  E-value=1.5  Score=38.75  Aligned_cols=40  Identities=28%  Similarity=0.262  Sum_probs=31.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .|++.++.||.+-..   +...|..|||+.+|+|+.+|+++..
T Consensus         4 ~ld~~~~~iL~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~   43 (150)
T 2w25_A            4 ALDDIDRILVRELAA---DGRATLSELATRAGLSVSAVQSRVR   43 (150)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            488889988886532   2579999999999999999975543

>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=84.66  E-value=2.1  Score=36.90  Aligned_cols=51  Identities=16%  Similarity=0.251  Sum_probs=36.3

Q ss_pred             HHHHHHHHHhc----CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          457 MRQHVRNLLTL----LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       457 l~~~L~~~L~~----L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      +...+...+..    |++.+..||..-+.   ..+.|..|||+.+|+++.+|.++..+
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    99999999887664   25899999999999999999765544

>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=84.65  E-value=1.3  Score=35.93  Aligned_cols=40  Identities=23%  Similarity=0.213  Sum_probs=31.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .|++.+..|+.....   +.+.|..|||+.+|+|+.+|++++.
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            578888888876542   2579999999999999999975443

>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=84.62  E-value=3.8  Score=34.86  Aligned_cols=51  Identities=10%  Similarity=0.021  Sum_probs=37.6

Q ss_pred             HHHHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          458 RQHVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       458 ~~~L~~~L--~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      ...+...+  ..|++.+..||...+.- ++.+.|..|||+.+|+++.+|..+..
T Consensus        20 ~~~~~~~~~~~~lt~~~~~iL~~l~~~-~~~~~~~~ela~~l~~~~~tvs~~l~   72 (141)
T 3bro_A           20 STRFDIFAKKYDLTGTQMTIIDYLSRN-KNKEVLQRDLESEFSIKSSTATVLLQ   72 (141)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHT-TTSCCBHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCCCcchHHHHHH
Confidence            34455555  35899999998876642 22379999999999999999975443

>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=84.61  E-value=1.5  Score=35.41  Aligned_cols=33  Identities=15%  Similarity=0.427  Sum_probs=24.1

Q ss_pred             cccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          481 GIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       481 GL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +|..|+..|..+||..||+|+..|.    |+|-+|.+
T Consensus        23 ~L~~~~~~Ta~~IAkkLg~sK~~vN----r~LY~L~k   55 (75)
T 1sfu_A           23 SLNTNDYTTAISLSNRLKINKKKIN----QQLYKLQK   55 (75)
T ss_dssp             TSCTTCEECHHHHHHHTTCCHHHHH----HHHHHHHH
T ss_pred             hCCCCcchHHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            3444466899999999999987775    55555543

>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=84.42  E-value=2.8  Score=35.89  Aligned_cols=47  Identities=13%  Similarity=0.185  Sum_probs=36.1

Q ss_pred             HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          460 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       460 ~L~~~L--~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .+...+  ..|++.+..||...+    +.+.|..|||+.+|+|+.+|..+..+
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  358999999987765    26899999999999999999754443

>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=84.36  E-value=1.5  Score=38.62  Aligned_cols=43  Identities=14%  Similarity=0.213  Sum_probs=31.9

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      |++.++.||.+--   .+.+.|..|||+.+|+|+.+|+++    +++|.+
T Consensus         1 ld~~~~~il~~L~---~~~~~~~~ela~~lg~s~~tv~~~----l~~L~~   43 (150)
T 2pn6_A            1 MDEIDLRILKILQ---YNAKYSLDEIAREIRIPKATLSYR----IKKLEK   43 (150)
T ss_dssp             CCHHHHHHHHHHT---TCTTSCHHHHHHHHTSCHHHHHHH----HHHHHH
T ss_pred             CChHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            5677778877543   235799999999999999999754    445544

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=84.11  E-value=1.6  Score=39.48  Aligned_cols=39  Identities=15%  Similarity=0.236  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      |++.++.||.+--.   +...|..|||+.+|+|+.+|+..++
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            56778888876432   3578999999999999999985543

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=83.95  E-value=1.8  Score=35.43  Aligned_cols=41  Identities=15%  Similarity=0.188  Sum_probs=29.0

Q ss_pred             CCHHHHH-HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          468 LNPKERC-IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       468 L~~rER~-VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      .++..+. |+.+..-   +.+.|..+||..+|||+.+|+++..+.
T Consensus         6 ys~e~k~~~v~~~~~---~~g~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            6 YSEEFKRDAVALYEN---SDGASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCHHHHHHHHHHHTT---GGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH---cCCChHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555553 4444331   027899999999999999999987653

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=83.65  E-value=3.3  Score=35.11  Aligned_cols=50  Identities=14%  Similarity=0.101  Sum_probs=37.5

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          458 RQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       458 ~~~L~~~L~--~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      ...+...+.  .|++.+..||..-+.   +.+.|..|||+.+|+|+.+|..+..+
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            334445553  589999998877654   36899999999999999999754433

>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=82.95  E-value=0.68  Score=41.47  Aligned_cols=39  Identities=13%  Similarity=0.027  Sum_probs=29.5

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      ++..+|.-|...+-    .++|..+||+.||||+.+|+.+..+
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            45555544444443    5799999999999999999998765

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=82.79  E-value=3.5  Score=35.00  Aligned_cols=41  Identities=7%  Similarity=0.046  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|++.+..||..-+.   +.+.|..|||+.+|+|+.+|..+..+
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            799999998887653   25799999999999999999754433

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=82.53  E-value=1.9  Score=34.70  Aligned_cols=49  Identities=29%  Similarity=0.346  Sum_probs=33.3

Q ss_pred             HHHHhcC-CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          462 RNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       462 ~~~L~~L-~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ..++..| ++.+..||.+..   .+.+.|..|||+.+|+|+.+|++.    +++|.+
T Consensus        15 ~~~~~~l~~~~~~~il~~l~---~~~~~s~~ela~~l~is~~tvs~~----l~~L~~   64 (99)
T 3cuo_A           15 AALLKAMSHPKRLLILCMLS---GSPGTSAGELTRITGLSASATSQH----LARMRD   64 (99)
T ss_dssp             HHHHHHHCSHHHHHHHHHHT---TCCSEEHHHHHHHHCCCHHHHHHH----HHHHHH
T ss_pred             HHHHHHhCChHHHHHHHHHH---hCCCcCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            3444444 356666665433   346899999999999999999754    455543

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=82.52  E-value=4.8  Score=35.21  Aligned_cols=50  Identities=16%  Similarity=0.074  Sum_probs=38.1

Q ss_pred             HHHHHHH---hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          459 QHVRNLL---TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       459 ~~L~~~L---~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      ..+...+   ..|++.|..||...+.   +.+.|..|||+.+|+++.+|.+++.+-
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   3699999999887664   258999999999999999997655443

>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=82.46  E-value=3.6  Score=33.74  Aligned_cols=50  Identities=26%  Similarity=0.336  Sum_probs=33.3

Q ss_pred             HHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          460 HVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       460 ~L~~~L~~L~-~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .+..++..|. |.-..||.+-.   + .++|..||++.+|+|+.+|++    .|++|++
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L~---~-~~~~~~ela~~l~is~~tvs~----~L~~L~~   62 (102)
T 3pqk_A           12 EVANLLKTLSHPVRLMLVCTLV---E-GEFSVGELEQQIGIGQPTLSQ----QLGVLRE   62 (102)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHHH---T-CCBCHHHHHHHHTCCTTHHHH----HHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH---h-CCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            3445555555 44445554433   2 469999999999999999975    5555654

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=82.29  E-value=2.7  Score=35.72  Aligned_cols=48  Identities=10%  Similarity=0.120  Sum_probs=36.2

Q ss_pred             HHHHHHHh-cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          459 QHVRNLLT-LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       459 ~~L~~~L~-~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      ..+...+. .|++.+..||..-+.   +.+.|..|||+.+|+++.+|..+..
T Consensus        26 ~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~   74 (140)
T 2nnn_A           26 ALFANGIGNGLTPTQWAALVRLGE---TGPCPQNQLGRLTAMDAATIKGVVE   74 (140)
T ss_dssp             HHHHHHCSSCCCHHHHHHHHHHHH---HSSBCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            33444443 799999998877653   2489999999999999999975443

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=81.93  E-value=4.1  Score=33.07  Aligned_cols=50  Identities=18%  Similarity=0.228  Sum_probs=33.4

Q ss_pred             HHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          460 HVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       460 ~L~~~L~~L~-~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .+..++..|. +....||.+-   .+ .+.|..|||+.+|+|+.+|+    +.+++|++
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L---~~-~~~~~~ela~~l~is~~tvs----~~L~~L~~   62 (98)
T 3jth_A           12 KAVVLLKAMANERRLQILCML---HN-QELSVGELCAKLQLSQSALS----QHLAWLRR   62 (98)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHT---TT-SCEEHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHH---hc-CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            3445555554 4444555433   23 58999999999999999996    45556654

>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=81.89  E-value=1.5  Score=35.88  Aligned_cols=44  Identities=11%  Similarity=0.079  Sum_probs=32.9

Q ss_pred             cCCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~-~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|+.++..||...+.-. +|.+.|..|||+.+|+++.+|.+++.+
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            47888888887665322 234489999999999999999765443

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=81.77  E-value=2.9  Score=34.66  Aligned_cols=45  Identities=11%  Similarity=0.101  Sum_probs=31.3

Q ss_pred             HHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          461 VRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       461 L~~~L~~L~-~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      +..++..|. +....||.+..   + .+.|..|||+.+|+|+.+|++++.
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 55566666542   2 469999999999999999975543

>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=81.75  E-value=1.7  Score=36.37  Aligned_cols=47  Identities=21%  Similarity=0.347  Sum_probs=34.8

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      ..+.+....||...+-  .|++.|..|||+.+|+|+.+|+    +++++|...
T Consensus        14 ~~~~~~~l~Il~~l~~--~g~~~s~~eLa~~lgvs~~tV~----~~L~~L~~~   60 (110)
T 1q1h_A           14 SLLGDDVIDVLRILLD--KGTEMTDEEIANQLNIKVNDVR----KKLNLLEEQ   60 (110)
T ss_dssp             TTSCSTTHHHHHHHHH--HCSCBCHHHHHHTTTSCHHHHH----HHHHHHHHH
T ss_pred             HHcChHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHH----HHHHHHHHC
Confidence            3455667777766542  3467999999999999999997    567777653

>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=81.69  E-value=4.6  Score=34.38  Aligned_cols=53  Identities=9%  Similarity=0.147  Sum_probs=39.4

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          457 MRQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       457 l~~~L~~~L~--~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      +...+...+.  .|++.+..||..-+. .++++.|..|||+.+|+++.+|..+..+
T Consensus        16 ~~~~~~~~~~~~~lt~~~~~vL~~l~~-~~~~~~t~~ela~~l~~~~~tvs~~l~~   70 (139)
T 3eco_A           16 MKQKADQKLEQFDITNEQGHTLGYLYA-HQQDGLTQNDIAKALQRTGPTVSNLLRN   70 (139)
T ss_dssp             HHHHHHHHHGGGTCCHHHHHHHHHHHH-STTTCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHh-cCCCCcCHHHHHHHhCCCcccHHHHHHH
Confidence            3445555553  589999999987764 2225899999999999999999765444

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=81.58  E-value=2.2  Score=39.02  Aligned_cols=41  Identities=17%  Similarity=0.157  Sum_probs=31.7

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      ..|++.++.||.+...   +...|..|||+.+|+|+.+|+.++.
T Consensus        13 ~~ld~~d~~IL~~L~~---~~~~s~~eLA~~lglS~~tv~~~l~   53 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKK---DARLTISELSEQLKKPESTIHFRIK   53 (171)
T ss_dssp             -CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4578888888876542   2478999999999999999976543

>3sqn_A Conserved domain protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MGA family; 2.31A {Enterococcus faecalis}

Probab=81.56  E-value=1.7  Score=46.57  Aligned_cols=105  Identities=15%  Similarity=0.108  Sum_probs=59.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC-CCCCcchhhhcccCCCCChhHHHHHHHHHHHHHHHHhcCCHHH
Q 009567          394 SPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW-ADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKE  472 (532)
Q Consensus       394 ~Pt~eEIA~~lgis~e~v~~ll~~~~~~iSLD~~v~-~d~~~~l~d~i~d~~~~~pee~~~~~~l~~~L~~~L~~L~~rE  472 (532)
                      ..|..+||+.+|+|...|+.-+..-+..+.-...+. ...+-.    +.........             .....+++.+
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            578999999999999999987765433221000010 011111    1111000000             0112244555


Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       473 R~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      |....+.+.|.. ++.|+.++|+.+.||++||.+-.++..+.|+
T Consensus        95 R~~~Il~~LL~~-~~isi~~Lae~l~VS~sTi~~DLk~i~~~L~  137 (485)
T 3sqn_A           95 ISIQLLKELLFT-KELVTTSFLSTSGVSYETLKRHIKKMNQALR  137 (485)
T ss_dssp             HHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHHHG
T ss_pred             HHHHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence            655555555543 5899999999999999999766655555443

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=81.48  E-value=2.2  Score=35.20  Aligned_cols=39  Identities=21%  Similarity=0.269  Sum_probs=28.4

Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       469 ~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      +|....||.....  + .++|..|||+.+|+|+++|++..+.
T Consensus        26 ~~~Rl~IL~~l~~--~-~~~~~~ela~~l~is~stvs~hL~~   64 (99)
T 2zkz_A           26 HPMRLKIVNELYK--H-KALNVTQIIQILKLPQSTVSQHLCK   64 (99)
T ss_dssp             SHHHHHHHHHHHH--H-SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH--C-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4666677733221  1 4799999999999999999876543

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=81.45  E-value=4.1  Score=34.80  Aligned_cols=41  Identities=22%  Similarity=0.299  Sum_probs=32.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  508 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie  508 (532)
                      ..|++.+..|+.+.+ +.+ .+.|..|||+.+|+|+.+|..+.
T Consensus        22 ~gl~~~~~~il~~L~-~~~-~~~t~~ela~~l~~~~stvs~~l   62 (152)
T 1ku9_A           22 HGLNKSVGAVYAILY-LSD-KPLTISDIMEELKISKGNVSMSL   62 (152)
T ss_dssp             TTCCHHHHHHHHHHH-HCS-SCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCChhHHHHHHHHH-HcC-CCCCHHHHHHHHCcCHHHHHHHH
Confidence            368999999988764 223 57999999999999999996544

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=81.43  E-value=3.1  Score=32.91  Aligned_cols=28  Identities=14%  Similarity=0.237  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .+.|..|||+.+|+|+.+|++    .+++|.+
T Consensus        13 ~~~s~~eLa~~lgvs~~tv~r----~L~~L~~   40 (81)
T 2htj_A           13 NGGKTAEIAEALAVTDYQARY----YLLLLEK   40 (81)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHH----HHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            468999999999999999975    4555544

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=81.43  E-value=4.7  Score=35.00  Aligned_cols=48  Identities=15%  Similarity=0.242  Sum_probs=36.9

Q ss_pred             HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          460 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       460 ~L~~~L--~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .+...+  ..|++.|..||..-+.   +.+.|..|||+.+|+++.+|.++..+
T Consensus        29 ~~~~~~~~~~lt~~q~~iL~~l~~---~~~~~~~eLa~~l~~~~~~vs~~l~~   78 (149)
T 4hbl_A           29 FYEKKLKQFGITYSQYLVMLTLWE---ENPQTLNSIGRHLDLSSNTLTPMLKR   78 (149)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHH---SSSEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            344444  3599999999887653   36899999999999999999765544

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=81.35  E-value=1.5  Score=36.74  Aligned_cols=38  Identities=18%  Similarity=0.209  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      +|...|+.+..-    .+.|..+||+.+|||..||+..+..-
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    34899999999999999999887753

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=81.25  E-value=3.7  Score=34.60  Aligned_cols=45  Identities=16%  Similarity=0.248  Sum_probs=32.3

Q ss_pred             HHHHHhc-CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          461 VRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       461 L~~~L~~-L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      +..++.. .++.+..||.+..-    .+.|+.|||+.+|+|+.+|++.++
T Consensus        22 ~~~~~~~l~~~~~~~il~~L~~----~~~s~~ela~~l~is~stvsr~l~   67 (119)
T 2lkp_A           22 VASTLQALATPSRLMILTQLRN----GPLPVTDLAEAIGMEQSAVSHQLR   67 (119)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHHH----CCCCHHHHHHHHSSCHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3344433 35677777776553    479999999999999999975544

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=81.24  E-value=9.9  Score=31.28  Aligned_cols=36  Identities=11%  Similarity=0.035  Sum_probs=28.1

Q ss_pred             HHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 009567          382 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI  417 (532)
Q Consensus       382 ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~  417 (532)
                      ++..-+.......++.++||+.+|+++..+..+...
T Consensus         6 ~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~   41 (108)
T 3mn2_A            6 QVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQR   41 (108)
T ss_dssp             HHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            344445555666789999999999999999888763

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=80.85  E-value=5.1  Score=34.81  Aligned_cols=50  Identities=6%  Similarity=0.133  Sum_probs=37.3

Q ss_pred             HHHHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          458 RQHVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       458 ~~~L~~~L--~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      ...+...+  ..|++.+..||...+.   ..+.|..|||+.+|+++.+|..++.+
T Consensus        29 ~~~~~~~l~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~i~~~tvs~~l~~   80 (155)
T 3cdh_A           29 SAQFHDHIRAQGLRVPEWRVLACLVD---NDAMMITRLAKLSLMEQSRMTRIVDQ   80 (155)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHSS---CSCBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            34444444  3699999988876543   35799999999999999999765443

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=80.70  E-value=4.6  Score=34.76  Aligned_cols=49  Identities=20%  Similarity=0.251  Sum_probs=37.3

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          459 QHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       459 ~~L~~~L~--~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      ..+...+.  .|++.+..||...+.   ..+.|..|||+.+|+++.+|.+++.+
T Consensus        29 ~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~   79 (150)
T 2rdp_A           29 QRGREILTNYPITPPQFVALQWLLE---EGDLTVGELSNKMYLACSTTTDLVDR   79 (150)
T ss_dssp             HHHHHHHTTSSSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCchhHHHHHHH
Confidence            34555553  589999998877653   24799999999999999999765544

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=80.69  E-value=4.6  Score=34.30  Aligned_cols=62  Identities=16%  Similarity=0.221  Sum_probs=44.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcc-cCCCCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHHHh
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESR----ALYRLKQSL  519 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL-~~~e~~Tl~EIAe~LgISrerVRqie~r----ALkKLR~~l  519 (532)
                      ...|...+..|++.|+.|..+..-= ..-..+|..|+|+..|+|..+|-+..++    ...-+|..+
T Consensus         5 ~~~I~~~~~~lt~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~gf~efk~~l   71 (107)
T 3iwf_A            5 LYKIDNQYPYFTKNEKKIAQFILNYPHKVVNMTSQEIANQLETSSTSIIRLSKKVTPGGFNELKTRL   71 (107)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHHHCHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHhCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence            3467788899999999998754420 0114799999999999999999765543    344444444

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=80.60  E-value=4.8  Score=34.11  Aligned_cols=51  Identities=6%  Similarity=0.017  Sum_probs=38.5

Q ss_pred             HHHHHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          457 MRQHVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       457 l~~~L~~~L--~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      +...+...+  ..|++.+..||..-+.   ..+.|..+||+.+|+++.+|.++..+
T Consensus        19 ~~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~~~~~la~~l~~~~~tvs~~l~~   71 (138)
T 1jgs_A           19 KDRLLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDR   71 (138)
T ss_dssp             HHHHHHHHHTTTTSCHHHHHHHHHHHH---HSSBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhhhcCCCHHHHHHHHHHHh---cCCCCHHHHHHHHCCChHHHHHHHHH
Confidence            344555555  3589999998877653   25789999999999999999765544

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=80.53  E-value=4.5  Score=35.08  Aligned_cols=41  Identities=5%  Similarity=0.050  Sum_probs=33.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|++.+..||..-+.   ..+.|..|||+.+|+++.+|.++..+
T Consensus        38 ~lt~~~~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~   78 (154)
T 2qww_A           38 GLTIQQLAMINVIYS---TPGISVADLTKRLIITGSSAAANVDG   78 (154)
T ss_dssp             TCCHHHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            699999999887654   25799999999999999999765544

---

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	532
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	3e-28
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	7e-27
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	7e-20
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	1e-19
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	6e-16
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	2e-15
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	6e-09
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	4e-07
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	8e-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	3e-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 =  108 bits (271), Expect = 3e-28
 Identities = 57/179 (31%), Positives = 92/179 (51%), Gaps = 30/179 (16%)

Query: 218 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIR------------------LEKEKSKLQ 259
           DP+R +L       LLT +EE +L  ++++ +                   + + K    
Sbjct: 2   DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGT 61

Query: 260 SQFGREPTLIEWAKAIGLSCRDLKSE------------LHSGNSSREKLINANLRLVVHV 307
           ++  + P L E      +   D K +               G ++R+ LI ANLRLVV +
Sbjct: 62  ARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSI 121

Query: 308 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 366
           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 =  109 bits (272), Expect = 7e-27
 Identities = 46/190 (24%), Positives = 84/190 (44%)

Query: 171 KQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETR 230
           + F Q R + ++      S   + +      R             + + + LF     + 
Sbjct: 142 EVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSD 201

Query: 231 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 290
               A          +     E+    LQ     E       + +    R +        
Sbjct: 202 TWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKAR 261

Query: 291 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 350
            ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA W
Sbjct: 262 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 321

Query: 351 WVRQTIRKAI 360
           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 = 81.9 bits (202), Expect = 7e-20
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 287 HSGNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCR 343
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 6   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 65

Query: 344 FASYAYWWVRQTIRKAI 360
             +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 = 81.3 bits (201), Expect = 1e-19
 Identities = 30/80 (37%), Positives = 51/80 (63%)

Query: 452 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 511
             + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +A
Sbjct: 3   AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62

Query: 512 LYRLKQSLGGKASYGYADLL 531
           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 = 70.1 bits (172), Expect = 6e-16
 Identities = 22/67 (32%), Positives = 41/67 (61%)

Query: 463 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 522
           ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +L+     +
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 523 ASYGYAD 529
               + 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 = 68.5 bits (168), Expect = 2e-15
 Identities = 22/57 (38%), Positives = 41/57 (71%)

Query: 461 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 517
           +   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 = 50.6 bits (121), Expect = 6e-09
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 507
            +  V K+ + + V+  ++ L  +E+ +++L F     +     EV  I   S  RV QL
Sbjct: 2   VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQL 57

Query: 508 ESRALYRLKQSL 519
           +++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 = 45.5 bits (108), Expect = 4e-07
 Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 9/82 (10%)

Query: 364 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MP 421
           SR +R          ++ E      ++    P  E++A+ +GI+ E+L + +        
Sbjct: 2   SRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI 55

Query: 422 LSMQQPVWADQDTTFQEITADT 443
           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 = 43.9 bits (104), Expect = 8e-07
 Identities = 10/56 (17%), Positives = 27/56 (48%)

Query: 365 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM 420
            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 = 42.7 bits (101), Expect = 2e-06
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLSM 424
           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 = 37.3 bits (87), Expect = 3e-04
 Identities = 14/63 (22%), Positives = 22/63 (34%), Gaps = 4/63 (6%)

Query: 457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 516
           +RQ V   +  L    R  + LR  ++     S  E+  I       VR    RA   + 
Sbjct: 8   LRQIVFRTIESLPEDLRMAITLRE-LDG---LSYEEIAAIMDCPVGTVRSRIFRAREAID 63

Query: 517 QSL 519
             +
Sbjct: 64  NKV 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	532
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	100.0
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.84
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.78
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.67
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
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.16
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.15
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.06
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.86
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.75
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.73
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.45
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.4
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.32
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	98.11
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.94
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.89
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.56
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	95.84
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	95.25
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.51
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	94.46
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	92.15
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	91.88
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.6
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	91.34
d1hlva1	66	DNA-binding domain of centromere binding protein B	90.86
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	89.9
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	89.49
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	87.61
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	87.3
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	87.13
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	86.93
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	86.88
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	86.63
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	86.58
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	86.46
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	86.45
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	86.39
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	86.07
d1zyba1	73	Probable transcription regulator BT4300, C-termina	85.6
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	85.33
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	85.27
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	85.09
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	84.58
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	84.38
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	84.07
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	83.96
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	83.26
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	82.89
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	82.85
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	82.7
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	82.52
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	81.83
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	80.94
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	80.63
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	80.53
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	80.44
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	80.25
d1y7ya1	69	Restriction-modification controller protein C.AhdI	80.15

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=100.00  E-value=5.4e-34  Score=268.06  Aligned_cols=150  Identities=37%  Similarity=0.633  Sum_probs=122.5

Q ss_pred             ChHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------------hhhCCCCcHHHH-------
Q 009567          217 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ------------------SQFGREPTLIEW-------  271 (532)
Q Consensus       217 ~d~l~~yl~~i~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~------------------~~~g~~pt~~ew-------  271 (532)
                      +||+++||++|+++||||++||++|+++|+.++.+.....+..                  ...+..|...+|       
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            4899999999999999999999999999998775544322221                  112223333322       


Q ss_pred             --HHHccCC---HHHHHHHHhhcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhh
Q 009567          272 --AKAIGLS---CRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAS  346 (532)
Q Consensus       272 --A~aag~~---~~~L~~~l~~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFST  346 (532)
                        .......   ...+....+.|..|+++||.+|++||++||++|.+.|.+++||||||+|||++|+++|||++|++|+|
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              2222221   24466777888999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhccc
Q 009567          347 YAYWWVRQTIRKAIFQHSRT  366 (532)
Q Consensus       347 YA~~wIr~aI~~~ir~~~r~  366 (532)
                      ||+|||+++|.+++++++|+
T Consensus       161 ya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         161 YATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHhCCC
Confidence            99999999999999998864

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

Probab=99.84  E-value=1.6e-21  Score=197.83  Aligned_cols=76  Identities=43%  Similarity=0.927  Sum_probs=72.6

Q ss_pred             hcHHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhh
Q 009567          288 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  363 (532)
Q Consensus       288 ~g~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~  363 (532)
                      ....|++.||..|++||++||++|.++|++++||+|+|++||++|+++|||.+|++|||||+||||++|.++++++
T Consensus       259 ~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         259 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             hccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHHHHHHhCC
Confidence            3347999999999999999999999999999999999999999999999999999999999999999999999874

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.78  E-value=2e-19  Score=149.56  Aligned_cols=75  Identities=24%  Similarity=0.377  Sum_probs=69.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCC---CCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHHHhhc
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  364 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~---g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~ir~~~  364 (532)
                      ...+++||..|++||.++|++|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|.+++|+..
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            3468999999999999999998664   78999999999999999999999999999999999999999999998754

>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=99.67  E-value=1.8e-17  Score=137.36  Aligned_cols=75  Identities=39%  Similarity=0.737  Sum_probs=71.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 009567          457 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL  531 (532)
Q Consensus       457 l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yldll  531 (532)
                      +++.|..+|+.|+|+|+.||.+||||++++++|+.|||+.||||+++|||++.+|++|||.......++.|++++
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            456788999999999999999999999999999999999999999999999999999999999899999999875

>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=2.7e-17  Score=130.16  Aligned_cols=66  Identities=33%  Similarity=0.614  Sum_probs=63.3

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 009567          464 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  529 (532)
Q Consensus       464 ~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l~~yld  529 (532)
                      +|+.|+|+|+.||.+||||++++++|++|||+.||||+++|||++.+|++|||.......+++|++
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=9.5e-16  Score=118.75  Aligned_cols=57  Identities=39%  Similarity=0.728  Sum_probs=54.3

Q ss_pred             HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          462 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       462 ~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      ..+|+.|+++|+.||.+||||++++++|++|||+.||||+++|||++.+|++|||+.
T Consensus         3 ~~~L~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR~~   59 (61)
T d1ku3a_           3 EKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH   59 (61)
T ss_dssp             SSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHhcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcC
Confidence            456899999999999999999999999999999999999999999999999999974

>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=8.6e-13  Score=103.97  Aligned_cols=70  Identities=29%  Similarity=0.414  Sum_probs=66.0

Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 009567          448 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  521 (532)
Q Consensus       448 pee~~~~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~  521 (532)
                      |++.+...+....|..+|+.|||++|+||.++|+    +++|++|||+.||+|.++|+++..+|+++||+.+.+
T Consensus         2 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~L~~   71 (71)
T d1rp3a2           2 VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQLKAKALERLREMLSN   71 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHT----SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHh----HhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHccC
Confidence            6777888889999999999999999999999998    999999999999999999999999999999998753

>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=99.16  E-value=5.5e-11  Score=93.03  Aligned_cols=63  Identities=22%  Similarity=0.153  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 009567          454 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  520 (532)
Q Consensus       454 ~~~l~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~  520 (532)
                      .++....|..+|+.||+++|+||.++|.    +++|++|||+.||+|.++|++...||+++||..++
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            3456778999999999999999999998    99999999999999999999999999999999875

>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=99.06  E-value=1.3e-10  Score=89.11  Aligned_cols=58  Identities=26%  Similarity=0.461  Sum_probs=55.1

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCCccc
Q 009567          367 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLSM  424 (532)
Q Consensus       367 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~~iSL  424 (532)
                      ||+|.|+.+.+++++++.+++.+++||+||.+|||+.+|  +++++|..++...+.++||
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            799999999999999999999999999999999999997  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=98.86  E-value=1.5e-09  Score=82.29  Aligned_cols=54  Identities=17%  Similarity=0.244  Sum_probs=51.2

Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc
Q 009567          365 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT  418 (532)
Q Consensus       365 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~  418 (532)
                      ++||+|+|+.+.++|++++.+.+.+++||+||.+|||+.+|+++++|..++...
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=98.75  E-value=1.6e-08  Score=85.85  Aligned_cols=55  Identities=24%  Similarity=0.220  Sum_probs=50.1

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      .-|||+||+||.+||.    +++|+.|||+.||||+++|++.++||+++||+....-++
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            4499999999999998    999999999999999999999999999999997555444

>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=98.73  E-value=1.6e-08  Score=85.88  Aligned_cols=55  Identities=24%  Similarity=0.244  Sum_probs=49.8

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  524 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~l~~~~l  524 (532)
                      ..|||++|.||.++|+    +++|++|||+.||||+++|+..++||+++||+....-++
T Consensus        15 ~lLp~~qR~v~~L~y~----~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~e~kL~l   69 (106)
T d1s7oa_          15 ALLTDKQMNYIELYYA----DDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   69 (106)
T ss_dssp             GGSCHHHHHHHHHHHH----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             hhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            4499999999999999    999999999999999999999999999999986554443

>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=98.45  E-value=1.2e-07  Score=74.71  Aligned_cols=69  Identities=16%  Similarity=0.155  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHhhHHHHHHHHHHHhhhhhCCcCCCchhhHHHHHHHHHHHHHH
Q 009567          290 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  360 (532)
Q Consensus       290 ~~Are~LI~~nlrLV~sIAkrY~~~g~~~eDLiQEG~iGLikAiekFDp~kG~rFSTYA~~wIr~aI~~~i  360 (532)
                      ..++++++..|.+.++.+|.++.++..+.+|++||.++.+|+..++|++.  .+|.+|++..+++.+.+++
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            36799999999999999999999999999999999999999999999874  4699999999999988765

>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=98.40  E-value=3.1e-08  Score=78.97  Aligned_cols=70  Identities=16%  Similarity=0.242  Sum_probs=57.8

Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCcchhhhccc
Q 009567          372 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITAD  442 (532)
Q Consensus       372 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~iSLD~~v~~d~~~~l~d~i~d  442 (532)
                      .+..+++++.++...|.+++||.||.+|||..|||++++|..++...  ..++|||.++.+ ++..+.+++++
T Consensus         4 s~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~d-~~~~~~e~lps   75 (77)
T d1rp3a1           4 QVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRD-FARDYSELIPS   75 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHTTTGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCccC-CCCchhccCCC
Confidence            34578899999999999999999999999999999999999998653  467899986643 34566676665

>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=98.32  E-value=7.6e-07  Score=69.54  Aligned_cols=53  Identities=13%  Similarity=0.322  Sum_probs=48.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 009567          458 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  515 (532)
Q Consensus       458 ~~~L~~~L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKL  515 (532)
                      .+.+...+..|+|+|++|+.+..     .|+|.+|||..||||..||+....++++||
T Consensus         3 ~~~~~~~~~~LT~rE~~vl~~l~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl   55 (70)
T d1yioa1           3 QDQLEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKL   55 (70)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence            45677888999999999999976     799999999999999999999999999998

>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=98.11  E-value=2.6e-06  Score=65.72  Aligned_cols=47  Identities=19%  Similarity=0.301  Sum_probs=44.1

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          465 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       465 L~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      +..|+|+|++|+.+.-     +|+|.+|||+.||||..+|+....++++||.
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            5689999999999887     7999999999999999999999999999984

>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=97.94  E-value=8.1e-06  Score=62.52  Aligned_cols=45  Identities=27%  Similarity=0.383  Sum_probs=42.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .|+++|++|+.+.-     +|+|.+|||+.||+|..+|+.+..++++||.
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            69999999998876     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=97.89  E-value=1.1e-05  Score=62.03  Aligned_cols=45  Identities=29%  Similarity=0.378  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .|+|+|++|+.+.-     +|+|.+|||+.||+|..+|+.+..++++||-
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     8999999999999999999999999999983

>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=97.56  E-value=5e-05  Score=61.36  Aligned_cols=45  Identities=22%  Similarity=0.297  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  516 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR  516 (532)
                      .|+++|++|+.+..     .|++.+|||+.||+|..+|+....++++||.
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            59999999999988     7999999999999999999999999999983

>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=95.84  E-value=0.0095  Score=43.77  Aligned_cols=39  Identities=31%  Similarity=0.479  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHHhh
Q 009567          250 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS  288 (532)
Q Consensus       250 ~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l~~  288 (532)
                      ++.++..+|...+|++||.+|.|+++|++.+++...+..
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            566788999999999999999999999999998776654

>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=95.25  E-value=0.01  Score=45.50  Aligned_cols=43  Identities=16%  Similarity=0.285  Sum_probs=35.7

Q ss_pred             cCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCC-CHHHHHHHHH
Q 009567          467 LLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGL-SKERVRQLES  509 (532)
Q Consensus       467 ~L~~rER~VL~L--RyGL~~~e~~Tl~EIAe~LgI-SrerVRqie~  509 (532)
                      .|+++|++||..  .|....|-+-|++|||+.+|+ |.++|+.++.
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            599999999987  344455688999999999999 8999987754

>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=94.51  E-value=0.029  Score=43.23  Aligned_cols=38  Identities=39%  Similarity=0.554  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHhhhCCCCcHHHHHHHccCCHHHHHHHH
Q 009567          249 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL  286 (532)
Q Consensus       249 ~~le~~~~~l~~~~g~~pt~~ewA~aag~~~~~L~~~l  286 (532)
                      .+++++...|+..+||+||.+|.|...||+.+++...+
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            36778999999999999999999999999998887654

>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=94.46  E-value=0.032  Score=39.37  Aligned_cols=37  Identities=16%  Similarity=0.251  Sum_probs=31.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL  507 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqi  507 (532)
                      .|++.+.+-++-.+-    .|.|..+||..||||+.||.++
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            477777777777665    7899999999999999999765

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=92.15  E-value=0.18  Score=37.11  Aligned_cols=39  Identities=31%  Similarity=0.558  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHhhhCCCCcHHHHHHHccC--CHHHHHHHHh
Q 009567          249 IRLEKEKSKLQSQFGREPTLIEWAKAIGL--SCRDLKSELH  287 (532)
Q Consensus       249 ~~le~~~~~l~~~~g~~pt~~ewA~aag~--~~~~L~~~l~  287 (532)
                      -++.++..+|...+|++||.+|.|++.|+  +.+.+...++
T Consensus        12 ~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~   52 (60)
T d1ku2a1          12 NKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLK   52 (60)
T ss_dssp             HHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGG
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHH
Confidence            35677889999999999999999999975  4555655443

>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=91.88  E-value=0.2  Score=36.83  Aligned_cols=40  Identities=20%  Similarity=0.385  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      |++.+++||...-.   +...|+.|||+.+|+|..+|+..+.+
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            67888899887654   35789999999999999999865543

>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=91.60  E-value=0.2  Score=36.59  Aligned_cols=40  Identities=15%  Similarity=0.344  Sum_probs=31.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      |++.++.||.+--.   +...|+.|||+.+|+|+++|.+++.+
T Consensus         1 lD~~D~kIl~~L~~---n~r~s~~~lA~~~gls~~~v~~Ri~~   40 (60)
T d1i1ga1           1 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRKRVKA   40 (60)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            46678888886553   25779999999999999999865543

>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=91.34  E-value=0.2  Score=36.94  Aligned_cols=41  Identities=20%  Similarity=0.146  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .|++.++.||...-.   +...|+.|||+.+|+|+++|.+++.+
T Consensus         2 klD~~D~~IL~~L~~---n~r~s~~~iA~~lgis~~tv~~Ri~~   42 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVRQ   42 (63)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            477888888877553   35789999999999999999865543

>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=90.86  E-value=0.15  Score=38.28  Aligned_cols=44  Identities=9%  Similarity=0.130  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      .|+..|+.=|..+|-  +|+.++..|||..|||++++|+.|.++-=
T Consensus         7 ~LT~~eK~~ii~~~e--~g~k~sq~eIA~~fGv~~STvs~IlKnK~   50 (66)
T d1hlva1           7 QLTFREKSRIIQEVE--ENPDLRKGEIARRFNIPPSTLSTILKNKR   50 (66)
T ss_dssp             CCCHHHHHHHHHHHH--HCTTSCHHHHHHHHTCCHHHHHHHHHTHH
T ss_pred             cCCHHHHHHHHHHHH--cCCcchHHHHHHHhCCChhHHHHHHHHHH
Confidence            466666655544442  34667999999999999999999988743

>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=89.90  E-value=0.42  Score=34.58  Aligned_cols=40  Identities=18%  Similarity=0.353  Sum_probs=30.3

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       468 L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      |++.++.||..--.   +...|+.|||+.+|+|+.+|....++
T Consensus         1 lD~~D~~Il~~L~~---n~r~s~~eiA~~l~ls~~~v~~Ri~~   40 (60)
T d2cyya1           1 LDEIDKKIIKILQN---DGKAPLREISKITGLAESTIHERIRK   40 (60)
T ss_dssp             CCHHHHHHHHHHHH---CTTCCHHHHHHHHCSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45667777776543   35779999999999999999765443

>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=89.49  E-value=0.17  Score=34.83  Aligned_cols=31  Identities=6%  Similarity=0.209  Sum_probs=26.3

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      +|..|+-     +++.-.+||+.|||++.+|-.+++
T Consensus        10 ~V~~L~~-----~G~gat~IAk~lgI~R~SVYR~L~   40 (43)
T d1gdta1          10 AVLNMWQ-----QGLGASHISKTMNIARSTVYKVIN   40 (43)
T ss_dssp             HHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHh
Confidence            4666664     899999999999999999987665

>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=87.61  E-value=0.27  Score=37.57  Aligned_cols=28  Identities=25%  Similarity=0.396  Sum_probs=24.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      ++|.+|||..+|+|+++|.    |++++|++.
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            7899999999999999995    788888774

>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=87.30  E-value=0.31  Score=38.09  Aligned_cols=36  Identities=19%  Similarity=0.244  Sum_probs=28.5

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          473 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       473 R~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      .++|.+..-   ++|+|..+||+.||||..+|+++..+.
T Consensus        12 ~~aV~l~~~---~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          12 RDAVALYEN---SDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHHTT---GGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHH---cCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            356666541   147999999999999999999998765

>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=87.13  E-value=0.3  Score=38.55  Aligned_cols=43  Identities=26%  Similarity=0.222  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHHHH--hcccCCCCCCHHHHHHHhC--CCHHHHHHHHH
Q 009567          467 LLNPKERCIVRLR--FGIEDGKPKSLSEVGNIFG--LSKERVRQLES  509 (532)
Q Consensus       467 ~L~~rER~VL~LR--yGL~~~e~~Tl~EIAe~Lg--ISrerVRqie~  509 (532)
                      .|++|+++||...  +.+..|.+-+.++|++.+|  +|..+||..+.
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            4899999998752  3356779999999999966  58999997653

>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=86.93  E-value=0.0058  Score=51.78  Aligned_cols=32  Identities=13%  Similarity=0.280  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +|+|++|||++||.|+..|+.++++|++++++
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            78999999999999999999999999998865

>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=86.88  E-value=0.27  Score=36.54  Aligned_cols=27  Identities=37%  Similarity=0.506  Sum_probs=23.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +.|.+|||..+|+|+++|.    |.|++|++
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            5899999999999999995    66777765

>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=86.63  E-value=0.35  Score=35.55  Aligned_cols=42  Identities=19%  Similarity=0.368  Sum_probs=30.5

Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          469 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       469 ~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +....+||.+-   .++...|.+|+|+.||||+.+|++.    +++|++
T Consensus         4 ~~~~~~iL~~L---~~~~~~s~~eLa~~l~vS~~ti~r~----i~~L~~   45 (63)
T d1biaa1           4 NTVPLKLIALL---ANGEFHSGEQLGETLGMSRAAINKH----IQTLRD   45 (63)
T ss_dssp             CHHHHHHHHHH---TTSSCBCHHHHHHHHTSCHHHHHHH----HHHHHH
T ss_pred             cHHHHHHHHHH---HHCCcCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            34445555543   4557899999999999999999865    455655

>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=86.58  E-value=0.86  Score=38.02  Aligned_cols=46  Identities=22%  Similarity=0.308  Sum_probs=36.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      -.|++.+-.|+.+-+. . ++++|..|||+.+|+|+.+|+.    ++++|-+
T Consensus        22 ~Gl~~~~~~i~~~L~~-~-~~plt~~ela~~l~vsk~~vs~----~l~~L~~   67 (151)
T d1ku9a_          22 HGLNKSVGAVYAILYL-S-DKPLTISDIMEELKISKGNVSM----SLKKLEE   67 (151)
T ss_dssp             TTCCHHHHHHHHHHHH-C-SSCEEHHHHHHHHTCCHHHHHH----HHHHHHH
T ss_pred             cCCCHHHHHHHHHHHh-C-CCCcCHHHHHHHhCCCcchHHH----HHHHHHH
Confidence            3589999999988873 3 3679999999999999999975    4555543

>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=86.46  E-value=0.52  Score=39.23  Aligned_cols=25  Identities=12%  Similarity=0.099  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      ++++..+||+.||||+.+|+.+..+
T Consensus        31 ~G~s~r~iA~~~~VS~~tV~k~l~r   55 (123)
T d1pdnc_          31 DGIRPCVISRQLRVSHGCVSKILNR   55 (123)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHCcCHHHHHHHHHH
Confidence            7899999999999999999887765

>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=86.45  E-value=0.36  Score=35.25  Aligned_cols=25  Identities=12%  Similarity=0.135  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .++|.+|+|+.+|||+.+|+++++.
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            4699999999999999999999974

>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=86.39  E-value=0.35  Score=36.84  Aligned_cols=29  Identities=34%  Similarity=0.491  Sum_probs=24.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      -++|.+|||..+|+|+++|.    +++++|++.
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    778888774

>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=86.07  E-value=0.46  Score=35.85  Aligned_cols=43  Identities=12%  Similarity=0.108  Sum_probs=37.7

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-CCCHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-GLSKERVRQLE  508 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~L-gISrerVRqie  508 (532)
                      +.|++.+++|+.+.-.-.+.+|.+..||+..| |++...|++..
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            46999999999998887777999999999999 89999987644

>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=85.60  E-value=0.33  Score=36.71  Aligned_cols=28  Identities=7%  Similarity=0.259  Sum_probs=24.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          487 PKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       487 ~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      ++|.+|||..+|+|+++|.    |++++|++.
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            5799999999999999994    788888764

>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=85.33  E-value=0.39  Score=36.49  Aligned_cols=29  Identities=14%  Similarity=0.099  Sum_probs=24.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  518 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~rALkKLR~~  518 (532)
                      -++|.+|||..+|+|+++|.    |+|++|++.
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    778888764

>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=85.27  E-value=0.92  Score=33.99  Aligned_cols=40  Identities=20%  Similarity=0.356  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCC-CHHHHHHHHHh
Q 009567          378 SKVLEAKRLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFI  417 (532)
Q Consensus       378 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgi-s~e~v~~ll~~  417 (532)
                      .++-.....+..++|..||..|||+.+|+ |+..|...+..
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            34445556677788999999999999999 78888887764

>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=85.09  E-value=0.57  Score=36.31  Aligned_cols=49  Identities=16%  Similarity=0.237  Sum_probs=38.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          459 QHVRNLLTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       459 ~~L~~~L~~L~~rER~VL~LRyGL~~---~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      ..|...+..|++.|+.|..+.  +++   -..+|.+|||+..|||..+|-+..+
T Consensus         7 ~~i~~~~~~Ls~~e~~ia~yi--l~~~~~~~~~si~~lA~~~~vS~sTi~Rf~k   58 (83)
T d2o3fa1           7 AIIQSMKHKLPPSERKLADYI--LAHPHKAIESTVNEISALANSSDAAVIRLCK   58 (83)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHH--HHCHHHHHTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHHHHH--HcCHHHHHHccHHHHHHHHCCCHHHHHHHHH
Confidence            457778899999999988543  332   2579999999999999999976544

>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=84.58  E-value=1.8  Score=35.27  Aligned_cols=55  Identities=11%  Similarity=0.091  Sum_probs=40.6

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          458 RQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       458 ~~~L~~~L~--~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      ...+...+.  .|++.|-.||..-+. .+|.+.|..||++.+|+++.+|.    +++++|-+
T Consensus        15 ~~~~~~~l~~~glt~~q~~vL~~l~~-~~~~~it~~ela~~~~~~~~~vs----~~l~~L~~   71 (135)
T d3broa1          15 STRFDIFAKKYDLTGTQMTIIDYLSR-NKNKEVLQRDLESEFSIKSSTAT----VLLQRMEI   71 (135)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHH-TTTSCCBHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH-cCCCCCCHHHHHHHHCcCHhHHH----HHHHHHHH
Confidence            334444443  489999999987764 34467999999999999999996    55566543

>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=84.38  E-value=0.52  Score=37.79  Aligned_cols=43  Identities=21%  Similarity=0.244  Sum_probs=33.7

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          466 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       466 ~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      -.|++.+..||...+-  .+.++|..|||+.+|+++.+|+.++.+
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            4699999999875542  125799999999999999999755443

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.07  E-value=0.75  Score=33.87  Aligned_cols=46  Identities=15%  Similarity=0.270  Sum_probs=29.8

Q ss_pred             CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          468 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       468 L~~rER~VL~LRyGL~-~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      |++..-.-|...|-|. .+..-+..+||+.||||+.+|.    ++++||.+
T Consensus         3 ls~s~EdYL~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt----~mvkrL~~   49 (63)
T d2isya1           3 LVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVS----QTVSRMER   49 (63)
T ss_dssp             TSSHHHHHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCchhHH----HHHHHHHH
Confidence            3333333344434332 3456899999999999999996    55666654

>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=83.96  E-value=0.57  Score=35.08  Aligned_cols=25  Identities=20%  Similarity=0.320  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .++|..|+|+.||||+.+|.+++..
T Consensus        13 ~gltQ~elA~~LGvs~~ti~~yE~G   37 (67)
T d2auwa1          13 NNLSLTTAAEALGISRRMVSYYRTA   37 (67)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            6799999999999999999998863

>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=83.26  E-value=0.94  Score=36.72  Aligned_cols=46  Identities=24%  Similarity=0.180  Sum_probs=35.3

Q ss_pred             HHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          461 VRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       461 L~~~L-~~L~~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      +++.- ..|+|-|.-.-.-++. +  .++|.++||+.+|+|+.+|++++.
T Consensus         6 ~EN~qR~~L~p~e~A~a~~~l~-~--~g~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_           6 IENLQRNELTPREIADFIGREL-A--KGKKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             HHHHHTTCCCHHHHHHHHHHHH-H--TTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             HHHHcccCCCHHHHHHHHHHHH-H--hCCCHHHHHHHHCCcHHHHHHHHH
Confidence            33444 4588888877666653 2  578999999999999999999875

>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=82.89  E-value=1.5  Score=34.50  Aligned_cols=51  Identities=22%  Similarity=0.245  Sum_probs=36.1

Q ss_pred             HHHHHHHhcCCHHHH-HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          459 QHVRNLLTLLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       459 ~~L~~~L~~L~~rER-~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      +.+.+++..|...-| .||.+-..    .+++..||++.+|+|+.+|++.+    +.|+.
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            356667778876555 44443332    57999999999999999998754    45554

>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=82.85  E-value=1.4  Score=34.87  Aligned_cols=50  Identities=12%  Similarity=0.230  Sum_probs=33.7

Q ss_pred             HHHHHHhcCCH-HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          460 HVRNLLTLLNP-KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       460 ~L~~~L~~L~~-rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .+..++..|.. .-..||.+-.   + .++|..||++.+|+|+++|++.+    ++|++
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            34455555554 4445554332   2 57999999999999999998764    45554

>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=82.70  E-value=0.63  Score=36.29  Aligned_cols=44  Identities=16%  Similarity=0.179  Sum_probs=32.8

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH-----HHHHHHHHhhc
Q 009567          474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR-----ALYRLKQSLGG  521 (532)
Q Consensus       474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r-----ALkKLR~~l~~  521 (532)
                      .|-.+|--    .++|.+++|+.+|+|+.+|.++++.     .+.+|.+.+..
T Consensus        15 ~i~~~r~~----~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~~   63 (89)
T d2o38a1          15 ALNAVIDR----ARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNA   63 (89)
T ss_dssp             HHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHH
T ss_pred             HHHHHHHH----cCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHHH
Confidence            34455555    7999999999999999999999972     25555554443

>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=82.52  E-value=0.71  Score=34.10  Aligned_cols=32  Identities=13%  Similarity=0.182  Sum_probs=27.1

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .|-.+|.-    .++|.+|+|+.+|||+.+|..+++
T Consensus        10 ~i~~~r~~----~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          10 VLQEHLRN----SGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHHT----TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHH----cCCCHHHHHHHHHcCHhHHHHHHc
Confidence            34455554    899999999999999999999996

>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=81.83  E-value=0.96  Score=33.09  Aligned_cols=39  Identities=18%  Similarity=0.209  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          470 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       470 ~rER~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      +|...||.+..  ......|..|+|+.||||+.||++-+..
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            44455665433  2224689999999999999999876643

>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=80.94  E-value=0.75  Score=33.57  Aligned_cols=25  Identities=24%  Similarity=0.405  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .++|.+|+|+.+|||+.+|.++++.
T Consensus        13 ~g~tq~elA~~~gis~~~is~~e~g   37 (66)
T d1utxa_          13 KKISQSELAALLEVSRQTINGIEKN   37 (66)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cCCCHHHHHHhcccCHHHHHHHHcC
Confidence            6899999999999999999999873

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.63  E-value=1.7  Score=32.01  Aligned_cols=33  Identities=18%  Similarity=0.199  Sum_probs=27.2

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 009567          474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  511 (532)
Q Consensus       474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rA  511 (532)
                      .||.+..     +++|-.+||+.|+||..+|..+.++-
T Consensus        22 Riv~~~~-----~G~s~r~aA~rf~VS~s~v~k~l~r~   54 (63)
T d1k78a1          22 RIVELAH-----QGVRPCDISRQLRVSHGCVSKILGRY   54 (63)
T ss_dssp             HHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            3556654     68999999999999999999887763

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.53  E-value=2.4  Score=30.45  Aligned_cols=51  Identities=12%  Similarity=0.086  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHhcccCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 009567          467 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  517 (532)
Q Consensus       467 ~L~~rER~VL~LRyGL~~~-e~~Tl~EIAe~LgISrerVRqie~rALkKLR~  517 (532)
                      .+++.+..+|...|..+.. ......+||..+|||...|+.+...-..+.|.
T Consensus         7 ~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           7 HFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            3678888999999876533 45678999999999999999999988888775

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=80.44  E-value=1.1  Score=33.09  Aligned_cols=36  Identities=11%  Similarity=0.120  Sum_probs=27.4

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 009567          474 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  512 (532)
Q Consensus       474 ~VL~LRyGL~~~e~~Tl~EIAe~LgISrerVRqie~rAL  512 (532)
                      .||.+-+-   ..+.|-.|||+.+|+|+.+|+.+...-.
T Consensus        10 ~Il~~l~~---~g~~sr~eLa~~~glS~~Tv~~~l~~L~   45 (71)
T d1z05a1          10 RVYKLIDQ---KGPISRIDLSKESELAPASITKITRELI   45 (71)
T ss_dssp             HHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHH---cCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45555442   2589999999999999999998776543

>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=80.25  E-value=0.94  Score=32.85  Aligned_cols=24  Identities=13%  Similarity=0.297  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLES  509 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~  509 (532)
                      .++|.+|+|+.+|||+.+|.++++
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            689999999999999999999986

>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=80.15  E-value=0.95  Score=33.23  Aligned_cols=25  Identities=24%  Similarity=0.231  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 009567          486 KPKSLSEVGNIFGLSKERVRQLESR  510 (532)
Q Consensus       486 e~~Tl~EIAe~LgISrerVRqie~r  510 (532)
                      .++|.+++|+.+|+|+.+|+++++.
T Consensus        21 ~gltq~~lA~~~gis~~~i~~~E~g   45 (69)
T d1y7ya1          21 KGLSQETLAFLSGLDRSYVGGVERG   45 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             cCCCHHHHHhHhCCCHHHHHHHHCC
Confidence            7899999999999999999999863