Citrus Sinensis ID: 008352

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------57
Protein Sequence
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccHHHHHHHcccHHHHHHHHcccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHcccHHHHHHHHHHHHcccccccccccccHHHHHHHHHHccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccEEEEEccccccccccHHHHHHHccHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccccccccHHHHHHHccccHHHHHHHHHHHHHHHHcccccccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHccccccccccccccccccccccccccccEEEccccccccEEccccccHHHccccccEcccccccHccHHHHHHHcccccccEEccccEccEEEcccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHcccccccccccccccccHHHccccccccHHHHHHHcccccccccccccccccHHcHHHHHcHcccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHcccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHc
Coil and Loop (DISEMBL)
meagrnllssppsfpsrtrvkhslsssasssssssVLMHneqsapavasvptssvarhfptsvllqeqrdeyrpllhmfkedktsqatsdsrnIETEAFFveeknsgdlDQLVQDLEHqflhwpdlwnlsppmkrgedpsvsltmqslsndteesvdaepfDAVALARKALSASKEAAslaenpklngaeftdisltsslgypleevkqfsqprflerrskkrkvskpqvtnhetynSRKASVKKKLsegfdrndplrlflwgpetrklltaDEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRdlkselhsgnssREKLINANLRLVVHVAKQYqgrgislhdLLQEGSMGLMKSVEkfkpqagcrfasYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIqegnhspdkedlaRRVGITVEKLERLIFITrmplsmqqpvwadqdtTFQEITadtgveipdisVQKQLMRQHVRNLLtllnpkerCIVRLRFgiedgkpkslsevgnIFGLSKERVRQLESRALYRLKQSLggkasygyadlli
Flexible Loop (DISEMBL)
meagrnllssppsfpsrtrVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMfkedktsqatsdsrNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAslaenpklngaeFTDISLTSslgypleevkqfsqprflerrskkrkvskpqvtnhetynsrkasvkkklsegfdrndplrlfLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLqsqfgreptLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFqhsrtirlpeNIYTLLSKVLEAKRLYIqegnhspdkedlarRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNlltllnpkerCIVRLRfgiedgkpkslsevgnifglskeRVRQLESRALYrlkqslggkasygyadlli
Low Complexity Region (SEG)
MEAGRNLLSSPPSFPSRTRVKHslsssasssssssVLMHNEQsapavasvptssvaRHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDavalarkalsaskeaaslaeNPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered region (IsUnstruct)
**************************************************************************************************FFV******DLDQLVQDLEHQFLHWPDLWNL******************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE*********FGREPTLIEWAKAIGLSCRDL************KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEG********LARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY*****
Disordered Region (DISOPRED)
**********PPSF*******************************************HFPTSVLLQEQRD*********************************************LEHQFLHW**************************************************************LNGAEFT***************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS*FGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL*******SPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered Region (DISEMBL)
******************************************************VARHFPTSVLLQEQRDEYRPLLHMFKED*********RNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQS**********AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLE*************TNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK********SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered Region (DISPRO)
*********************************SSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM**********************VDAEPFDAVALARKALSASKEAASLAENPKLN****************************************************************DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPV*ADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFExxxxxxxxxxxxxxxxxxxxxFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
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	569	2.2.26 [Sep-21-2011]
Q9LD95	547	RNA polymerase sigma fact	yes	no	0.947	0.985	0.551	1e-168
P26683	390	RNA polymerase sigma fact	yes	no	0.586	0.856	0.373	2e-66
O22056	572	RNA polymerase sigma fact	no	no	0.594	0.590	0.381	3e-65
P38023	399	RNA polymerase sigma fact	yes	no	0.523	0.746	0.394	1e-63
P74565	425	RNA polymerase sigma fact	N/A	no	0.544	0.729	0.342	6e-58
P52322	416	RNA polymerase sigma fact	no	no	0.525	0.718	0.345	1e-56
Q31ME3	320	RNA polymerase sigma fact	no	no	0.525	0.934	0.386	5e-56
Q03066	416	RNA polymerase sigma-C fa	no	no	0.527	0.721	0.360	8e-53
Q31QG5	320	RNA polymerase sigma fact	no	no	0.528	0.940	0.382	3e-52
Q59996	404	Probable RNA polymerase s	N/A	no	0.523	0.737	0.348	5e-52

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

 Score =  591 bits (1524), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 318/577 (55%), Positives = 407/577 (70%), Gaps = 38/577 (6%)

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

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

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

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

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

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

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

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

Query: 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 532
           FQEIT D+G+E P +SV KQLMR HVRNLL +L+PKER I++LRFGI+ GK +SLSE+G 
Sbjct: 451 FQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGE 510

Query: 533 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 569
           I+GLSKERVRQLESRALYRLKQ++     + YADLL+
Sbjct: 511 IYGLSKERVRQLESRALYRLKQNMNSHGLHAYADLLV 547

Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Regulates transcription in chloroplast in a DG1-dependent manner. Involved in light-dependent chloroplast development. Required during early plant development and primary leaf formation.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  254 bits (648), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 130/348 (37%), Positives = 220/348 (63%), Gaps = 14/348 (4%)

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

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

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

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

Query: 446 EKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 505
           EKL  +    ++P+S++ P+  ++D+   +     G E P+  V K L+R+ +  +L  L
Sbjct: 271 EKLRFIAKSAQLPISLETPIGKEEDSRLGDFIESDG-ETPEDQVSKNLLREDLEKVLDSL 329

Query: 506 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           +P+ER ++RLR+G++DG+ K+L E+G IF +++ER+RQ+E++AL +L+
Sbjct: 330 SPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 377

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

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

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

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

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

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

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

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

Query: 452 IFITRMPLSMQQPVWADQDTTFQEITAD-TGVEIPDISVQKQLMRQHVRNLLTLLNPKER 510
           +   + P S+ Q +  +Q+    E+ AD   V   DI + K+ MRQ +  +L  L  +E+
Sbjct: 455 LLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILI-KEFMRQDLDKVLDSLGTREK 513

Query: 511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
            ++R RFG+EDG+ K+L E+G + G+S+ERVRQ+ES A  +LK
Sbjct: 514 QVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLK 556

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

Arabidopsis thaliana (taxid: 3702)

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

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

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

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

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

Query: 435 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 494
           E++A R+ +T+EKL  +    ++P+S++ P+  ++D+   +     G E P+  V K L+
Sbjct: 269 EEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDEVAKNLL 327

Query: 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           R+ +  +L+ L+P+ER ++RLR+G++DG+ K+L E+G +F +++ER+RQ+E++AL +L+
Sbjct: 328 REDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLR 386

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

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

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

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

Query: 239 RKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQ 298
           RK +VKKK        D +R++L      +LL A+EE EL  QI DL+ LE  +  L  Q
Sbjct: 59  RKDAVKKKPYT----EDSIRIYLQEIGRIRLLRAEEEIELARQIADLLELELIRDNLTLQ 114

Query: 299 FGREPTLIEWAKAI----------------GLSCRDLKSELHSGNS-------------- 328
             R+P+ +EW K +                    +D+ S L + ++              
Sbjct: 115 LERQPSELEWGKQVWKLETAKQRLVGDKKKEPKKKDIDSYLANPDNELSLENEWSQQPNK 174

Query: 329 --------------SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFK 374
                         +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF 
Sbjct: 175 NFAAFRRRLFLDRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 234

Query: 375 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDK 434
            + G +F++YA WW+RQ I +AI   SRTIRLP ++Y  +S++ +  +L  QE    P +
Sbjct: 235 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTE 294

Query: 435 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 494
           E++A ++ +T+EKL  +    ++P+S++ P+  ++D+   +     G E P+  V K L+
Sbjct: 295 EEIAEKMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDEVSKNLL 353

Query: 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           R+ + N+L  L+P+ER ++RLR+G++DG+ K+L E+G IF +++ER+RQ+E++AL +L+
Sbjct: 354 REDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 412

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

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

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

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

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

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

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

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

Query: 456 RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRL 515
           ++P+S++ P+  ++D+   +     G E P+  V K L+R+ + N+L  L+P+ER ++RL
Sbjct: 307 QLPISLETPIGKEEDSRLGDFIEADG-ETPEDEVSKNLLREDLENVLDTLSPRERDVLRL 365

Query: 516 RFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
           R+G++DG+ K+L E+G IF +++ER+RQ+E++AL +L+ 
Sbjct: 366 RYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 404

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

Microcystis aeruginosa (taxid: 1126)

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

 Score =  219 bits (558), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 116/300 (38%), Positives = 188/300 (62%), Gaps = 1/300 (0%)

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

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

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

Query: 435 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 494
            +LA  + + +E++   I + R P+S+   V   QDT  QE+  D     P   V+++ +
Sbjct: 191 SELAEVLELPLEQVREYIQMNRQPVSLDVKVGDSQDTELQELLEDEQSS-PSDYVEQESL 249

Query: 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
           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 (530), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 124/344 (36%), Positives = 190/344 (55%), Gaps = 44/344 (12%)

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

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

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

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

Query: 451 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKER 510
           ++      +S++  V  D+DT   E+    GV  P+  + ++ +++ +++LL  L  +ER
Sbjct: 299 VLLRVPRSVSLETKVGKDKDTELGELLETDGV-TPEEMLMRESLQRDLQHLLADLTSRER 357

Query: 511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
            ++ +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 (525), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 116/303 (38%), Positives = 188/303 (62%), Gaps = 2/303 (0%)

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

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

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

Query: 433 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 492
              +LA  + +T  ++   +   R PLS+   V  +QDT   ++  +T    P+    + 
Sbjct: 189 TLPELAAALDLTPAQVRDYLEKARHPLSLDLRVGDNQDTELGDLL-ETDCTTPEEFTLQA 247

Query: 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552
            MR+ +  LL  L  ++R ++ LR+G+EDG+  +L+ +G+   +S+ERVRQLE  AL+ L
Sbjct: 248 SMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRERVRQLEREALHTL 307

Query: 553 KQS 555
           +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 =  206 bits (523), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 119/341 (34%), Positives = 189/341 (55%), Gaps = 43/341 (12%)

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

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

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

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

Query: 452 IFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERC 511
           +      +S++  V  D+DT   ++  +T  + P+  + ++ ++  ++ +L  L P+E+ 
Sbjct: 288 LTQVPRSVSLELKVGQDKDTELMDLL-ETDTQSPEDELMREALQNDMQEILLDLTPREQE 346

Query: 512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552
           ++ 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	569
297741628	561	unnamed protein product [Vitis vinifera]	0.975	0.989	0.631	0.0
224068757	535	predicted protein [Populus trichocarpa]	0.938	0.998	0.626	0.0
359481391	572	PREDICTED: RNA polymerase sigma factor r	0.991	0.986	0.627	0.0
255556952	548	RNA polymerase sigma factor rpoD, putati	0.961	0.998	0.619	0.0
356536959	571	PREDICTED: RNA polymerase sigma factor r	0.989	0.985	0.584	1e-178
356548319	574	PREDICTED: RNA polymerase sigma factor r	0.991	0.982	0.569	1e-178
449451030	562	PREDICTED: RNA polymerase sigma factor s	0.973	0.985	0.56	1e-172
312282671	547	unnamed protein product [Thellungiella h	0.947	0.985	0.556	1e-169
297827203	546	RNA polymerase sigma-70 factor [Arabidop	0.945	0.985	0.554	1e-168
18404292	547	RNApolymerase sigma-subunit F [Arabidops	0.947	0.985	0.551	1e-166

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

 Score =  718 bits (1853), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/575 (63%), Positives = 440/575 (76%), Gaps = 20/575 (3%)

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

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

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

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

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

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

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

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

Query: 475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF 534
           E+TADTG+EIPD+SV KQLMRQHVRNLL +L PKER I+RLRFGI DG P++LSE+G +F
Sbjct: 467 EVTADTGIEIPDVSVAKQLMRQHVRNLLHVLTPKERRIIRLRFGIGDGIPRTLSEIGLVF 526

Query: 535 GLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 569
           G SKERVRQLE RAL++LKQ L       Y DLL+
Sbjct: 527 GFSKERVRQLEQRALHKLKQCLSSHGLESYTDLLV 561

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 =  714 bits (1844), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/568 (62%), Positives = 437/568 (76%), Gaps = 34/568 (5%)

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

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

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

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

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

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

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

Query: 421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADT 480
           KR YIQEGNH P  E++ARRVGI ++KLE+L+  TR PLSMQQ VW+DQ+TTFQEITADT
Sbjct: 387 KRSYIQEGNHQPTAEEIARRVGIAIDKLEKLLCFTRTPLSMQQTVWSDQNTTFQEITADT 446

Query: 481 GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKER 540
            +EIPD+SV KQLMR+H+R LL +L+ KER I+RLRFGIEDGK KSLSE+GN+FGLSKER
Sbjct: 447 EIEIPDMSVAKQLMRKHIRGLLNILSLKERRIIRLRFGIEDGKQKSLSEIGNVFGLSKER 506

Query: 541 VRQLESRALYRLKQSLGGKASYGYADLL 568
           VRQLESRALY+LKQ +G      YADLL
Sbjct: 507 VRQLESRALYKLKQCVGSHGLDAYADLL 534

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  712 bits (1839), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/577 (62%), Positives = 440/577 (76%), Gaps = 13/577 (2%)

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

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

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

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

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

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

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

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

Query: 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 532
           FQE+TADTG+EIPD+SV KQLMRQHVRNLL +L PKER I+RLRFGI DG P++LSE+G 
Sbjct: 476 FQEVTADTGIEIPDVSVAKQLMRQHVRNLLHVLTPKERRIIRLRFGIGDGIPRTLSEIGL 535

Query: 533 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 569
           +FG SKERVRQLE RAL++LKQ L       Y DLL+
Sbjct: 536 VFGFSKERVRQLEQRALHKLKQCLSSHGLESYTDLLV 572

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  702 bits (1811), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 353/570 (61%), Positives = 431/570 (75%), Gaps = 23/570 (4%)

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

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

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

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

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

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

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

Query: 420 AKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITAD 479
           AKR YI EGNH+P KE+LA+R+GIT  +LERL+++ RMPLSMQQ VWADQ+TTFQEITAD
Sbjct: 399 AKRSYIMEGNHNPTKEELAKRIGITTVRLERLLYMARMPLSMQQTVWADQETTFQEITAD 458

Query: 480 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 539
             VEIP++ V KQLMR+HV +LL +LNP+ER I+RLR+GIEDGK KSLSE+G++FGLSKE
Sbjct: 459 IEVEIPELCVAKQLMRKHVLSLLNILNPRERKIIRLRYGIEDGKKKSLSEIGSVFGLSKE 518

Query: 540 RVRQLESRALYRLKQSLGGKASYGYADLLI 569
           RVRQLESRALY+LKQ L       YADLL+
Sbjct: 519 RVRQLESRALYKLKQCLASHGLEAYADLLV 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 =  632 bits (1631), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 337/577 (58%), Positives = 429/577 (74%), Gaps = 14/577 (2%)

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

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

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

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

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

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

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

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

Query: 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 532
           FQEITAD  VE  D++V+KQLMR+HV N+L++L+PKER I+RLR+G EDG+ KSLSE+G+
Sbjct: 475 FQEITADPTVEATDVTVEKQLMRRHVLNVLSVLHPKERRIIRLRYGFEDGEQKSLSEIGD 534

Query: 533 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 569
           IFGLSKERVRQLE RALY+LK+ L  +    Y DLL+
Sbjct: 535 IFGLSKERVRQLEIRALYKLKKCLVKQGLDAYVDLLL 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 =  630 bits (1626), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 330/579 (56%), Positives = 422/579 (72%), Gaps = 15/579 (2%)

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

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

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

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

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

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

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

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

Query: 471 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV 530
           TTFQEITAD  VE  D+SV+KQLMRQHV N+L++L+PKER I+RLR+G EDG+ KSLSE+
Sbjct: 476 TTFQEITADPTVEATDVSVEKQLMRQHVLNVLSILHPKERRIIRLRYGFEDGEQKSLSEI 535

Query: 531 GNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 569
           G+IFGLSKERVRQLE RALY+LK+ L  +    Y DLL+
Sbjct: 536 GDIFGLSKERVRQLEIRALYKLKKCLVKQGLDAYVDLLL 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 =  610 bits (1572), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 322/575 (56%), Positives = 414/575 (72%), Gaps = 21/575 (3%)

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

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

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

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

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

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

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

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

Query: 474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 533
           QEITAD+ V+ PD+SV+++LMR+H+RNLL++L+PKER I+RLRFGIEDG+ K+L E+GN+
Sbjct: 467 QEITADSEVDTPDVSVERELMRRHIRNLLSILSPKERRIIRLRFGIEDGREKTLLEIGNM 526

Query: 534 FGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 568
           FGLSKERVRQLE+RALY+LK+    +    YADLL
Sbjct: 527 FGLSKERVRQLENRALYKLKRCCNSQGLGAYADLL 561

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  600 bits (1548), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 321/577 (55%), Positives = 404/577 (70%), Gaps = 38/577 (6%)

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

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

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

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

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

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

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

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

Query: 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 532
           FQE+T D+G+E P +SV KQLMR HVRNLL +L+PKE+ I++LRFGI+ GK +SLSE+G 
Sbjct: 451 FQEVTPDSGIETPSMSVGKQLMRNHVRNLLNVLSPKEKRIIKLRFGIDGGKQRSLSEIGE 510

Query: 533 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 569
           I+GLSKERVRQLESRALYRLKQ++       YADLL+
Sbjct: 511 IYGLSKERVRQLESRALYRLKQNMSSHGLNAYADLLV 547

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  598 bits (1543), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 320/577 (55%), Positives = 408/577 (70%), Gaps = 39/577 (6%)

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

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

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

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

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

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

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

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

Query: 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 532
           FQEIT D+G+E P +SV KQ+MR HVRNLL +L+PKER I++LRFGI+ GK +SLSE+G 
Sbjct: 450 FQEITPDSGIETPTMSVGKQMMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGE 509

Query: 533 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 569
           I+GLSKERVRQLESRALYRLKQ +     + YADLL+
Sbjct: 510 IYGLSKERVRQLESRALYRLKQHMNSHGLHAYADLLV 546

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  591 bits (1524), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 318/577 (55%), Positives = 407/577 (70%), Gaps = 38/577 (6%)

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

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

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

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

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

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

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

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

Query: 473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN 532
           FQEIT D+G+E P +SV KQLMR HVRNLL +L+PKER I++LRFGI+ GK +SLSE+G 
Sbjct: 451 FQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGE 510

Query: 533 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI 569
           I+GLSKERVRQLESRALYRLKQ++     + YADLL+
Sbjct: 511 IYGLSKERVRQLESRALYRLKQNMNSHGLHAYADLLV 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	569
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.827	0.861	0.541	7.7e-146
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.622	0.618	0.492	8.3e-90
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.594	0.590	0.381	1.6e-63
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.421	0.382	0.377	1.5e-50
TIGR_CMR|DET_0551	520	DET_0551 "RNA polymerase sigma	0.405	0.444	0.370	6e-48
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.483	0.743	0.357	2.6e-47
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.630	0.622	0.312	1.8e-46
TIGR_CMR|CJE_1081	622	CJE_1081 "RNA polymerase sigma	0.502	0.459	0.310	4.7e-46
TIGR_CMR|GSU_1525	328	GSU_1525 "RNA polymerase sigma	0.418	0.725	0.347	4.7e-46
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.435	0.767	0.382	7.9e-46

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

 Score = 1265 (450.4 bits), Expect = 7.7e-146, Sum P(2) = 7.7e-146
 Identities = 266/491 (54%), Positives = 340/491 (69%)

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

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

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

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

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

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

Query:   439 RRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHV 498
               VG++ EKL++L++ TR PLSMQQP+W+DQDTTFQEIT D+G+E P +SV KQLMR HV
Sbjct:   417 GHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHV 476

Query:   499 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558
             RNLL +L+PKER I++LRFGI+ GK +SLSE+G I+GLSKERVRQLESRALYRLKQ++  
Sbjct:   477 RNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNS 536

Query:   559 KASYGYADLLI 569
                + 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:   214 RFLERRSKKRKVSKPQVTNHETY--NSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLT 271
             R LERRSK+R   +  + +      NS+K    KK     + ++P +LFL   ET + LT
Sbjct:   216 RLLERRSKRRYAPRASIADVSCSADNSKKKEKSKKYGRVLEPDEPFKLFLRDRETTEFLT 275

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

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

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

Query:   452 IFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERC 511
                TR P SMQ  VW+D+  TFQEIT D  VE PD+SV + +MRQ VR+ L +L+P+E+ 
Sbjct:   455 RAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEPPDLSVDRMMMRQQVRDFLGILSPREKE 514

Query:   512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL 568
             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:   214 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 272
             R  ER++++ K  +   +   +  +  +  KK+L ++  D NDPLR       + KLLT 
Sbjct:   216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275

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

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

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

Query:   452 IFITRMPLSMQQPVWADQDTTFQEITADT-GVEIPDISVQKQLMRQHVRNLLTLLNPKER 510
             +   + P S+ Q +  +Q+    E+ AD   V   DI + K+ MRQ +  +L  L  +E+
Sbjct:   455 LLSPKPPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILI-KEFMRQDLDKVLDSLGTREK 513

Query:   511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
              ++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:   325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASY 384
             + N +++++I ANLRLVV +AK+Y  RG+   DL+QEG++GLMK+V+KF  + G +F++Y
Sbjct:   386 TANRAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTY 445

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

Query:   445 VEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTL 504
             VEK+ +++ I + P+S++ P+  D  +TF +   D     P+ +     +R+    +L+ 
Sbjct:   506 VEKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLADLREITTKVLST 565

Query:   505 LNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 563
             L PKE  I+R+RFGI + GK  +L EVG +F +++ER+RQ+E++AL +L+     +   G
Sbjct:   566 LTPKEERILRMRFGIGKSGKDHTLEEVGRLFNVTRERIRQIEAKALRKLRHPSRARKLRG 625

Query:   564 Y 564
             +
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:   322 ELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
             E+ +  + R  LI ANLRLVV VAK++ GRG+ L DL+QEG++GL+++VEKF    G +F
Sbjct:   277 EIDAKRAERH-LIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKF 335

Query:   382 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRV 441
             ++YA WW+RQ I +AI   +RTIR+P ++   ++K+L   R   Q+    P  +++A  +
Sbjct:   336 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIAVEM 395

Query:   442 GITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNL 501
              +  EK+  +  ++++P+S++ P+  ++D+   +   D     P  +  +QL+++ +  +
Sbjct:   396 DLPPEKVREIAKVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTV 455

Query:   502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
             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:   274 EEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL 333
             +E +L   I + I ++        + GR P L    + I L+ R  K E      ++ KL
Sbjct:    83 DEVDLDLTIPEGIAIDDPVRMYLKEIGRVPLLTP-EEEIELAKR--KEE--GDEEAKRKL 137

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

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

Query:   454 ITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIV 513
             I + P+S++ P+  ++D+   +   D   + P       L+R+ +  +L  L  +E+ ++
Sbjct:   258 IAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDEVLKTLTEREQKVL 317

Query:   514 RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
             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:   193 DISLTSSLGYPLEEVKQFSQPR---FLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSE 249
             D+ L ++L   LEE    +  R     ER+  K K+++  VT+    +   A + ++L E
Sbjct:   192 DVRL-AALNAELEEESLSASRRQELLAERQELKEKLAE-MVTSLRLKDRHIAKIAQRLKE 249

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

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

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

Query:   419 EAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA 478
                R  +QE    P  E++A R+ + ++K+ +++ I + P+S++ P+  ++D+   +   
Sbjct:   430 RTSRQLVQEIGREPSPEEIAERMNLPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIE 489

Query:   479 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 538
             D GV  P  +V K  + +    +L  L P+E  ++R+RFGI +    +L EVG  F +++
Sbjct:   490 DKGVVSPLEAVIKANLSEQTARVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTR 549

Query:   539 ERVRQLESRALYRLK 553
             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:   275 EFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI 334
             E  +++   ++ +L + K   +  F  E + +   K I      +K      + ++ ++ 
Sbjct:   333 ETTMVSTYMEIKKLFQTKEASEKSFDLEKSRL---KEI---LEQIKRGKKISDEAKGRMA 386

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

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

Query:   455 TRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVR 514
             T+ P+S++ P+  + D  F +   D     P   + K  +++ +  +L  LN +E+ ++R
Sbjct:   507 TKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKDDLKEQIDEVLDQLNDREKAVIR 566

Query:   515 LRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD 566
             +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:   317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 375
             ++L   +  G+ ++R+K+I +NLRLVV +AK+Y  RG+   DL++EG+MGL+K+VE+FK 
Sbjct:    79 KELAGRIAKGDKAARDKMIESNLRLVVKIAKRYINRGLPFLDLIEEGNMGLIKAVERFKL 138

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

Query:   436 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 495
             ++A  + +    + RL+ + +   S+++P+  + D    +   DT    P + ++     
Sbjct:   199 EVATEMKVNSAYVRRLMVLLKKTYSIERPMGENSDYFLIDTIEDTSTVSPAVLLEDLNKY 258

Query:   496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
             + 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:   305 LIEWAKAIGLSC-RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGS 363
             L+E  K +G +  RDL + +  G ++R  L+ ANLRLVV +AK+Y GRG+ L DL+QEG+
Sbjct:    61 LLETRKRLGENRKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGN 120

Query:   364 MGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL 423
             +GL++++EKF    G +F++YA WW+RQ I + +   SRTIRLP ++   ++K+   KR 
Sbjct:   121 LGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRE 180

Query:   424 YIQE-GNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGV 482
               Q  G  + D E+LA   GI ++K+  L+  +R P+S+  PV ++++    +   D   
Sbjct:   181 MHQHLGREATD-EELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEA 239

Query:   483 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 542
                + +V  +L+   +R++L  L+ +E  ++RLRFG++DG+P++L ++G +FGLS+ERVR
Sbjct:   240 MSAENAVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVR 299

Query:   543 QLESRALYRLK 553
             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	0.5511	0.9472	0.9853	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	569
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	3e-97
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	1e-81
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	3e-78
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	7e-75
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	6e-73
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	6e-73
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	4e-69
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	4e-61
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	2e-58
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-56
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	4e-56
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	7e-54
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	1e-44
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	3e-31
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	8e-30
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	3e-27
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	3e-27
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	2e-24
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	6e-22
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	4e-21
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	1e-20
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	5e-19
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	7e-19
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	1e-17
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	6e-17
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	9e-17
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	2e-15
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	2e-13
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	9e-13
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	1e-12
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	2e-12
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	3e-12
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	8e-12
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	7e-11
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	2e-10
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	5e-10
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	7e-10
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	1e-09
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	4e-09
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	2e-08
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	9e-07
PRK08295	208	PRK08295, PRK08295, RNA polymerase factor sigma-70	1e-04
TIGR02859	198	TIGR02859, spore_sigH, RNA polymerase sigma-H fact	1e-04
COG1595	182	COG1595, RpoE, DNA-directed RNA polymerase special	0.002
PRK12427	231	PRK12427, PRK12427, flagellar biosynthesis sigma f	0.002

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

 Score =  297 bits (763), Expect = 3e-97
 Identities = 126/285 (44%), Positives = 194/285 (68%), Gaps = 1/285 (0%)

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

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

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

Query: 449 ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 508
             L+   R P+S+  PV  ++DT   ++  D G   P+  V+++ +RQ + +LL  L P+
Sbjct: 195 RELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLRQDLESLLAELTPR 253

Query: 509 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           ER ++RLRFG++ G+P +L+E+G    LS+ERVRQ+E++AL +L+
Sbjct: 254 ERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393). Length = 298

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

 Score =  259 bits (664), Expect = 1e-81
 Identities = 121/317 (38%), Positives = 206/317 (64%), Gaps = 8/317 (2%)

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

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

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

Query: 418 LEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE-I 476
            +  ++  QE    P +E++A  + +T+EKL  +    ++P+S++ P+  ++D+   + I
Sbjct: 226 KKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI 285

Query: 477 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL 536
            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: 537 SKERVRQLESRALYRLK 553
           ++ER+RQ+E++AL +L+
Sbjct: 344 TRERIRQIEAKALRKLR 360

Length = 373

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

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

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

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

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

Query: 429 NHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS 488
              P  E++A  +G++ +K+  ++     P+S+  P+  D+D+   +   D     P+ +
Sbjct: 203 GREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELGDFLEDDKSVSPEDA 262

Query: 489 VQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547
           V+++ +++ +  +L   L  +ER ++RLRFG++DG+PK+L E+G  FG+S+ERVRQ+E++
Sbjct: 263 VERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAK 322

Query: 548 ALYRLK 553
           AL +L+
Sbjct: 323 ALRKLR 328

Length = 342

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

 Score =  240 bits (615), Expect = 7e-75
 Identities = 122/294 (41%), Positives = 185/294 (62%), Gaps = 1/294 (0%)

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

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

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

Query: 449 ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 508
              + + R P+S+   V  +QDT   E+  D G   PD  + ++L+RQ + NLL  L P+
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELSELLEDEGPS-PDQYITQELLRQDLNNLLAELTPQ 270

Query: 509 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY 562
           +R ++ LRFG+EDGK  SL++VG    LS+ERVRQLE +AL  L++       Y
Sbjct: 271 QREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRRANVKEY 324

Length = 327

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

 Score =  232 bits (594), Expect = 6e-73
 Identities = 91/224 (40%), Positives = 155/224 (69%)

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

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

Query: 450 RLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKE 509
            +  I + P+S++ P+  ++D+   +   DT +E PD    K+L+R+ +  +L  L  +E
Sbjct: 122 EIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTERE 181

Query: 510 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
             ++R+R+G+ DG+P +L EVG  F +++ER+RQ+ES+AL +L+
Sbjct: 182 EKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLR 225

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc [Transcription, Transcription factors]. Length = 238

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

 Score =  235 bits (601), Expect = 6e-73
 Identities = 121/308 (39%), Positives = 189/308 (61%), Gaps = 1/308 (0%)

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

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

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

Query: 435 EDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM 494
            +LA  + +T +++   +   R PLS+   V  +QDT   E+  DTG    D + Q  L 
Sbjct: 188 GELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFATQSSL- 246

Query: 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
           +  +  L+  L P+++ ++ LRFG+EDG+P +L+++G    +S+ERVRQ+E  AL +L++
Sbjct: 247 QLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306

Query: 555 SLGGKASY 562
                  Y
Sbjct: 307 RKANIQEY 314

Length = 317

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

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

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

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

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

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

Query: 453 FITRMP--LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRN----LLTLLN 506
            + R+P  +S++  V  D+DT   ++     +E  DIS ++ LMR+ ++     LL  L 
Sbjct: 299 -LLRVPRSVSLETKVGKDKDTELGDL-----LETDDISPEEMLMRESLQRDLQHLLADLT 352

Query: 507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
            +ER ++R+RFG+ DG   SL+E+G    LS+ERVRQ+ES+AL +L+Q
Sbjct: 353 SRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ 400

Length = 415

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

 Score =  204 bits (521), Expect = 4e-61
 Identities = 111/302 (36%), Positives = 186/302 (61%), Gaps = 17/302 (5%)

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

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

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

Query: 433 DKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ 492
           D E+LA   GI  EK+  L+  +R P+S+  PV +D++    +   D+     + +V   
Sbjct: 192 D-EELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAG 250

Query: 493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552
           L+   +R++L  L+ +E+ ++RLRFG++DG+P++L ++G +FGLS+ERVRQ+E   + +L
Sbjct: 251 LLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKL 310

Query: 553 KQ 554
           + 
Sbjct: 311 RN 312

Length = 324

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

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

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

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

Query: 449 ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPK 508
            R++ +     S+  P+  D   +  +  AD     P+  VQ   ++Q +   L  LN +
Sbjct: 167 SRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNER 226

Query: 509 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
           +R ++  RFG+   +P +L EV    GL++ERVRQ++  AL +L++ L
Sbjct: 227 QREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393) [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]. Length = 285

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

 Score =  197 bits (504), Expect = 1e-56
 Identities = 105/290 (36%), Positives = 170/290 (58%), Gaps = 21/290 (7%)

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

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

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

Query: 444 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 503
           T EK+  +    R P+S+ + +  + D+ F +   D+    P  +V   L++  ++ +L 
Sbjct: 387 TPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLE 446

Query: 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
            L+ +E  ++R+RFG+ DG+PK+L E+G ++G+++ER+RQ+ES+ L +L+
Sbjct: 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496

Length = 509

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

 Score =  191 bits (488), Expect = 4e-56
 Identities = 86/229 (37%), Positives = 144/229 (62%)

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

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

Query: 448 LERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 507
           + R++ +     S+  P+  D + +  +I AD     P+ + Q   M+Q +   L  LN 
Sbjct: 206 VSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELND 265

Query: 508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
           K+R ++  RFG+   +  +L +V    GL++ERVRQ++  AL RL++ L
Sbjct: 266 KQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314

Length = 325

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

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

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

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

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

Query: 427 EGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD 486
           E    P  E++A  + +  EK+  ++ I + P+S++ P+  + D+   +   D     P 
Sbjct: 228 ELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPA 287

Query: 487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES 546
                +L+++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E+
Sbjct: 288 DHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEA 347

Query: 547 RALYRLKQ 554
           +AL +L+ 
Sbjct: 348 KALRKLRH 355

Length = 367

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

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

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

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

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

Query: 456 RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRL 515
           + P+S++ P+  D+D+   +   D   E+P  +  ++ +R+   ++L  L P+E  ++R+
Sbjct: 508 KEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRM 567

Query: 516 RFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           RFGI+     +L EVG  F +++ER+RQ+E++AL +L+
Sbjct: 568 RFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605

Length = 619

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

 Score =  121 bits (306), Expect = 3e-31
 Identities = 64/247 (25%), Positives = 124/247 (50%), Gaps = 19/247 (7%)

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

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

Query: 433 DKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ 490
             E++A  +GI  E+    +        LS+ + V  D D    +      +E PD  V+
Sbjct: 128 TDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDDQ-----IENPDDGVE 182

Query: 491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550
           K+ + + ++  +  L  +E+ ++ LR+  E     +  E+  + G+S+ RV +L  +A+ 
Sbjct: 183 KEELLEILKEAIEPLPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVSRLHKKAIK 238

Query: 551 RLKQSLG 557
           +L++ L 
Sbjct: 239 KLRKELN 245

Length = 247

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

 Score =  118 bits (297), Expect = 8e-30
 Identities = 72/240 (30%), Positives = 128/240 (53%), Gaps = 25/240 (10%)

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

Query: 392 TIRKAIFQHSRTIRLPENIYTLLSKVL------EAKRLYIQEGNHSPDK-EDLARRVGIT 444
            I + I ++ R +++     T   + L        KRL   +G  +P++ E +A  +G++
Sbjct: 99  EIHEYILRNWRLVKVAT---TKAQRKLFFNLRKMKKRL---QGWLNPEEVEAIAEELGVS 152

Query: 445 VEKLERLIFITRMP---LSMQQPVWADQDTTFQEIT--ADTGVEIPDISVQKQ---LMRQ 496
               E     +R+    +S+   +  D+D     I    D   +  D   ++Q   L RQ
Sbjct: 153 ER--EVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDTLEEEQWEELQRQ 210

Query: 497 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
            + N L  L+ + R I+  R+  +D    +L E+   +G+S ER+RQ+E  A+ +LK +L
Sbjct: 211 ALANALGSLDARSRRIIEARWLDDD--KLTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]. Length = 270

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

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

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

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

Query: 450 RLIFITRM--PLSMQQPVWADQDTTFQEIT-ADT-GVEIPDISVQKQLMRQHVRNLLTLL 505
             +        LS+   +  D       I   DT G E  D +++    R  ++ LL  L
Sbjct: 125 EALEAGNAYQALSLDASIEDDDGD---PIALLDTLGDE--DDALETVEDRLALKPLLAAL 179

Query: 506 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
             +ER I+ LRF  ED   K+ SE+    G+S+  V +L  RAL +L++ L
Sbjct: 180 PERERRILLLRF-FED---KTQSEIAERLGISQMHVSRLLRRALKKLREQL 226

This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage. Length = 227

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

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

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

Query: 389 VRQTI------------------RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNH 430
           +R +I                  +KA+F + R +R              A+   + + + 
Sbjct: 101 IRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLR--------------AR---LAQADE 143

Query: 431 SPDKEDLARRV----GITVEKLERLIFITRMP-LSMQQPVWADQDTTFQEITA--DTGVE 483
              K+++ R +    G+++  +E +      P  S+  P   + +   + +    D    
Sbjct: 144 ELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDS-P 202

Query: 484 IPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 539
           +PD  V+     +  R+ +   L  LN +E  I+R R   ED    +L  +G   G+SKE
Sbjct: 203 LPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRED--GATLEALGEELGISKE 260

Query: 540 RVRQLESRALYRLKQSL 556
           RVRQ+E+RAL +L+++L
Sbjct: 261 RVRQIEARALEKLRRAL 277

Length = 289

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

 Score =  102 bits (258), Expect = 2e-24
 Identities = 71/250 (28%), Positives = 126/250 (50%), Gaps = 38/250 (15%)

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

Query: 392 TIRKAIFQHSRTIRLPENIYTL---------LSKVLEAKRLYIQEGNHSPDK-EDLARRV 441
            I + I ++ R ++    + T          L K    KRL    G  +P++ E +A  +
Sbjct: 112 EIHEYILRNWRIVK----VATTKAQRKLFFNLRKA--KKRL----GWLNPEEVEMVAEEL 161

Query: 442 GITVE---KLERLIFITRMP---LSMQQPVWADQDTTFQEIT--ADTGVEIPDISVQKQL 493
           G++ E   ++E      R+     S+  P+  D + +        D   +  D+  +   
Sbjct: 162 GVSEEEVREMES-----RLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNW 216

Query: 494 MRQHVRNL---LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550
             Q    L   L  L+ + R I+  R+  +D    +L E+   +G+S ERVRQ+E  A+ 
Sbjct: 217 EDQRRALLADALEGLDERSRDIIEARWLDDD--KSTLQELAAEYGVSAERVRQIEKNAMK 274

Query: 551 RLKQSLGGKA 560
           +LK ++   A
Sbjct: 275 KLKAAIEAAA 284

Length = 284

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

 Score = 95.0 bits (237), Expect = 6e-22
 Identities = 67/244 (27%), Positives = 133/244 (54%), Gaps = 21/244 (8%)

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

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

Query: 436 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQ-DTTF--QEITADTGVE---IPDISV 489
           ++A+ + +  E++   +   + P+S+ +P++ D  D  +   +I+ +   +   + +I++
Sbjct: 144 EIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKNKDENWLEEIAL 203

Query: 490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 549
            K+ M++        LN +E+ I+ LRF     + K+  EV    G+S+ +V +LE  AL
Sbjct: 204 -KEAMKK--------LNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAAL 250

Query: 550 YRLK 553
             ++
Sbjct: 251 KHMR 254

Length = 258

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

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

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

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

Query: 436 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 495
           ++A+ + +  E++   +   + P+S+ +P++ D          D    +  IS +K    
Sbjct: 141 EIAKELKVPQEEVVFALDAIQDPVSLFEPIYND--------GGDPIYVMDQISDEKNKDS 192

Query: 496 QHVRNL-----LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550
           Q +  +     +  LN +E+ I+ +RF   +GK +   EV    G+S+ +V +LE  AL 
Sbjct: 193 QWLEGIALKEAMKRLNEREKMILNMRF--FEGKTQ--MEVAEEIGISQAQVSRLEKAALK 248

Query: 551 RLKQ 554
            +++
Sbjct: 249 HMRK 252

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 254

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

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

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

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

Query: 443 ITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI--TADTGVEIPDISVQKQLMRQHVRN 500
           ++ E++   +   R P S+   V  D       +   AD G E  D  ++K  +++ +  
Sbjct: 125 VSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKGSEDSDW-LEKIALKEAISK 183

Query: 501 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
               L+ +ER I+ LR+     K K+ +EV N+ G+S+ +V +LE + L ++K+ L
Sbjct: 184 ----LDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 231

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

 Score = 80.7 bits (200), Expect = 5e-19
 Identities = 27/71 (38%), Positives = 44/71 (61%)

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

Query: 393 IRKAIFQHSRT 403
           I  A+ +  RT
Sbjct: 61  IIDALRKQRRT 71

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

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

 Score = 85.5 bits (212), Expect = 7e-19
 Identities = 57/227 (25%), Positives = 103/227 (45%), Gaps = 56/227 (24%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           +R  LI  NLRLV H+ K++   G  + DL+  G++GL+K+++ F P  G R A+YA   
Sbjct: 49  ARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYA--- 105

Query: 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
             + I   I  H R +                K+                          
Sbjct: 106 -ARCIENEILMHLRAL----------------KK-------------------------- 122

Query: 449 ERLIFITRMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 505
                 T+  +S+Q P+  D+   + +  +I    G  + +  V+  L  + +   L++L
Sbjct: 123 ------TKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQ-VELNLEIKKLYKKLSVL 175

Query: 506 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 552
           + +ER ++ +R+G+ DG+ K+  E+  I G+S+  V ++E RAL +L
Sbjct: 176 DGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKL 222

The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 227

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

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

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

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

Query: 443 ITVEKLERLIFITRMPLSMQQPVWADQD---TTFQEITADTGVEIPDISVQKQLMRQHVR 499
           +T E++      +R P S+ + V  +     T   +I   +  +  D    K+ +R+   
Sbjct: 146 VTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSEEDWFDKIALKEAIRE--- 202

Query: 500 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 558
                L+ +ER IV LR+     K K+ SEV    G+S+ +V +LE + L ++K+ L  
Sbjct: 203 -----LDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLDE 252

Length = 252

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

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

Query: 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAY 386
            S++  LI  NLRLVV++A++++  GI + DL+  G++GL+K+V  F P    + A+YA 
Sbjct: 51  ESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYA- 109

Query: 387 WWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 446
                         SR I   EN      ++L    +Y++  N                 
Sbjct: 110 --------------SRCI---EN------EIL----MYLRRNNK---------------- 126

Query: 447 KLERLIFITRMPLSMQQPV---WADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 503
                   TR  +S  +P+   W   +    ++   T  +I    +++++ R+ +R  L 
Sbjct: 127 --------TRSEVSFDEPLNVDWDGNELLLSDVLG-TDSDIVYKYLEEEVDRELLRKALA 177

Query: 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
            LN +E+ I+ LRFG+  G  K+  EV ++ G+S+  + +LE R L RLK+ +
Sbjct: 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEI 230

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 234

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

 Score = 79.2 bits (196), Expect = 9e-17
 Identities = 56/234 (23%), Positives = 113/234 (48%), Gaps = 19/234 (8%)

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

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

Query: 449 ERL---IFITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 503
            +    I    + +S+ + +    D   +  +   D   E P+  ++++ +R+ +   + 
Sbjct: 117 RQALNEINALSL-VSLDE-LLESGDDGGSLIDRIEDDKSEDPEEELEREELREALAEAIE 174

Query: 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557
            L+ +E+ ++ L +  E     +L E+G + GL++ RV Q+ S+AL +L+  L 
Sbjct: 175 SLSEREQLVLSLYYYEE----LNLKEIGEVLGLTESRVSQIHSQALKKLRAKLS 224

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium. Length = 224

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

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

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           +R  LI  NLRLV H+ K+++  G  + DL+  G++GL+K++E F    G + A+YA   
Sbjct: 50  ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA--- 106

Query: 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSP---DKEDLARRVGITV 445
             + I   I  H R           L K    K + +Q+    P   DKE          
Sbjct: 107 -ARCIENEILMHLRN----------LKKTK--KEVSLQD----PIGVDKEG--------- 140

Query: 446 EKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL 505
                        +S+   + +++D   +++         ++ ++ + + + +  L    
Sbjct: 141 -----------NEISLIDILGSEEDDVIEQV---------ELKMEVEKLYKKIDIL---- 176

Query: 506 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
           + +E+ ++ +R+G+ +GK K+  E+    G+S+  V ++E RAL +L + L
Sbjct: 177 DEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227

Length = 233

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

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

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

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

Query: 449 E--RLIFITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDISVQKQLM-RQHVRNLLT 503
           +  +L    R PLS+  PV  D+D  T+  ++  D        S Q     R  ++  L 
Sbjct: 147 QEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPDPRYR----SFQLAQEDRIRLQQALA 202

Query: 504 LLNPKERCIVRLRF 517
            L  + R ++   F
Sbjct: 203 QLEERTREVLEFVF 216

Length = 256

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

 Score = 68.1 bits (167), Expect = 9e-13
 Identities = 61/235 (25%), Positives = 110/235 (46%), Gaps = 17/235 (7%)

Query: 331 EKLINANLRLV-VHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 387
           ++LI   + LV  HV +   G  + +S  DL   G +GL  ++EKF P    +F +YA +
Sbjct: 25  DELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASF 84

Query: 388 WVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 446
                IR AI    R    LP ++     KV  A     Q    +   +++A  +G+T E
Sbjct: 85  ----RIRGAIIDGLRKEDWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEE 140

Query: 447 KLERLI---FITRMPLSM-QQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLL 502
           ++E  +   F   + LS+ ++    D          D     P+  + K+ + + +   +
Sbjct: 141 EVEATMNEGFFANL-LSIDEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKI 199

Query: 503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557
             L+ KE+ ++ L +  E     +L+E+G +  LS  R+ Q+ S+AL++LK+ L 
Sbjct: 200 KQLSEKEQLVISLFYKEE----LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250

Length = 251

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

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

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

Query: 473 FQEITADTGVEIPD 486
             ++  D   E P+
Sbjct: 62  LGDLLEDDDAESPE 75

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

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

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

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

Query: 390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL- 448
              +R+    +S ++++P  +  L  ++  A     Q    +P   +LA  +G+  E++ 
Sbjct: 102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVV 161

Query: 449 ERLIFITRM-PLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNP 507
           E L+  +    LS+     +  D       ADT  ++ D  + +   R+ +R LL  L  
Sbjct: 162 EGLVAGSAYNTLSIDSGGGSGDDDARA--IADTLGDV-DAGLDQIENREALRPLLAALPE 218

Query: 508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 557
           +ER ++ LRF     +  + +++    G+S+  V +L ++ L RL+  L 
Sbjct: 219 RERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264

Length = 264

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

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

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

Query: 388 WVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEK 447
             R  I   + +  R  R  + +  LL      +    Q        E+    +   +EK
Sbjct: 59  IARNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQ--------EEEREALREALEK 110

Query: 448 L---ERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLL 502
           L   ER + +    L         +  +++EI    G+ +  +  + +  R+ +R LL
Sbjct: 111 LPEREREVLV----LRYL------EGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158

This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs. Length = 158

>gnl|CDD|218139 pfam04545, Sigma70_r4, Sigma-70, region 4

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

Query: 501 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
            L  L P+ER ++ LRFG    +  +L E+G   G+S+ERVRQ+E RAL +L++
Sbjct: 1   ALASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50

Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. Length = 50

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

 Score = 62.2 bits (152), Expect = 7e-11
 Identities = 55/245 (22%), Positives = 114/245 (46%), Gaps = 24/245 (9%)

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

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

Query: 438 ARRVGITVEKL-ERLI---FITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQL 493
           A ++G+++E+  E L+         +   +    D     ++   +  ++     ++ + 
Sbjct: 118 AEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQDEDPLQ----QLEDEE 173

Query: 494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           +R+ +   +  L  +E+ ++ L +  E     +L E+G + G+S+ RV Q+ S+A+ RL+
Sbjct: 174 LREALVEAIESLPEREQLVLSLYYQEE----LNLKEIGAVLGVSESRVSQIHSQAIKRLR 229

Query: 554 QSLGG 558
             LG 
Sbjct: 230 ARLGE 234

Length = 236

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

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

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

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

Query: 442 GITVEKLE----RLIFITRMPLSMQQPVWADQDT-TFQEITADTGVEIPDISVQKQLMRQ 496
           GI++E+      +L   + + L+       + D  +  +         PD   +++ +++
Sbjct: 145 GISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKR 204

Query: 497 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
            +   +  L  +E+ ++ L +  ED    +L E+G + G+++ R+ QL ++A+ +L+  L
Sbjct: 205 VIVEAIKTLPEREKKVLILYY-YED---LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260

Query: 557 G 557
            
Sbjct: 261 A 261

Length = 268

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

 Score = 60.0 bits (145), Expect = 5e-10
 Identities = 61/236 (25%), Positives = 106/236 (44%), Gaps = 16/236 (6%)

Query: 330 REKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAY 386
           R+ LI   L LV +VA +        +   DL   G  GL+++VE+F P+   RF  YA 
Sbjct: 25  RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84

Query: 387 WWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 446
           + ++  I   I    +   +P +++   +K+ +A     Q     P   +L   + I+ +
Sbjct: 85  FLIKAAI---IDDLRKQDWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQ 141

Query: 447 KLERLIFITR----MPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRN 500
           +L       R    + L+ + P  +D +     +E  AD   E     V K+     +  
Sbjct: 142 ELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERIADERAETGYDVVDKKEFSSILAE 201

Query: 501 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
            +  L  KER ++ L +  E      L E+G I G+S+ RV Q+ S+AL +L+ +L
Sbjct: 202 AILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKLRATL 253

Length = 257

>gnl|CDD|100119 cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

 Score = 54.4 bits (132), Expect = 7e-10
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           R+ +   L  L  +ER ++ LRFG    +  S  E+  I G+S+  VRQ   RAL +L+
Sbjct: 1   RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP). Length = 55

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

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

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

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

Query: 449 ERLIFITRM-----PLSMQQPVWADQD---TTFQEITA--DTGVEIPDISVQKQLMRQHV 498
           E +     M      LS+   + AD D    T  +I    + G E      +++++ + +
Sbjct: 151 EAM----EMGKSYQALSVDHSIEADSDGSTVTLLDIVGQQEDGYE----LTEQRMILEKI 202

Query: 499 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
              L +L+ +E+ I++  F IE+    S  E G   G+S+  V +L+ +A+ +L+++ 
Sbjct: 203 ---LPVLSDREKSIIQCTF-IEN---LSQKETGERLGISQMHVSRLQRQAIKKLREAA 253

Length = 257

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

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

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

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

Length = 234

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

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

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

Query: 390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLE 449
              I++ +   + ++ +P  I  L  K+ +A          SP   ++A  +G++ E++ 
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150

Query: 450 RLIFITR--MPLSMQQPVWADQDTTFQEITADTG-VEIPDISVQKQLMRQHVRNLLTLLN 506
            ++ + +    LS+   + AD D +        G VE      +++++   +  +L +L+
Sbjct: 151 EIMEMGQSYRALSVDDVIEADSDGSTVARLDSVGEVEDGYDQTERRMV---LEKILPILS 207

Query: 507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS 555
            +E+ I+   F  E+   K   E G   G+S+  V +L+ +A+ +LK++
Sbjct: 208 EREKSIIHCTF-EENLSQK---ETGERLGISQMHVSRLQRQAISKLKEA 252

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

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

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

Query: 499 RNLLTL----LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
           R LL      L+ +E+ I+ LRFG+  G+ K+  EV ++ G+S+  + +LE R + RLK+
Sbjct: 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228

Length = 234

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

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

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

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

Length = 208

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

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

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

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

Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs in Listeria score above the noise cutoff to This model, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 198

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

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

Query: 462 QQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIED 521
           ++   A  +                  +  +   + +R  L  L P++R    LR+ +E 
Sbjct: 85  RKRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRY-LEG 143

Query: 522 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 563
               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 = 39.8 bits (93), Expect = 0.002
 Identities = 52/230 (22%), Positives = 98/230 (42%), Gaps = 28/230 (12%)

Query: 332 KLINANLRLVVHVAKQ--YQGRG-ISLHDLLQEGSMGLMKSVEKF-KPQAGCRFASYAYW 387
           K +NA L LV  V +Q  +Q    I   D+ Q   MGL++++ ++  P     FA+YA  
Sbjct: 19  KYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDEQ--FAAYAV- 75

Query: 388 WVRQTIRKAIFQHSRTIRL-PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE 446
                IR AI    R +   P  +     K  +A R   +   H P+ E+++  + +T E
Sbjct: 76  ---HRIRGAILDELRELDWRPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAE 132

Query: 447 KLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS--VQKQLM-RQHVRNLLT 503
           +                   A    +  E+ A         S  +++ ++   +++  L+
Sbjct: 133 EY----------QEYLLLENAGTLESLDELLALEAHNDILQSRDLEENIIIEDNLKQALS 182

Query: 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
            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	569
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	100.0
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	100.0
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	100.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	100.0
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	100.0
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	100.0
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	100.0
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	100.0
PRK08215	258	sporulation sigma factor SigG; Reviewed	100.0
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	100.0
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	100.0
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	100.0
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	100.0
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	100.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	100.0
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
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.9
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.89
PRK12513	194	RNA polymerase sigma factor; Provisional	99.89
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.89
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.89
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.89
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.88
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.87
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.87
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.87
PRK12519	194	RNA polymerase sigma factor; Provisional	99.87
PRK12514	179	RNA polymerase sigma factor; Provisional	99.87
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.87
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.87
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.87
PRK11922	231	RNA polymerase sigma factor; Provisional	99.87
PRK12524	196	RNA polymerase sigma factor; Provisional	99.87
PRK12537	182	RNA polymerase sigma factor; Provisional	99.86
PRK12538	233	RNA polymerase sigma factor; Provisional	99.86
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.86
PRK12534	187	RNA polymerase sigma factor; Provisional	99.86
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.86
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.85
PRK12515	189	RNA polymerase sigma factor; Provisional	99.85
PRK12526	206	RNA polymerase sigma factor; Provisional	99.85
PRK12542	185	RNA polymerase sigma factor; Provisional	99.85
PRK11924	179	RNA polymerase sigma factor; Provisional	99.85
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.84
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.84
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.84
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.84
PRK12543	179	RNA polymerase sigma factor; Provisional	99.84
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.84
PRK12531	194	RNA polymerase sigma factor; Provisional	99.84
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.83
PRK12536	181	RNA polymerase sigma factor; Provisional	99.83
PRK12522	173	RNA polymerase sigma factor; Provisional	99.83
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.83
PRK12520	191	RNA polymerase sigma factor; Provisional	99.83
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.83
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.83
PRK12539	184	RNA polymerase sigma factor; Provisional	99.83
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.82
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.81
PRK12533	216	RNA polymerase sigma factor; Provisional	99.81
PRK12529	178	RNA polymerase sigma factor; Provisional	99.81
PRK12512	184	RNA polymerase sigma factor; Provisional	99.81
PRK12518	175	RNA polymerase sigma factor; Provisional	99.81
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.81
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.81
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.81
PRK12516	187	RNA polymerase sigma factor; Provisional	99.81
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.8
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.8
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.8
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.8
PRK12528	161	RNA polymerase sigma factor; Provisional	99.79
PRK12545	201	RNA polymerase sigma factor; Provisional	99.79
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.79
PRK12547	164	RNA polymerase sigma factor; Provisional	99.79
PRK12532	195	RNA polymerase sigma factor; Provisional	99.78
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.78
PRK12541	161	RNA polymerase sigma factor; Provisional	99.78
PRK12530	189	RNA polymerase sigma factor; Provisional	99.78
PRK12544	206	RNA polymerase sigma factor; Provisional	99.78
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.78
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.78
PRK12535	196	RNA polymerase sigma factor; Provisional	99.78
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.78
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.77
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.77
PRK12540	182	RNA polymerase sigma factor; Provisional	99.77
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.76
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.75
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.75
PRK12517	188	RNA polymerase sigma factor; Provisional	99.75
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.74
PRK12546	188	RNA polymerase sigma factor; Provisional	99.74
PRK12511	182	RNA polymerase sigma factor; Provisional	99.74
PRK12525	168	RNA polymerase sigma factor; Provisional	99.73
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.7
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.69
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.66
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.65
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.64
PRK09191	261	two-component response regulator; Provisional	99.52
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.52
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.45
PF07638	185	Sigma70_ECF: ECF sigma factor	99.38
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.25
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.23
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	99.04
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	98.93
PRK06930	170	positive control sigma-like factor; Validated	98.65
PRK00118	104	putative DNA-binding protein; Validated	98.43
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.29
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.18
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.13
PRK04217	110	hypothetical protein; Provisional	98.1
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.04
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	97.97
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	97.95
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	97.94
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.81
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.67
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.63
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.59
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.57
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.51
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.43
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.33
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.31
PRK10840	216	transcriptional regulator RcsB; Provisional	97.26
PRK13870	234	transcriptional regulator TraR; Provisional	97.26
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.24
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.24
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.24
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.22
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	97.18
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	97.16
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	97.11
COG2197	211	CitB Response regulator containing a CheY-like rec	97.06
COG4566	202	TtrR Response regulator [Signal transduction mecha	97.01
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	96.97
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.9
PRK09483	217	response regulator; Provisional	96.87
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.79
PRK15369	211	two component system sensor kinase SsrB; Provision	96.71
COG3413	215	Predicted DNA binding protein [General function pr	96.65
PRK01381	99	Trp operon repressor; Provisional	96.48
PRK10651	216	transcriptional regulator NarL; Provisional	96.48
PRK09390	202	fixJ response regulator FixJ; Provisional	96.44
COG1356	143	tfx Transcriptional regulator [DNA replication, re	96.41
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.21
COG1342	99	Predicted DNA-binding proteins [General function p	96.2
PRK15320	251	transcriptional activator SprB; Provisional	95.98
COG4941	415	Predicted RNA polymerase sigma factor containing a	95.97
PRK10403	215	transcriptional regulator NarP; Provisional	95.92
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	95.5
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.5
PRK09935	210	transcriptional regulator FimZ; Provisional	95.47
PRK13558	665	bacterio-opsin activator; Provisional	95.24
PRK04841	903	transcriptional regulator MalT; Provisional	95.24
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	95.05
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	94.81
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	94.64
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.56
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	94.51
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	94.38
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	94.25
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	94.14
PRK15418	318	transcriptional regulator LsrR; Provisional	94.08
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	93.5
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	93.46
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	93.41
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	93.14
PRK05901	509	RNA polymerase sigma factor; Provisional	92.78
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	92.67
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	92.53
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.27
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	92.25
PHA00675	78	hypothetical protein	92.22
PF13730	55	HTH_36: Helix-turn-helix domain	92.14
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	91.83
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	91.58
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	91.37
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	91.27
PRK07598	415	RNA polymerase sigma factor SigC; Validated	90.9
PF13518	52	HTH_28: Helix-turn-helix domain	90.79
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	90.57
smart00351	125	PAX Paired Box domain.	90.32
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	90.21
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	90.08
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	89.99
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	89.99
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	89.69
PHA02591	83	hypothetical protein; Provisional	88.98
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	88.92
PRK11083	228	DNA-binding response regulator CreB; Provisional	88.87
PF10668	60	Phage_terminase: Phage terminase small subunit; In	88.87
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	88.74
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	88.11
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	87.83
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	87.72
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	87.7
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	87.52
PHA02547	179	55 RNA polymerase sigma factor; Provisional	87.1
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	86.97
cd00131	128	PAX Paired Box domain	86.75
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	86.55
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	86.27
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	86.2
PRK15479	221	transcriptional regulatory protein TctD; Provision	86.16
PRK12423	202	LexA repressor; Provisional	85.77
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	85.75
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	85.73
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	85.59
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	85.54
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	85.39
PRK05949	327	RNA polymerase sigma factor; Validated	85.34
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	85.23
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	84.71
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	84.36
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	84.03
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	83.89
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	83.86
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	83.85
PRK10046	225	dpiA two-component response regulator DpiA; Provis	83.83
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	83.59
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	83.53
PF12728	51	HTH_17: Helix-turn-helix domain	83.34
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	83.26
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	83.23
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	83.06
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	82.99
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	82.91
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	82.63
COG3355	126	Predicted transcriptional regulator [Transcription	82.52
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	82.49
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	82.39
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	82.36
PRK07405	317	RNA polymerase sigma factor SigD; Validated	82.28
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	82.28
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	82.27
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	82.26
COG3415	138	Transposase and inactivated derivatives [DNA repli	82.14
CHL00148	240	orf27 Ycf27; Reviewed	82.03
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	81.49
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	81.36
PRK07670	251	RNA polymerase sigma factor SigD; Validated	81.27
TIGR01764	49	excise DNA binding domain, excisionase family. An	81.18
PRK00215	205	LexA repressor; Validated	80.55
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	80.51
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	80.36
PRK13413	200	mpi multiple promoter invertase; Provisional	80.22

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=1.3e-64  Score=539.81  Aligned_cols=315  Identities=38%  Similarity=0.648  Sum_probs=299.0

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHhhhhCCCCcHHHHHHHc
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI  312 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~--------------------le~~~~~l~~~~g~~pt~~ewA~a~  312 (569)
                      .+|+++.||++|++.||||++||++|+++||.++.                    |++++..|++++|++||..|||.++
T Consensus        58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~  137 (415)
T PRK07598         58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA  137 (415)
T ss_pred             CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence            57899999999999999999999999999999999                    8999999999999999999999554


Q ss_pred             ----------------------CCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhh
Q 008352          313 ----------------------GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSV  370 (569)
Q Consensus       313 ----------------------g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAi  370 (569)
                                            |+++++|+..++.|..|+++||.+|+++|++||++|.++|++++||||||++|||+|+
T Consensus       138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rav  217 (415)
T PRK07598        138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAV  217 (415)
T ss_pred             CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence                                  5566677777788999999999999999999999999999999999999999999999


Q ss_pred             hhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHH
Q 008352          371 EKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLER  450 (569)
Q Consensus       371 ekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~  450 (569)
                      ++|||++|++|+|||+||||++|.+++++++|+||+|.|+...+++++++.+.+.+++||.|+.+|||+.+|+++++|+.
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             HHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHH
Q 008352          451 LIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV  530 (569)
Q Consensus       451 ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EI  530 (569)
                      ++...+.++|||.+++++++..+.+++.++ ..+|++.+...++...|..+|..||++||.||.|||||+||+++|++||
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 VLLRVPRSVSLETKVGKDKDTELGDLLETD-DISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEI  376 (415)
T ss_pred             HHHHccCCcccccccCCCccccHHHhccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHH
Confidence            999999999999999988888888887654 3478888999999999999999999999999999999999999999999


Q ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 008352          531 GNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL  568 (569)
Q Consensus       531 Ae~LGISrerVRqie~RALkKLR~~l~~~~L~~yldll  568 (569)
                      |+.||||+++||+++++|++|||+.-....+++|++.|
T Consensus       377 A~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~~~  414 (415)
T PRK07598        377 GRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLELL  414 (415)
T ss_pred             HHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHHhc
Confidence            99999999999999999999999998999999999765

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=8.8e-62  Score=514.37  Aligned_cols=312  Identities=37%  Similarity=0.728  Sum_probs=299.9

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~  332 (569)
                      ..|++..||++|+++|+||+|||++|+++|+.++.+++++.+|+...|++|+..+||.++|++..+|..++..|..|++.
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             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (569)
Q Consensus       333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~  412 (569)
                      ||.+|+++|+++|++|.++|.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|++++++||+|.|+..
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             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  492 (569)
Q Consensus       413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~  492 (569)
                      .+++++++...+.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++++. .+|++.+...
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            999999999999999999999999999999999999999888888999999998777778888888763 4788888888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 008352          493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA  565 (569)
Q Consensus       493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl  565 (569)
                      .++..|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+......|+.|+
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            9999999999999999999999999999889999999999999999999999999999999999888898886

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=2.8e-61  Score=504.09  Aligned_cols=311  Identities=40%  Similarity=0.676  Sum_probs=297.5

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~  332 (569)
                      .+|++..||++|+++|+||++||++|+++|+.++.+++.+..|+..+|++|+..+||.++++++.+|+..++.|+.|++.
T Consensus        16 ~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~   95 (327)
T PRK05949         16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQK   95 (327)
T ss_pred             CCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHH
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (569)
Q Consensus       333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~  412 (569)
                      ||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
T Consensus        96 Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~  175 (327)
T PRK05949         96 MIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITE  175 (327)
T ss_pred             HHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  492 (569)
Q Consensus       413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~  492 (569)
                      .+++++++.+.+.+++||.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|.. .+|++.+...
T Consensus       176 ~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~~  254 (327)
T PRK05949        176 KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQE  254 (327)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHHH
Confidence            999999999999999999999999999999999999999998899999999998777777888888765 5789989999


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352          493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  566 (569)
Q Consensus       493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld  566 (569)
                      .+...|..+|+.||++||.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+.  ...++.|+.
T Consensus       255 ~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~  326 (327)
T PRK05949        255 LLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA  326 (327)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            999999999999999999999999999999999999999999999999999999999999994  356777764

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

Probab=100.00  E-value=1.6e-60  Score=492.44  Aligned_cols=298  Identities=44%  Similarity=0.755  Sum_probs=285.6

Q ss_pred             cHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHH
Q 008352          255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  334 (569)
Q Consensus       255 d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI  334 (569)
                      |++..||++++++|+||+|||.+|+++++.+..++..+.+|+.+.|++|+..+||+++|+++.+|+..++.|..|++.||
T Consensus         1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv   80 (298)
T TIGR02997         1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI   80 (298)
T ss_pred             CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence            36788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  414 (569)
Q Consensus       335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l  414 (569)
                      .+|+++|++||++|.++|.+++||+||||+|||+|+++|||++|++|+|||+||||++|.+++.+++++||+|.++...+
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             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352          415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  494 (569)
Q Consensus       415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el  494 (569)
                      ++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.+.+++. ..+|++.+...++
T Consensus       161 ~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~~  239 (298)
T TIGR02997       161 NKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERESL  239 (298)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHHH
Confidence            999999999999999999999999999999999999999888999999998776666777777774 4578889999999


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ...|..+|+.||++||.||.+||||+|++++|++|||+.||||++||||++++|++|||
T Consensus       240 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr  298 (298)
T TIGR02997       240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR  298 (298)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            99999999999999999999999999989999999999999999999999999999996

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

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=3.1e-60  Score=494.52  Aligned_cols=311  Identities=38%  Similarity=0.641  Sum_probs=296.4

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~  332 (569)
                      .+|++..||++|+++|+||+|||.+|+++|+.++.+++++..|+.++|++|+..+||.++++++.+|+..++.|+.|++.
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             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (569)
Q Consensus       333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~  412 (569)
                      ||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.++..
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             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  492 (569)
Q Consensus       413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~  492 (569)
                      .+++++++...+.+.+|+.|+.+|||+.+|+++++|..++.....++|||.+++++++..+.++++++. ..|++.+...
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            999999999999999999999999999999999999999988888999999998777777888888764 5789989999


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352          493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  566 (569)
Q Consensus       493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld  566 (569)
                      +++..|..+|+.||++||.||.+||||+|++++|++|||+.||||++||||++.+|++|||+.  ...+..|+.
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            999999999999999999999999999999999999999999999999999999999999995  456777764

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=6e-59  Score=507.21  Aligned_cols=302  Identities=34%  Similarity=0.614  Sum_probs=277.6

Q ss_pred             CCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHH
Q 008352          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE  331 (569)
Q Consensus       252 ~~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are  331 (569)
                      ...|++..||++|+++|+||++||++|+++|+.+..++..   +.       ...+|+..   ...+|.+.++.|..|++
T Consensus       208 ~~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~~---~~~~l~~~~~~g~~Ar~  274 (509)
T PRK05901        208 ATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDPE---LRRDLQWIGRDGKRAKN  274 (509)
T ss_pred             ccccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchhh---hhhhhhhhccchHHHHH
Confidence            3568999999999999999999999999999876433321   11       11234422   45778888999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH
Q 008352          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  411 (569)
Q Consensus       332 ~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~  411 (569)
                      +||.+|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+.
T Consensus       275 ~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~  354 (509)
T PRK05901        275 HLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMV  354 (509)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHH
Q 008352          412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  491 (569)
Q Consensus       412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~  491 (569)
                      ..++++.++.+.+.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|.....|++.+..
T Consensus       355 e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~~  434 (509)
T PRK05901        355 ETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSF  434 (509)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHHH
Confidence            99999999999999999999999999999999999999999988899999999987777788899998877789999999


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352          492 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  566 (569)
Q Consensus       492 ~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld  566 (569)
                      ..++..|..+|..|++|||.||.+||||++++++|++|||+.||||++|||||+.+||+|||+......|+.|++
T Consensus       435 ~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~  509 (509)
T PRK05901        435 TLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD  509 (509)
T ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            999999999999999999999999999999999999999999999999999999999999999998899999975

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

Probab=100.00  E-value=1e-58  Score=480.86  Aligned_cols=314  Identities=36%  Similarity=0.654  Sum_probs=289.0

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh-hhCCCCcHH---------------HHHHHcCCCH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC  316 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~-~~g~~pt~~---------------ewA~a~g~~~  316 (569)
                      ..|.+..|+.+++..+++++++|.++.+.++....+......+.. ..+..|+..               +|+.....++
T Consensus         7 ~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E   86 (342)
T COG0568           7 SADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE   86 (342)
T ss_pred             chhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence            356888999999999999999999999999887766666677776 677888876               6666555554


Q ss_pred             -HHHHHHHhccH---HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          317 -RDLKSELHSGN---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       317 -~~L~~~l~~G~---~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                       ..|..++..|.   .|+.+||.+|+|||++||++|.|+|+++.||||||+|||++|+++|||++||+|||||+||||++
T Consensus        87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqa  166 (342)
T COG0568          87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQA  166 (342)
T ss_pred             HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHH
Confidence             66777777763   69999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  472 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  472 (569)
                      |.++|.+++|+||+|.|+...+++++++.+.+.+++|++|+.+|||+.+|+++++|+.++.....++|||.+++++++..
T Consensus       167 I~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~  246 (342)
T COG0568         167 ITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSE  246 (342)
T ss_pred             HHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998889


Q ss_pred             hhhcccCCCCCChhHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352          473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  551 (569)
Q Consensus       473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~-L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK  551 (569)
                      +.|+++|+...+|++.+....+.+.+...|.. |+++|+.||++|||++|+++.|++|||+.+|||++|||||+.+|++|
T Consensus       247 l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~K  326 (342)
T COG0568         247 LGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRK  326 (342)
T ss_pred             HHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence            99999999887999999999999999999999 99999999999999999999999999999999999999999999999


Q ss_pred             HHH-HhhcCchhhhhh
Q 008352          552 LKQ-SLGGKASYGYAD  566 (569)
Q Consensus       552 LR~-~l~~~~L~~yld  566 (569)
                      ||. ......+++|++
T Consensus       327 Lr~~~~~~~~~~~~l~  342 (342)
T COG0568         327 LRRHPERSALLRSYLD  342 (342)
T ss_pred             HHHhhhhhhHHHHhhC
Confidence            994 444555677764

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=7.2e-58  Score=477.58  Aligned_cols=300  Identities=36%  Similarity=0.629  Sum_probs=275.6

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~  332 (569)
                      .+|++..||++++++|+||+|||.+|+++|+.+..++..           |+..+|....  ...++...++.|..|+++
T Consensus        24 ~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~   90 (324)
T PRK07921         24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRH   90 (324)
T ss_pred             CCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHH
Confidence            357899999999999999999999999999987655543           2223332111  346788899999999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (569)
Q Consensus       333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~  412 (569)
                      ||..|+++|+++|++|.++|.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+..
T Consensus        91 Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~  170 (324)
T PRK07921         91 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE  170 (324)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  492 (569)
Q Consensus       413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~  492 (569)
                      .+++++++...+.+.+||.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+...
T Consensus       171 ~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~  250 (324)
T PRK07921        171 QVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAG  250 (324)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999998888899999999877777888999887666888888889


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhh
Q 008352          493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA  565 (569)
Q Consensus       493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl  565 (569)
                      +++..|..+|+.|+++|+.||.+||||+||+++|++|||+.||||++|||||+.+|++|||.......|+.|+
T Consensus       251 ~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~  323 (324)
T PRK07921        251 LLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA  323 (324)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999999999999999999999999998888888885

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2.4e-54  Score=458.52  Aligned_cols=276  Identities=36%  Similarity=0.704  Sum_probs=262.4

Q ss_pred             CCCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHH
Q 008352          251 FDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSR  330 (569)
Q Consensus       251 ~~~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Ar  330 (569)
                      ...+|++..||++|+++|+||++||.+|+++++.                                        ++..|+
T Consensus        92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~  131 (367)
T PRK09210         92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAK  131 (367)
T ss_pred             cccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHH
Confidence            3457899999999999999999999999988764                                        235899


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  410 (569)
Q Consensus       331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~  410 (569)
                      +.||..|+++|+++|++|.+++.+++||+||||||||+|+++|||.+|++|+|||+||||++|.++|+++.|+||+|.|+
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             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHH
Q 008352          411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  490 (569)
Q Consensus       411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~  490 (569)
                      ...++++.++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|....+|++.+.
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            99999999999999999999999999999999999999999998888999999998777778899999887778999999


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352          491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  566 (569)
Q Consensus       491 ~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld  566 (569)
                      ...++..|..+|..||++||.||.+||||+||+++|++|||+.||||++||||++.+||+|||+......|+.|++
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=2.3e-51  Score=461.79  Aligned_cols=239  Identities=34%  Similarity=0.698  Sum_probs=232.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (569)
Q Consensus       328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP  407 (569)
                      .|+++||.+|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|++++|+||+|
T Consensus       380 ~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip  459 (619)
T PRK05658        380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP  459 (619)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  487 (569)
Q Consensus       408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee  487 (569)
                      +|+...+++++++...+.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|....+|++
T Consensus       460 ~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~  539 (619)
T PRK05658        460 VHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPID  539 (619)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHH
Confidence            99999999999999999999999999999999999999999999998889999999998888778999999988788999


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352          488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  566 (569)
Q Consensus       488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld  566 (569)
                      .+....++..|..+|..||+||+.||++||||++++++|++|||+.||||++||||++.+|++|||+......|+.|+|
T Consensus       540 ~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~  618 (619)
T PRK05658        540 AAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD  618 (619)
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence            9999999999999999999999999999999998899999999999999999999999999999999999999999987

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

Probab=100.00  E-value=1.3e-47  Score=384.01  Aligned_cols=238  Identities=39%  Similarity=0.753  Sum_probs=227.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (569)
Q Consensus       329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~  408 (569)
                      |+++||..|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
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             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352          409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  488 (569)
Q Consensus       409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~  488 (569)
                      ++...++++.++...+.+++|+.||.+|||+.+|++++++..++......+|||.+++++++.++.+.++|+...+|++.
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~  160 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY  160 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence            99999999999999999999999999999999999999999998888889999999877766678888888877788888


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352          489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  566 (569)
Q Consensus       489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld  566 (569)
                      +...++...|..+|+.||++||.||.++|||++++++|++|||+.||||+++|+|++.+|++|||+.+....|+.|+|
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            888889999999999999999999999999998899999999999999999999999999999999999999999976

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

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=100.00  E-value=1.4e-44  Score=378.19  Aligned_cols=272  Identities=35%  Similarity=0.567  Sum_probs=253.5

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~  332 (569)
                      ..|.++.|+.+|+..|+||+++|.+|+.+++.                                        ++..|++.
T Consensus        51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~   90 (325)
T PRK05657         51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR   90 (325)
T ss_pred             cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence            56788999999999999999999999987654                                        45689999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (569)
Q Consensus       333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~  412 (569)
                      ||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||++|.++++++.+.|++|.++..
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             HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHH
Q 008352          413 LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQ  492 (569)
Q Consensus       413 ~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~  492 (569)
                      .++++.++...+.+.+|+.|+.+|||+.+|+++++|..++.......|+|.++..+...++.+.+.+....+|+..+...
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            99988899999999999999999999999999999999998888889999998777666778888877666889989888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 008352          493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY  564 (569)
Q Consensus       493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~y  564 (569)
                      +....|..+|..||+++|.||.+||||.+.+++|++|||+.||||++||++++++|+++||+.+...++..+
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            889999999999999999999999999888999999999999999999999999999999999998887643

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=2.4e-44  Score=370.74  Aligned_cols=264  Identities=26%  Similarity=0.451  Sum_probs=226.4

Q ss_pred             cHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHH
Q 008352          255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  334 (569)
Q Consensus       255 d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI  334 (569)
                      +..+.||++++++|+||+++|.+|+.+++.                                       .++..|+++||
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            466789999999999999999999987642                                       14568999999


Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH--
Q 008352          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT--  412 (569)
Q Consensus       335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~--  412 (569)
                      ..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++++|+|.+...  
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--chhhcccCCCCCChh
Q 008352          413 LLSKVLEAKRLYIQ---EGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQDT--TFQEITADTGVEIPD  486 (569)
Q Consensus       413 ~l~ki~ka~~~l~~---~~gr~Pt~eEIA~~lgis~e~v~~ll~-~~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~~pe  486 (569)
                      ...++++.+..+.+   .+|+.|+.+|||+.||+++++|..+.. ....++|||.+++++++.  ++.+.+.++.. +|+
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 445799999998765443  57788877643 566


Q ss_pred             HHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          487 ISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       487 e~l~~----~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      +.+..    .+....|..+|+.||++||.||.+||+.  ++++|++|||+.||||++||+|++++|++|||..+....
T Consensus       206 ~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~~  281 (289)
T PRK07500        206 EQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRALLSQS  281 (289)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            55443    3456789999999999999999999962  378999999999999999999999999999999987543

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=2.6e-44  Score=369.63  Aligned_cols=262  Identities=27%  Similarity=0.477  Sum_probs=223.9

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~  332 (569)
                      +.+++..|++++++.|+||.++|.+|+.+++.                                       .++..|++.
T Consensus        12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~~   52 (284)
T PRK06596         12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAKQ   52 (284)
T ss_pred             CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHHH
Confidence            55789999999999999999999999886532                                       144689999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHH
Q 008352          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYT  412 (569)
Q Consensus       333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~  412 (569)
                      ||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.+++++++++|++|.+...
T Consensus        53 Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~~  132 (284)
T PRK06596         53 LVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQ  132 (284)
T ss_pred             HHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999889999987642


Q ss_pred             --HHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCCcccCCCCCCCCC--cchhhcccCCCCCChhH
Q 008352          413 --LLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF-ITRMPLSMQQPVWADQD--TTFQEITADTGVEIPDI  487 (569)
Q Consensus       413 --~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~-~~~~~~SLD~~v~~d~~--~~l~d~i~D~~~~~pee  487 (569)
                        ...++.+....+.  .+++|+.+|||+.+|+++++|..++. .....+|||.+++++++  .++.+.++|+. .+|++
T Consensus       133 ~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~~  209 (284)
T PRK06596        133 RKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPAD  209 (284)
T ss_pred             HHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCchH
Confidence              2344444444443  35899999999999999999999875 33478999999865532  45778887764 46776


Q ss_pred             HHHHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          488 SVQKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       488 ~l~~~----el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      .++..    +++..|..+|+.||++||.||.+||+. + +++|++|||+.||||++||||++++|++|||+.+..
T Consensus       210 ~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~  282 (284)
T PRK06596        210 VLEEDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA  282 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            66654    357889999999999999999999973 2 689999999999999999999999999999998764

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=1.2e-43  Score=362.08  Aligned_cols=258  Identities=28%  Similarity=0.501  Sum_probs=217.0

Q ss_pred             HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHH
Q 008352          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (569)
Q Consensus       256 ~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~  335 (569)
                      ++..||++++++|+|+.++|.+|+.++..                                       .++..|++.||.
T Consensus         2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv~   42 (270)
T TIGR02392         2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLVL   42 (270)
T ss_pred             hHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence            57789999999999999999999886432                                       145689999999


Q ss_pred             HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH--HH
Q 008352          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY--TL  413 (569)
Q Consensus       336 ~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~--~~  413 (569)
                      .|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++.++++|+|.+..  ..
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            9999999999999999999999999999999999999999999999999999999999999999988899997654  33


Q ss_pred             HHHHHHHHHHHHHhcCCCC-CHHHHHHHhCCCHHHHHHHHHhc-CCCcccCCCCCCCCC--cchhhcccCCCCCChhHHH
Q 008352          414 LSKVLEAKRLYIQEGNHSP-DKEDLARRVGITVEKLERLIFIT-RMPLSMQQPVWADQD--TTFQEITADTGVEIPDISV  489 (569)
Q Consensus       414 l~ki~ka~~~l~~~~gr~P-t~eEIA~~lgis~e~v~~ll~~~-~~~~SLD~~v~~d~~--~~l~d~i~D~~~~~pee~l  489 (569)
                      ..++.+....+.  +++.| +.+|||+.+|+++++|.+++... ...+|||.+++++++  ..+.+.+.|+. .+|++.+
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            444544444442  32555 69999999999999999986533 347999999866443  25667777765 3677666


Q ss_pred             HHH----HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          490 QKQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       490 ~~~----el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      ...    .++..|..+|..||++||.||.+||+.  ++++|++|||+.||||+++|+|++++|++|||+.+.
T Consensus       200 ~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~  269 (270)
T TIGR02392       200 EEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA  269 (270)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence            543    356789999999999999999999962  368999999999999999999999999999998764

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

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=4.8e-43  Score=356.81  Aligned_cols=220  Identities=24%  Similarity=0.393  Sum_probs=201.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (569)
Q Consensus       328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP  407 (569)
                      .++++||.+|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+|
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--chhhcccCCCCC
Q 008352          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDT--TFQEITADTGVE  483 (569)
Q Consensus       408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~  483 (569)
                      +++...+++++++...+.+++|+.||.+|||+.+|+++++|.+++..  ...++|||.+++++++.  .+.+.++     
T Consensus       120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~-----  194 (264)
T PRK07122        120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLG-----  194 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccC-----
Confidence            99999999999999999999999999999999999999999998864  45689999998654322  2333332     


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      +++..++..+....|..+|+.||+++|.||.++|+    +++|++|||+.||||.++|++++++|+++||..+
T Consensus       195 ~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l  263 (264)
T PRK07122        195 DVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL  263 (264)
T ss_pred             CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence            34556667777888999999999999999999998    8999999999999999999999999999999876

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=2.2e-41  Score=342.96  Aligned_cols=228  Identities=25%  Similarity=0.408  Sum_probs=201.9

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~-g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      ++..|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++++.++
T Consensus        22 gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~  101 (256)
T PRK07408         22 PSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT  101 (256)
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCe
Confidence            345899999999999999999999876 6679999999999999999999999999999999999999999999999999


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc--chhhcccC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT--TFQEITAD  479 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~v~~d~~~--~l~d~i~D  479 (569)
                      ||+|+++...+++++++...+.+++|++|+.+|||+.+|+++++|..++.  .....+|||.++.++++.  .+.+.+++
T Consensus       102 vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d  181 (256)
T PRK07408        102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD  181 (256)
T ss_pred             eeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCC
Confidence            99999999999999999999999999999999999999999999999864  345689999987554332  45566665


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          480 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       480 ~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      +... +.  ....+....|..+|..||+++|.||.++|+    +++|++|||+.||||.++|++++.+|+++||+.+...
T Consensus       182 ~~~~-~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~  254 (256)
T PRK07408        182 PRYR-SF--QLAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE  254 (256)
T ss_pred             cccc-hh--hhhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence            4322 11  123345677999999999999999999998    8999999999999999999999999999999988654

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=8.5e-41  Score=343.37  Aligned_cols=272  Identities=35%  Similarity=0.561  Sum_probs=248.3

Q ss_pred             CCCCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHH
Q 008352          250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS  329 (569)
Q Consensus       250 ~~~~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~A  329 (569)
                      .....|.+..||.+|+.+|.||.++|.+|+.+++.                                        ++..|
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~a   47 (285)
T TIGR02394         8 ETRVADVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFEA   47 (285)
T ss_pred             ccCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHHH
Confidence            34467899999999999999999999999887654                                        34689


Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (569)
Q Consensus       330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~  409 (569)
                      ++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+||+.|||+.++.+++.++.+.+++|.+
T Consensus        48 ~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~  127 (285)
T TIGR02394        48 RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVH  127 (285)
T ss_pred             HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  489 (569)
Q Consensus       410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l  489 (569)
                      +...++.+.+..+.+.+.+|+.|+.+++|..+|++++++..++.......|+|.++..+....+.+.+.++...+|++.+
T Consensus       128 ~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~  207 (285)
T TIGR02394       128 VIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLV  207 (285)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHH
Confidence            99999998888888888889999999999999999999999998877889999887665555566666666556788889


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      ...+....|..+|..||+++|.||.++|||.+.+++|++|||+.||||.++|++++++|+++||+.+...++
T Consensus       208 ~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~  279 (285)
T TIGR02394       208 QNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV  279 (285)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999999999999999999999999988777999999999999999999999999999999999986554

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=100.00  E-value=8.7e-40  Score=330.55  Aligned_cols=243  Identities=27%  Similarity=0.444  Sum_probs=215.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 008352          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (569)
Q Consensus       264 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~s  343 (569)
                      .+++|+||++||.+|+.+++.                                        ++..|++.||..|+++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence            468899999999998876653                                        3458999999999999999


Q ss_pred             HHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHH
Q 008352          344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  423 (569)
Q Consensus       344 IArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~  423 (569)
                      +|++|.+++.+++||+||||+|||+++++|||.+|.+|+||++|||+|.|.++++++. .||+|+++...++++.++...
T Consensus        50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~  128 (254)
T TIGR02850        50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK  128 (254)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999975 889999999999999999999


Q ss_pred             HHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhcccCCCCCChhHHHHHHHHHHHHHHH
Q 008352          424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL  501 (569)
Q Consensus       424 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~~pee~l~~~el~e~L~~a  501 (569)
                      +.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++.  .+.+.+.|+.. .++    ....+..|..+
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            999999999999999999999999999998888899999987544332  45666665432 122    22344578999


Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      |..|++++|.||.+||+    +++|++|||+.||+|+++|++++++|++|||+.+
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    8999999999999999999999999999999753

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=100.00  E-value=1.5e-39  Score=329.86  Aligned_cols=227  Identities=26%  Similarity=0.391  Sum_probs=204.8

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~---~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~  401 (569)
                      ++..|+++||..|+++|+++|++|.+   .+++++||+|||+||||+|+++|||++|++|+|||.||||++|.+++++..
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   356899999999999999999999999999999999999999999999987


Q ss_pred             cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCC--CC--Ccchhh
Q 008352          402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWA--DQ--DTTFQE  475 (569)
Q Consensus       402 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~--d~--~~~l~d  475 (569)
                      +   +|+++...++++.++...+.+.+||.|+.+|||+.+|+++++|..++....  .++|||.++..  ++  +.++.+
T Consensus       100 ~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~  176 (257)
T PRK05911        100 W---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE  176 (257)
T ss_pred             C---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence            5   899999999999999999999999999999999999999999999886553  46899987643  21  235677


Q ss_pred             cccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          476 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       476 ~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      .++|.....|++.+...+....|..+|+.||++||.||.++|+    +++|++|||+.||||+++|++++.+|+++||+.
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            8888766678888888888999999999999999999999998    899999999999999999999999999999998


Q ss_pred             hhc
Q 008352          556 LGG  558 (569)
Q Consensus       556 l~~  558 (569)
                      +..
T Consensus       253 l~~  255 (257)
T PRK05911        253 LSA  255 (257)
T ss_pred             HHh
Confidence            754

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=100.00  E-value=1.9e-38  Score=321.27  Aligned_cols=243  Identities=27%  Similarity=0.463  Sum_probs=214.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 008352          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (569)
Q Consensus       264 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~s  343 (569)
                      .+++|+|+++|+..|+.+++.                                        ++..|++.||..|+++|++
T Consensus        13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~   52 (258)
T PRK08215         13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS   52 (258)
T ss_pred             CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence            457789999999988876653                                        3568999999999999999


Q ss_pred             HHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHH
Q 008352          344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRL  423 (569)
Q Consensus       344 IArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~  423 (569)
                      +|++|.+++.+++||+|||++|||+++++||+.+|++|+||+++||+++|.++++++. .||+|+++.....++.++...
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--chhhcccCCCCCChhHHHHHHHHHHHHHHH
Q 008352          424 YIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVRNL  501 (569)
Q Consensus       424 l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~~pee~l~~~el~e~L~~a  501 (569)
                      +.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++.  ++.+.++++.. .++    .......|..+
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            999999999999999999999999999988777888999988654432  34555554422 222    22334578899


Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      |+.||++++.||.++|+    +++|++|||+.||||.++|++++++|+++||+.+
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

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

Probab=100.00  E-value=2.1e-38  Score=318.14  Aligned_cols=223  Identities=27%  Similarity=0.504  Sum_probs=202.9

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~-~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      ++..++ .||+.|+|||.+||++|.+++. +.+||+|-|+|||++|+++|||++|.+|+|||...|+++|.+++|++. .
T Consensus        21 g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~   98 (247)
T COG1191          21 GDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-S   98 (247)
T ss_pred             cCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-C
Confidence            345788 9999999999999999998877 999999999999999999999999999999999999999999999999 9


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCCCCCcchhhcccCCC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTG  481 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~d~~~~l~d~i~D~~  481 (569)
                      |++|+.+....+++..+...+.+++||+||++|||+.+|++.+++..++....  ..+|+|..+..+++..     .++.
T Consensus        99 v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~  173 (247)
T COG1191          99 VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQ  173 (247)
T ss_pred             ccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhc
Confidence            99999999999999999999999999999999999999999999999887654  6788887765444333     2233


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      ..+|.+.+++.+..+.|.+++..|++|||.||.+||.    +++|++|||++||||..+|+|++++|++|||+.+..
T Consensus       174 ~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~  246 (247)
T COG1191         174 IENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK  246 (247)
T ss_pred             cccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence            4467788888888889999999999999999999998    999999999999999999999999999999998753

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=100.00  E-value=4.4e-37  Score=313.13  Aligned_cols=249  Identities=20%  Similarity=0.363  Sum_probs=221.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 008352          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (569)
Q Consensus       264 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~s  343 (569)
                      -+++|+||.++|.+|+.+++.                                       .++..+++.|+..|.++|+.
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            478999999999999987653                                       13468999999999999999


Q ss_pred             HHHHhh-C--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHH
Q 008352          344 VAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEA  420 (569)
Q Consensus       344 IArry~-~--~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka  420 (569)
                      +|++|. +  .+.+++||+||||+|||+++++||+.+|++|+||++||||+.|.+++++..   ++|+++....++++++
T Consensus        47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~  123 (268)
T PRK06288         47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERA  123 (268)
T ss_pred             HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHH
Confidence            999986 2  567899999999999999999999999999999999999999999999654   6899999999999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCC---CcchhhcccCCCCCChhHHHHHHHHH
Q 008352          421 KRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQ---DTTFQEITADTGVEIPDISVQKQLMR  495 (569)
Q Consensus       421 ~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~---~~~l~d~i~D~~~~~pee~l~~~el~  495 (569)
                      ...+.+.+|+.|+.+|||+.+|++.+++..++...  ....|||..+..++   ...+.+.++++...+|++.+...+..
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            99999999999999999999999999999987643  45789988763222   23466777776667888888888889


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      ..|..+|..||+++|.||.++|+    +++|++|||+.||+|.++|++++.+|+++||.++..
T Consensus       204 ~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  262 (268)
T PRK06288        204 RVIVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE  262 (268)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999998    899999999999999999999999999999998864

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=100.00  E-value=1.9e-36  Score=305.87  Aligned_cols=244  Identities=23%  Similarity=0.356  Sum_probs=215.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHH
Q 008352          268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ  347 (569)
Q Consensus       268 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArr  347 (569)
                      |.||+++|.+|+.+++.                                       .++..|+++|+..|.++|+++|++
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            66899999888876653                                       134589999999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHh
Q 008352          348 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE  427 (569)
Q Consensus       348 y~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~  427 (569)
                      |.+++.+++||+||||+|||+++++||++.|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+.+.
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--CCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcC
Q 008352          428 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL  505 (569)
Q Consensus       428 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L  505 (569)
                      +|+.|+.+|+|+.+|++.+++..++...  ....|||.++..+++......+ + ....|++.+...+....|..+|+.|
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            9999999999999999999998887643  4578999888655443222221 1 1224666677777888899999999


Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          506 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       506 ~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      |+++|.||.++|+    +++|++|||+.||||.++|++++.+|+++||+.+
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=1.2e-36  Score=302.60  Aligned_cols=223  Identities=29%  Similarity=0.469  Sum_probs=199.0

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      .++..|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|.||++|||++.|.++++++. .
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            345699999999999999999999999999999999999999999999999999999999999999999999999986 8


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhcccCCC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTG  481 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~i~D~~  481 (569)
                      |++|+++....+++.++...+..++|+.||.+|||+.+|++++++..++.....+.|||.++.++++.  ++.+.+.++.
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            99999999999999999999999999999999999999999999999988878889999888655432  3456665543


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      .  +++   .......|..+++.||+++++||.++|+    +++|++|||+.||||+++|++++++|++|||..|
T Consensus       166 ~--~~~---~~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l  231 (231)
T TIGR02885       166 S--EDS---DWLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL  231 (231)
T ss_pred             c--cHH---hHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence            2  222   2223557889999999999999999998    8999999999999999999999999999999864

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.

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

Probab=100.00  E-value=5.5e-36  Score=296.93  Aligned_cols=221  Identities=28%  Similarity=0.452  Sum_probs=198.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (569)
Q Consensus       327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl  406 (569)
                      ..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+|+++||+.+|.+|+||+++||++.|.++++++.+.+++
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--cchhhcccCCCC
Q 008352          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM--PLSMQQPVWADQD--TTFQEITADTGV  482 (569)
Q Consensus       407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~--~~SLD~~v~~d~~--~~l~d~i~D~~~  482 (569)
                      |.++...+++++++...+.+.+|+.|+.+|+|+.+|++++++..++.....  ..|||.++.++++  ..+.+.+.    
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~----  157 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG----  157 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence            999999999999999999999999999999999999999999998876554  8999988763222  12233322    


Q ss_pred             CChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          483 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       483 ~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                       +++..+...+....|..+|..||+++++||.++|+    +++|++|||+.||+|+++|++++++|+++||+.+
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             34455556677788999999999999999999998    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=2.8e-35  Score=297.02  Aligned_cols=225  Identities=24%  Similarity=0.369  Sum_probs=202.4

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccc
Q 008352          326 GNSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (569)
Q Consensus       326 G~~Are~LI~~nlrLV~sIArry~~---~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r  402 (569)
                      +..|++.||..|.++|+++|++|.+   ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+|.|.++++++. 
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            4589999999999999999999965   678999999999999999999999999999999999999999999999876 


Q ss_pred             ceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH--hcCCCcccCCCCCCCCCc-chhhcccC
Q 008352          403 TIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF--ITRMPLSMQQPVWADQDT-TFQEITAD  479 (569)
Q Consensus       403 ~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~--~~~~~~SLD~~v~~d~~~-~l~d~i~D  479 (569)
                        ++|.++...+++++++...+.+.+|+.|+.+|||+.+|++.++|..++.  ....++|||.++.++++. .+.+.+.+
T Consensus        99 --~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~  176 (251)
T PRK07670         99 --WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRD  176 (251)
T ss_pred             --CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhcC
Confidence              6999999999999999999999999999999999999999999999876  456789999988654433 23344455


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          480 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       480 ~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      ....++++.+...+....|..+|..||+++|+||.++|+    +++|++|||+.||+|.++|+++++||+++||.++.
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            555578888888888889999999999999999999998    99999999999999999999999999999999875

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=1.6e-34  Score=292.21  Aligned_cols=243  Identities=24%  Similarity=0.355  Sum_probs=214.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHH
Q 008352          268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ  347 (569)
Q Consensus       268 ~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArr  347 (569)
                      |.|+++||.+|..+++.                                       .++..|++.||..|.++|+++|++
T Consensus         8 ~~l~~~e~~~li~~~~~---------------------------------------~gd~~a~~~l~~~~~~~v~~~a~~   48 (257)
T PRK08583          8 TKLTKEEVNKWIAEYQE---------------------------------------NQDEEAQEKLVKHYKNLVESLAYK   48 (257)
T ss_pred             CcCChHHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHHHHHH
Confidence            77999999888776543                                       134689999999999999999999


Q ss_pred             hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHh
Q 008352          348 YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQE  427 (569)
Q Consensus       348 y~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~  427 (569)
                      |.+++.+++||+||||+|||+++++||+..|.+|.||+++||+|.|.++++++.+.+++|+++....++++++...+...
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---chhhcccCCCCCChhHHHHHHHHHHHHHHHH
Q 008352          428 GNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDT---TFQEITADTGVEIPDISVQKQLMRQHVRNLL  502 (569)
Q Consensus       428 ~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~---~l~d~i~D~~~~~pee~l~~~el~e~L~~aL  502 (569)
                      .++.|+.+++|+.+|++.+++..+....  ....|+|.+++.+++.   .+.+..     ..|++.+...+....|..+|
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     24566667777778899999


Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      ..||+++|+||.++|+    +++|++|||+.||||.++|++++++|+++||..+..
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    899999999999999999999999999999998754

>PRK05572 sporulation sigma factor SigF; Validated

Probab=100.00  E-value=1.9e-34  Score=291.25  Aligned_cols=244  Identities=28%  Similarity=0.430  Sum_probs=212.8

Q ss_pred             ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHH
Q 008352          262 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV  341 (569)
Q Consensus       262 ~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV  341 (569)
                      +.-...|.||.+++.+|..+++.                                        ++..|++.|+..|.++|
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            44567899999999888765442                                        34589999999999999


Q ss_pred             HHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHH
Q 008352          342 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAK  421 (569)
Q Consensus       342 ~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~  421 (569)
                      +++|++|.+++.+++||+|||++++|+++++||+.+|.+|.||+++||++.|.+++++.. .|++|+++....++++++.
T Consensus        46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~  124 (252)
T PRK05572         46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK  124 (252)
T ss_pred             HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999998889999999999999999999884 7899999999999999999


Q ss_pred             HHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc--chhhcccCCCCCChhHHHHHHHHHHHHH
Q 008352          422 RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT--TFQEITADTGVEIPDISVQKQLMRQHVR  499 (569)
Q Consensus       422 ~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~--~l~d~i~D~~~~~pee~l~~~el~e~L~  499 (569)
                      ..+..++||.|+..|+|+.+|++++++..+......+.||+.++.+++..  ++.+.+.++..   +    .......|.
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            99999999999999999999999999999888777889999887654322  23344433221   1    123356789


Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          500 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       500 ~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      .+|+.||+++++||.++|+    +++|++|||+.+|+|.++|++++++|+++||..+.
T Consensus       198 ~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~  251 (252)
T PRK05572        198 EAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD  251 (252)
T ss_pred             HHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999998    89999999999999999999999999999998774

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

Probab=100.00  E-value=1.2e-34  Score=287.37  Aligned_cols=217  Identities=23%  Similarity=0.419  Sum_probs=195.9

Q ss_pred             HHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352          333 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (569)
Q Consensus       333 LI~~nlrLV~sIArry~~---~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~  409 (569)
                      |+..|.++|+++|++|.+   ++.+++||+|||++|||+++++|||++|++|+||+++||++.+.+++++..   ++|.+
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   789999999999999999999999999999999999999999999999875   58999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCC-CCcchhhcccCCCCCChh
Q 008352          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWAD-QDTTFQEITADTGVEIPD  486 (569)
Q Consensus       410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d-~~~~l~d~i~D~~~~~pe  486 (569)
                      ....+++++++...+.+.+|+.|+.+|+|+.+|+++++|..++..  .....|+|....++ +...+.+.++++...+|+
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE  157 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence            999999999999999999999999999999999999999999853  34567888766543 234566666655556888


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      +.+...+....|..+|+.||+++|+||.++|+    +++|++|||+.||+|.++|++++++|+++||+++
T Consensus       158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l  223 (224)
T TIGR02479       158 EELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL  223 (224)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence            88888888899999999999999999999998    8999999999999999999999999999999875

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=100.00  E-value=2.5e-34  Score=287.50  Aligned_cols=208  Identities=21%  Similarity=0.328  Sum_probs=179.3

Q ss_pred             HHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352          331 EKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (569)
Q Consensus       331 e~LI~~nlrLV~sIArry~~---~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP  407 (569)
                      ..|+..|+++|.++|++|.+   .+.+.+||+|||++|||+|+++|||.+| +|+|||+|||||+|.+++++..+   +|
T Consensus        18 ~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~---~~   93 (231)
T PRK12427         18 GKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW---RP   93 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---CC
Confidence            45778899999999999874   4679999999999999999999998666 89999999999999999998654   68


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITADTGVEIP  485 (569)
Q Consensus       408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p  485 (569)
                      +++....++++++...+.+++|+.|+.+|||+.+|+++++|.+++..  .....|||.+++++++..   .+.+   ..+
T Consensus        94 r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~~~  167 (231)
T PRK12427         94 RRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---RDL  167 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---CCH
Confidence            88899999999999999999999999999999999999999998763  456899999886654322   2221   123


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      ++.   ......|..++..||+++|.||.++|+    +++|++|||+.||||.++|+|++++|++|||.+
T Consensus       168 ~~~---~~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~  230 (231)
T PRK12427        168 EEN---IIIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF  230 (231)
T ss_pred             HHH---HHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            322   234567899999999999999999998    899999999999999999999999999999964

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=100.00  E-value=3.4e-33  Score=279.18  Aligned_cols=225  Identities=23%  Similarity=0.406  Sum_probs=198.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~---~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~  401 (569)
                      .|.-+++.|+..|.++|+++|++|.   +++.+++||+||||+|||+++++|||++|.+|+||+++||+|.|.++++++.
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            4677999999999999999999997   6789999999999999999999999999999999999999999999999986


Q ss_pred             cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCCcccCCCCCCCCCcchhhcccC
Q 008352          402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFI--TRMPLSMQQPVWADQDTTFQEITAD  479 (569)
Q Consensus       402 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~--~~~~~SLD~~v~~d~~~~l~d~i~D  479 (569)
                      +   +|..+.....++.++...+.+.+|++|+.+|||+.+|++.++|..++..  ....+|++..++++++. +.. ..+
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   6888888888888899999999999999999999999999999998874  34567888876554432 222 223


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          480 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       480 ~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      +...+|++.+...+....|..+|+.||+++|.||.++|.    +++|++|||+.||||.++|++++.+|+++||+.+..
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            334467888888888899999999999999999999998    899999999999999999999999999999998754

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.96  E-value=3.6e-28  Score=242.63  Aligned_cols=210  Identities=25%  Similarity=0.451  Sum_probs=171.1

Q ss_pred             HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHH
Q 008352          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (569)
Q Consensus       256 ~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~  335 (569)
                      .+..|+.+++..|+||+++|..|...++.                                        ++..|++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence            56789999999999999999888766542                                        34689999999


Q ss_pred             HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHH
Q 008352          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  415 (569)
Q Consensus       336 ~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~  415 (569)
                      .|.++|+++|.+|.+++.+.+||+|||++++|+++++||+++|.+|.||+++|+++.+.+++++..+..           
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            999999999999999999999999999999999999999988899999999999999999998754210           


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC---CCcchhhcccCCCCCChhHHHHHH
Q 008352          416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTGVEIPDISVQKQ  492 (569)
Q Consensus       416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d---~~~~l~d~i~D~~~~~pee~l~~~  492 (569)
                                                               ...+++.....+   ....+.+.+.+. .+.+++.+..+
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 008352          493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      +..+.|..+|+.||+++|+||.++|++.+.+++|++|||+.||||.++|+++++||+++||+.+..
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            778889999999999999999999977666899999999999999999999999999999998764

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.93  E-value=1.2e-24  Score=216.61  Aligned_cols=179  Identities=30%  Similarity=0.543  Sum_probs=141.8

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++..|++.|+..|.++|+++|.+|.++..+++||+||+|+++|+++++|+++.+.+|.||+++|++|.+.+++++..+..
T Consensus        45 gd~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~  124 (227)
T TIGR02846        45 GDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTK  124 (227)
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhccc
Confidence            34689999999999999999999999999999999999999999999999988889999999999999999998754210


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC---CCcchhhcccCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD---QDTTFQEITADTG  481 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d---~~~~l~d~i~D~~  481 (569)
                                                                          ...+++.....+   ....+.+...+ .
T Consensus       125 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~  151 (227)
T TIGR02846       125 ----------------------------------------------------GEVSLQDPIGVDKEGNEISLIDILGS-D  151 (227)
T ss_pred             ----------------------------------------------------cceeccccccCCcccCcccHHHHhcC-C
Confidence                                                                001111111000   01112222222 1


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      ...+++.+...+..+.|..+|+.||+++|+||.++|.++..+++|++|||++||+|.++|++++++|+++||+.+
T Consensus       152 ~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~  226 (227)
T TIGR02846       152 GDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL  226 (227)
T ss_pred             CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            234566666666677899999999999999999999765558999999999999999999999999999999865

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=2.3e-24  Score=214.93  Aligned_cols=180  Identities=28%  Similarity=0.539  Sum_probs=139.6

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+.++++++.+..
T Consensus        49 gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~  128 (234)
T PRK08301         49 GDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK  128 (234)
T ss_pred             cCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            34589999999999999999999999999999999999999999999999988889999999999999999998764210


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC--CC-CcchhhcccCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA--DQ-DTTFQEITADTG  481 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~--d~-~~~l~d~i~D~~  481 (569)
                                                                          ...+++.+...  ++ .....+...+. 
T Consensus       129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-  155 (234)
T PRK08301        129 ----------------------------------------------------AEVSFDEPLNIDWDGNELLLSDVLGTD-  155 (234)
T ss_pred             ----------------------------------------------------cccccccccccccCCCcccHHHhccCc-
Confidence                                                                00111111100  00 00111222211 


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      ...++..+......+.|..+|+.||+++|+||.++|+|...+++|++|||+.||||.++|+++++||+++||+.+.
T Consensus       156 ~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~  231 (234)
T PRK08301        156 NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN  231 (234)
T ss_pred             ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            1123334455555667999999999999999999996544489999999999999999999999999999999875

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.92  E-value=1.3e-23  Score=210.05  Aligned_cols=181  Identities=30%  Similarity=0.541  Sum_probs=141.1

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++..|++.|+..|.+.|+++|++|.+++.+.+||+||+++++|+++++|++..+++|.||++.+++|.+.++++++.+..
T Consensus        49 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~  128 (234)
T TIGR02835        49 GDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTR  128 (234)
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence            34689999999999999999999999999999999999999999999999988888999999999999999998765210


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC---CCCCcchhhcccCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW---ADQDTTFQEITADTG  481 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~---~d~~~~l~d~i~D~~  481 (569)
                                                                          ...+++....   .+......+... +.
T Consensus       129 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~~  155 (234)
T TIGR02835       129 ----------------------------------------------------SEVSFDEPLNVDWDGNELLLSDVLG-TD  155 (234)
T ss_pred             ----------------------------------------------------CcccccccccCCCCCCcchHHHhcC-CC
Confidence                                                                0011111110   000001111111 11


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      .+.+++.+......+.|..+|+.||+++|.||.++|++.+++++|++|||+.||||..+|+++..+|+++||+.+..
T Consensus       156 ~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~  232 (234)
T TIGR02835       156 SDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR  232 (234)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            12233444555566789999999999999999999976555899999999999999999999999999999998754

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=8.3e-23  Score=198.91  Aligned_cols=195  Identities=22%  Similarity=0.329  Sum_probs=149.5

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      ++++.++..+..| ..|++.|+..|.++|+.+|++|.+++.+.+||+||++++||+++.+||+.+|.+|.||++.++++.
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            4456666666555 599999999999999999999999999999999999999999999999988789999999999999


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT  471 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~-d~~~  471 (569)
                      +.+++++..+..+.+.                                               ....|.+.++.+ +.+.
T Consensus        89 ~~d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~  121 (208)
T PRK08295         89 IITAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDR  121 (208)
T ss_pred             HHHHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccch
Confidence            9999876432111000                                               011223332211 1222


Q ss_pred             chhhcccCCCCCChhHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          472 TFQEITADTGVEIPDISVQKQLMRQHV-RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       472 ~l~d~i~D~~~~~pee~l~~~el~e~L-~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      .+.+.+.++...+|++.+...+....+ ..++..||+++|.||.+ |.    +++|++|||+.||+|.++|+..+.||++
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            344444444444677666655555555 45679999999999999 77    8999999999999999999999999999


Q ss_pred             HHHHHhhcCc
Q 008352          551 RLKQSLGGKA  560 (569)
Q Consensus       551 KLR~~l~~~~  560 (569)
                      +||+++....
T Consensus       197 ~Lr~~l~~~~  206 (208)
T PRK08295        197 KLEKYLENRE  206 (208)
T ss_pred             HHHHHHHhhc
Confidence            9999886543

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.90  E-value=2.7e-22  Score=192.66  Aligned_cols=176  Identities=16%  Similarity=0.250  Sum_probs=143.9

Q ss_pred             CCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       314 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      ++++.|+..+..|+ .|++.|+..|.++|+.+|++|.+++.+.+|++||+|+++|+++.+|++. +.+|.+|++..+++.
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            45566777666554 9999999999999999999999999999999999999999999999986 457999999999999


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  472 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  472 (569)
                      +.++++++.+.                                                        +.+. .       
T Consensus        84 ~~d~~R~~~~~--------------------------------------------------------~~~~-~-------   99 (186)
T PRK05602         84 CYDRLRRRREV--------------------------------------------------------PVED-A-------   99 (186)
T ss_pred             HHHHHHhcCCC--------------------------------------------------------Cccc-c-------
Confidence            99998865310                                                        0000 0       


Q ss_pred             hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                       .+ ..+. ...++..+...+....+..+|..||+++|+||.++|.    +++|++|||+.||+|..+|+++++||+++|
T Consensus       100 -~~-~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~L  172 (186)
T PRK05602        100 -PD-VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVDALESLLARGRRAL  172 (186)
T ss_pred             -cc-cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence             00 0011 1135555666666778999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCch
Q 008352          553 KQSLGGKAS  561 (569)
Q Consensus       553 R~~l~~~~L  561 (569)
                      |+.+...+.
T Consensus       173 r~~l~~~~~  181 (186)
T PRK05602        173 RAQLADLPG  181 (186)
T ss_pred             HHHHHhccc
Confidence            999876553

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.89  E-value=6.1e-22  Score=191.15  Aligned_cols=191  Identities=23%  Similarity=0.325  Sum_probs=144.8

Q ss_pred             CCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       314 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      |++..|+..+..|+ .|++.|+..|.+.|+++|+++.++..+++||+||+|+++|+++.+|++..+..|.||++.+|++.
T Consensus         4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~   83 (198)
T TIGR02859         4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQ   83 (198)
T ss_pred             cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHH
Confidence            45667777776665 99999999999999999999999999999999999999999999999987779999999999999


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCC-CCCc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWA-DQDT  471 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~-d~~~  471 (569)
                      +.++++...+..+.+                                               .....|++.+... +++.
T Consensus        84 ~~~~~r~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~  116 (198)
T TIGR02859        84 IITAIKTATRQKHIP-----------------------------------------------LNSYVSLNKPIYDEESDR  116 (198)
T ss_pred             HHHHHHHHHHhcccc-----------------------------------------------hhhhcCcccccccccccc
Confidence            988886532110000                                               0011223322211 1112


Q ss_pred             chhhcccCCCCCChhHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          472 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       472 ~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L-~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      ++.+.+.+....+|++.+...+....|.++|+.| ++.++.|+. +|.    +++|++|||+.||+|.++|+..++||++
T Consensus       117 ~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~  191 (198)
T TIGR02859       117 TLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SYL----DGKSYQEIACDLNRHVKSIDNALQRVKR  191 (198)
T ss_pred             hHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            2333333222346777777777778899999995 566666665 566    8999999999999999999999999999


Q ss_pred             HHHHHh
Q 008352          551 RLKQSL  556 (569)
Q Consensus       551 KLR~~l  556 (569)
                      +||+.+
T Consensus       192 ~L~~~l  197 (198)
T TIGR02859       192 KLEKYL  197 (198)
T ss_pred             HHHHhc
Confidence            999875

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

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=5.6e-22  Score=191.68  Aligned_cols=181  Identities=18%  Similarity=0.251  Sum_probs=145.9

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      .++..++..+..| ..|++.|+..|.+.|+++|+++.++..+.+|++||+|+++|+++++|++.  ..|.+|++.++++.
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            3456666666655 49999999999999999999999999999999999999999999999975  36999999999999


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  472 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  472 (569)
                      +.+++++..+....+                                                     .+.    +.  .
T Consensus        89 ~~~~~R~~~~~~~~~-----------------------------------------------------~~~----~~--~  109 (194)
T PRK12513         89 LIDHWRRHGARQAPS-----------------------------------------------------LDA----DE--Q  109 (194)
T ss_pred             HHHHHHHhccccccc-----------------------------------------------------ccc----ch--h
Confidence            999998765321100                                                     000    00  0


Q ss_pred             hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                      . ....+ ....|+..+...+....|..+|+.||+++|.||.++|+    +++|++|||+.||+|.++|++++.||+++|
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 12256666667777888999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCch
Q 008352          553 KQSLGGKAS  561 (569)
Q Consensus       553 R~~l~~~~L  561 (569)
                      |+.+...++
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=99.89  E-value=8.9e-22  Score=190.83  Aligned_cols=175  Identities=17%  Similarity=0.189  Sum_probs=139.4

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 008352          316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  394 (569)
Q Consensus       316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~  394 (569)
                      ...|+..+..| ..|++.|+..|.++|+++|.+|.++..+.+|++||+|+++|+++++||+.+| .|.+|++..++|.+.
T Consensus        17 ~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~   95 (194)
T PRK09646         17 LDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAV   95 (194)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHH
Confidence            45566655555 5999999999999999999999999999999999999999999999998765 799999999999999


Q ss_pred             HHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008352          395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  474 (569)
Q Consensus       395 ~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~  474 (569)
                      ++++++.+..+.                                                       +.....   .   
T Consensus        96 d~~r~~~~~~~~-------------------------------------------------------~~~~~~---~---  114 (194)
T PRK09646         96 DRVRSEQAASQR-------------------------------------------------------EVRYGA---R---  114 (194)
T ss_pred             HHHHhhcccccc-------------------------------------------------------cccccc---c---
Confidence            999876421000                                                       000000   0   


Q ss_pred             hcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       475 d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +.  +.....+++.+...+..+.|..+|..||+++|.||.++|.    +++|++|||+.||+|..+|+++++||+++||.
T Consensus       115 ~~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~  188 (194)
T PRK09646        115 NV--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPLGTVKTRMRDGLIRLRD  188 (194)
T ss_pred             cc--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence            00  0011123344444555678999999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhhc
Q 008352          555 SLGG  558 (569)
Q Consensus       555 ~l~~  558 (569)
                      ++..
T Consensus       189 ~l~~  192 (194)
T PRK09646        189 CLGV  192 (194)
T ss_pred             Hhcc
Confidence            8854

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.89  E-value=1e-21  Score=187.76  Aligned_cols=179  Identities=17%  Similarity=0.257  Sum_probs=140.0

Q ss_pred             HHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 008352          317 RDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (569)
Q Consensus       317 ~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~  395 (569)
                      +.|+..+..| ..|+..|+..|.+.|+.+|++|.+++.+++|++||+++++|+++.+|++..  .|.+|++..+++.+.+
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            3455555444 599999999999999999999999999999999999999999999999865  5999999999999999


Q ss_pred             HHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008352          396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE  475 (569)
Q Consensus       396 ~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d  475 (569)
                      ++++..+...                                                       ++.....++.....+
T Consensus        84 ~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~  108 (187)
T TIGR02948        84 RLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMES  108 (187)
T ss_pred             HHHhhccccc-------------------------------------------------------ccccccCcccccccc
Confidence            9876431100                                                       000000000001111


Q ss_pred             cccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          476 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       476 ~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      ...+. .+.|++.+...+....+..+|..||+++|.||.++|.    +++|++|||+.||+|.++|++.+.||+++||..
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 2256666677777778999999999999999999998    899999999999999999999999999999998


Q ss_pred             hh
Q 008352          556 LG  557 (569)
Q Consensus       556 l~  557 (569)
                      +.
T Consensus       184 l~  185 (187)
T TIGR02948       184 LR  185 (187)
T ss_pred             hh
Confidence            75

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

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.89  E-value=1.4e-21  Score=186.73  Aligned_cols=180  Identities=15%  Similarity=0.234  Sum_probs=141.8

Q ss_pred             HHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 008352          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  394 (569)
Q Consensus       316 ~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~  394 (569)
                      .+.|+..+..|+ .+++.|+..|.++|+++|+++.++..+++|++||++++||+++.+|++..  .|.+|++..+++.+.
T Consensus         5 ~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~   82 (187)
T PRK09641          5 IKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTI   82 (187)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHH
Confidence            344555555554 99999999999999999999999999999999999999999999999853  699999999999999


Q ss_pred             HHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008352          395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  474 (569)
Q Consensus       395 ~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~  474 (569)
                      ++++++.+..                                                       +++.....++.....
T Consensus        83 d~~R~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~  107 (187)
T PRK09641         83 DRLRKRKPDY-------------------------------------------------------YLDAEVAGTEGLTMY  107 (187)
T ss_pred             HHHHhcCccc-------------------------------------------------------cccccccCCcchhhh
Confidence            9988754210                                                       000000011111111


Q ss_pred             hcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       475 d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +.+.+. ...|++.+...+....|..+|+.||+++++||.++|.    ++++++|||+.||||.++|++.+.||+++||+
T Consensus       108 ~~~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~  182 (187)
T PRK09641        108 SQLAAD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSLKEISEILDLPVGTVKTRIHRGREALRK  182 (187)
T ss_pred             cccccC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            111111 2246667777777788999999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhh
Q 008352          555 SLG  557 (569)
Q Consensus       555 ~l~  557 (569)
                      .+.
T Consensus       183 ~l~  185 (187)
T PRK09641        183 QLR  185 (187)
T ss_pred             HHh
Confidence            875

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.88  E-value=2.3e-21  Score=186.72  Aligned_cols=171  Identities=23%  Similarity=0.307  Sum_probs=137.9

Q ss_pred             HHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          318 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       318 ~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~----g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      .|+..+..| ..|++.|+..|.+.|+++|.++.++    +.+++|++||+|+++|+++.+|++. +..|.+|++..+++.
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 5999999999999999999998765    3689999999999999999999864 457999999999999


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  472 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  472 (569)
                      +.++++++.+....                                                     ..+ .        
T Consensus        92 ~~d~~r~~~r~~~~-----------------------------------------------------~~~-~--------  109 (189)
T PRK09648         92 VADAHRAAGRDKAV-----------------------------------------------------PTE-E--------  109 (189)
T ss_pred             HHHHHHHhCCCccc-----------------------------------------------------ccc-c--------
Confidence            99999876521100                                                     000 0        


Q ss_pred             hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                      ..+...  ...+|++.+...+..+.|..+|..||+++|+||.++|+    +++|++|||+.||||..+|++.++||+++|
T Consensus       110 ~~~~~~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L  183 (189)
T PRK09648        110 VPERPS--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGSTPGAVRVAQHRALARL  183 (189)
T ss_pred             cccccc--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            000000  11256666677777788999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhh
Q 008352          553 KQSLG  557 (569)
Q Consensus       553 R~~l~  557 (569)
                      |+.+.
T Consensus       184 r~~l~  188 (189)
T PRK09648        184 RAEIE  188 (189)
T ss_pred             HHHhc
Confidence            99764

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

Probab=99.87  E-value=4.5e-21  Score=180.33  Aligned_cols=163  Identities=20%  Similarity=0.344  Sum_probs=134.7

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++..|++.|+..|.+.+++++.++.++..+++|++||+++.+|+++++|+...+ .|.+|++.++++.+.++++++.+..
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            455999999999999999999999988899999999999999999999997555 8999999999999999998765211


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  484 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~  484 (569)
                      ..                                                     +.+.         ..+...  ....
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 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      |++.+...+..+.+..+|..|||++|+||.++|.    +|+|++|||+.||||..+|++...||+++||+.+
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            6666666677788999999999999999999998    8999999999999999999999999999999864

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.87  E-value=6.2e-21  Score=180.26  Aligned_cols=172  Identities=19%  Similarity=0.236  Sum_probs=137.2

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      .++..|++.|+..|.++|++++++|.+++.+.+|++||++++||+++++|+  .+.+|.+|++.++++.+.+++++..+.
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            355689999999999999999999999999999999999999999999999  446899999999999999998875421


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  483 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~  483 (569)
                      ...+                                                    +++  ..+.++....+...+  ..
T Consensus        84 ~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~~--~~  107 (182)
T PRK09652         84 PPAS----------------------------------------------------DVD--AEEAEDFDLADALRD--IS  107 (182)
T ss_pred             CCcc----------------------------------------------------ccc--ccccccccccccccc--cc
Confidence            1000                                                    000  000000011111111  12


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      +|++.+...+....+..+|..||+++|+||.++|.    .++|++|||+.||+|..+|++.+.||+++||+.+.
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            46667777777888999999999999999999998    89999999999999999999999999999999875

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.87  E-value=5.7e-21  Score=183.10  Aligned_cols=176  Identities=18%  Similarity=0.270  Sum_probs=135.3

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352          315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (569)
Q Consensus       315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  393 (569)
                      ++..+...+..| ..|++.|+..|.+.|+.++++|.+++.+++|++||+++++|+++++|++.. ..|.+|++..+++.+
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             HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352          394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  473 (569)
Q Consensus       394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  473 (569)
                      .+++++..+...                                                    ....+     ......
T Consensus        88 ~d~~rk~~~~~~----------------------------------------------------~~~~~-----~~~~~~  110 (186)
T PRK13919         88 VDHVRRRAARPQ----------------------------------------------------PLEPD-----EREPEA  110 (186)
T ss_pred             HHHHHhhhcccc----------------------------------------------------ccccc-----cccccc
Confidence            999987531100                                                    00000     000000


Q ss_pred             hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .+ .+     .+..........+.|..+|..||+++|+||.++|.    +++|++|||+.||+|..+|+..++||+++||
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     11111122233457899999999999999999998    9999999999999999999999999999999


Q ss_pred             HHhhc
Q 008352          554 QSLGG  558 (569)
Q Consensus       554 ~~l~~  558 (569)
                      +.+..
T Consensus       181 ~~l~~  185 (186)
T PRK13919        181 EVLRE  185 (186)
T ss_pred             HHhcC
Confidence            98753

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=4.6e-21  Score=185.09  Aligned_cols=174  Identities=23%  Similarity=0.293  Sum_probs=137.4

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 008352          316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  394 (569)
Q Consensus       316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~  394 (569)
                      +..|+..+..| ..|++.|+..|.+.|+++++++.++..+.+|++||+|+++|+. ..|++..+ .|.||++.++++.+.
T Consensus        16 ~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~   93 (194)
T PRK12519         16 DAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAI   93 (194)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHH
Confidence            45566655544 5999999999999999999999999899999999999999976 67887654 799999999999999


Q ss_pred             HHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008352          395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  474 (569)
Q Consensus       395 ~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~  474 (569)
                      ++++++.+.....                           .+.                        +.           
T Consensus        94 d~~Rk~~~~~~~~---------------------------~~~------------------------~~-----------  111 (194)
T PRK12519         94 DRLRSRRSRQRLL---------------------------ERW------------------------QQ-----------  111 (194)
T ss_pred             HHHHhcccccchh---------------------------hhh------------------------hh-----------
Confidence            9998764210000                           000                        00           


Q ss_pred             hcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       475 d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +...+.....+++.+...+....|..+|..||+++++||.++|.    +|+|++|||+.||+|..+|++++.||+++||+
T Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~  187 (194)
T PRK12519        112 ELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGIPLGTVKARARQGLLKLRE  187 (194)
T ss_pred             hhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            00000011245555666666678999999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhh
Q 008352          555 SLG  557 (569)
Q Consensus       555 ~l~  557 (569)
                      .+.
T Consensus       188 ~l~  190 (194)
T PRK12519        188 LLQ  190 (194)
T ss_pred             HHH
Confidence            874

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=7.1e-21  Score=181.53  Aligned_cols=173  Identities=14%  Similarity=0.165  Sum_probs=137.9

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352          315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (569)
Q Consensus       315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  393 (569)
                      +...|+..+..| ..|+..|+..|.+.|+.+|.++.++..+.+|++||+|+++|+++++|++.. ..|.||++..++|.+
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            344555555444 599999999999999999999999999999999999999999999998754 369999999999999


Q ss_pred             HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352          394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  473 (569)
Q Consensus       394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  473 (569)
                      .++++++.+.. .                                                     .++      ..   
T Consensus        84 ~d~~R~~~~~~-~-----------------------------------------------------~~~------~~---  100 (179)
T PRK12514         84 IDRLRARKAVA-V-----------------------------------------------------DID------EA---  100 (179)
T ss_pred             HHHHHhcCCcc-c-----------------------------------------------------ccc------cc---
Confidence            99998754210 0                                                     000      00   


Q ss_pred             hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .+. .+. ...|++.+...+....|..+|..||+++|+||.++|.    +|+|++|||+.||+|..+|++.+.||+++||
T Consensus       101 ~~~-~~~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr  174 (179)
T PRK12514        101 HDL-ADP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPLNTMRTWLRRSLLKLR  174 (179)
T ss_pred             hhc-ccc-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence            000 001 1245555555555567899999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhh
Q 008352          554 QSLG  557 (569)
Q Consensus       554 ~~l~  557 (569)
                      +++.
T Consensus       175 ~~l~  178 (179)
T PRK12514        175 ECLS  178 (179)
T ss_pred             HHhc
Confidence            9874

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.87  E-value=1e-20  Score=181.19  Aligned_cols=181  Identities=16%  Similarity=0.210  Sum_probs=141.1

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352          315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (569)
Q Consensus       315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  393 (569)
                      ++..|+..+..| ..+++.|+..|.+.|+.+|+++.++..+.+||+||+++++|+++++|++.  ..|.+|++..+++.+
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            345666666655 48999999999999999999999999999999999999999999999975  369999999999999


Q ss_pred             HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352          394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  473 (569)
Q Consensus       394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  473 (569)
                      .++++++.+.....                                                  ..+.+.      ....
T Consensus        84 ~~~~r~~~r~~~~~--------------------------------------------------~~~~~~------~~~~  107 (190)
T TIGR02939        84 KNHLVAQGRRPPTS--------------------------------------------------DVEIED------AEHF  107 (190)
T ss_pred             HHHHHHhccCCCcc--------------------------------------------------cccccc------hhhh
Confidence            99887544211000                                                  000000      0000


Q ss_pred             hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .+........+|++.+...+....|..+|..||+++|+||.++|.    ++++++|||+.||+|..+|+..+.||+++||
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            000000011246666677777788999999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhh
Q 008352          554 QSLG  557 (569)
Q Consensus       554 ~~l~  557 (569)
                      +++.
T Consensus       184 ~~l~  187 (190)
T TIGR02939       184 IRLR  187 (190)
T ss_pred             HHhh
Confidence            9885

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.87  E-value=4.9e-21  Score=177.73  Aligned_cols=151  Identities=21%  Similarity=0.253  Sum_probs=123.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (569)
Q Consensus       327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl  406 (569)
                      ..|++.|+..|.++|+++++++ ++..+++|++|||++++|+++++|++..| .|.+|++..+++.+.++++++.+..  
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            3689999999999999999986 56679999999999999999999998766 7999999999999999998753100  


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  486 (569)
Q Consensus       407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe  486 (569)
                                            .                                 ... .+              +.|+
T Consensus        79 ----------------------~---------------------------------~~~-~~--------------~~~~   88 (154)
T PRK06759         79 ----------------------E---------------------------------KCV-CV--------------GEYE   88 (154)
T ss_pred             ----------------------c---------------------------------ccc-cc--------------CCCc
Confidence                                  0                                 000 00              0111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      +.+...+....|..+|..||+++|+||.++|+    +++|.+|||+.||+|..+|+++..||+++||+.
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            22233344567999999999999999999998    999999999999999999999999999999974

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.87  E-value=1e-20  Score=182.77  Aligned_cols=174  Identities=14%  Similarity=0.181  Sum_probs=141.1

Q ss_pred             CCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHH
Q 008352          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRG---ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWV  389 (569)
Q Consensus       314 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g---~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wI  389 (569)
                      ++++.|+..+..|+ .|++.|+..|.+.|++++.++.+++   .+.+|++||+++++|+++++|++..+ .|.||++..+
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            45677777777665 9999999999999999999998863   47899999999999999999997654 7999999999


Q ss_pred             HHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 008352          390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ  469 (569)
Q Consensus       390 RqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~  469 (569)
                      ++.+.++++++.+...+                                                    .+.+.      
T Consensus        82 rn~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------  103 (189)
T PRK06811         82 KYKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------  103 (189)
T ss_pred             HHHHHHHHHHhcccccc----------------------------------------------------ccchh------
Confidence            99999999876521000                                                    00000      


Q ss_pred             CcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          470 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       470 ~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      .      .. ....++++.+...+....|..+|..||+++|.||.++|.    +|+|++|||+.||+|..+|++.+.||+
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 011245666666777788999999999999999999998    899999999999999999999999999


Q ss_pred             HHHHHHhh
Q 008352          550 YRLKQSLG  557 (569)
Q Consensus       550 kKLR~~l~  557 (569)
                      ++||....
T Consensus       173 ~~Lr~~~~  180 (189)
T PRK06811        173 KKLQKNKL  180 (189)
T ss_pred             HHHHHccc
Confidence            99998643

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=9.7e-21  Score=188.96  Aligned_cols=173  Identities=19%  Similarity=0.245  Sum_probs=138.1

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++..|++.|+..|.+.|+++|+++.+++.+.+||+||+|+++|+++++|++.  ..|.+|++..+++.+.+++++..+..
T Consensus        27 gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~  104 (231)
T PRK11922         27 GDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLV  104 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccc
Confidence            4568999999999999999999999999999999999999999999999986  47999999999999999988765321


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  484 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~  484 (569)
                      .++.                            .                      ..+ .... ++  ...... ....+
T Consensus       105 ~~~~----------------------------~----------------------~~~-~~~~-~~--~~~~~~-~~~~~  129 (231)
T PRK11922        105 NLAE----------------------------M----------------------VMA-STIA-GG--ERTPLA-DPAED  129 (231)
T ss_pred             cchh----------------------------c----------------------ccc-cccc-cc--cccccC-cccCC
Confidence            1100                            0                      000 0000 00  000001 11235


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      |++.+...+..+.|..+|..||+++|+||.++|.    +++|++|||+.||+|.++|++++.||+++||+.+..
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            6677777788888999999999999999999988    899999999999999999999999999999998864

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=1.3e-20  Score=182.95  Aligned_cols=177  Identities=19%  Similarity=0.215  Sum_probs=143.3

Q ss_pred             CCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       314 ~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      +++..|+..+..|+ .|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.+|++..+++.
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             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  472 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  472 (569)
                      +.++++++.+.                                                      ...++. .   .   
T Consensus        90 ~~d~~Rk~~~~------------------------------------------------------~~~~~~-~---~---  108 (196)
T PRK12524         90 CTDRLRRRRRA------------------------------------------------------SVDLDD-A---P---  108 (196)
T ss_pred             HHHHHHhhcCC------------------------------------------------------CCCccc-c---c---
Confidence            99998865310                                                      000000 0   0   


Q ss_pred             hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                        +. .+. ...+++.+...+....|..+|+.||+++|+||.|+|.    ++++++|||+.||||..+|++++.||+++|
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 1235556666677788999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCc
Q 008352          553 KQSLGGKA  560 (569)
Q Consensus       553 R~~l~~~~  560 (569)
                      |.++...+
T Consensus       181 r~~l~~~~  188 (196)
T PRK12524        181 AALLAGQR  188 (196)
T ss_pred             HHHHHhcc
Confidence            99987543

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.3e-20  Score=180.75  Aligned_cols=172  Identities=13%  Similarity=0.161  Sum_probs=137.2

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352          315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (569)
Q Consensus       315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  393 (569)
                      +...|+..+.+| ..|++.|+..|.+.|+.++.++.++..+.+|++||+|+.+|+.+++|++.. ..|.+|++..+++.+
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            345566666655 499999999999999999999999999999999999999999999998644 379999999999999


Q ss_pred             HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352          394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  473 (569)
Q Consensus       394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  473 (569)
                      .+++++..+...+                                                       +.     ..   
T Consensus        88 ~d~~r~~~~~~~~-------------------------------------------------------~~-----~~---  104 (182)
T PRK12537         88 LNVLRDTRREVVL-------------------------------------------------------DD-----DA---  104 (182)
T ss_pred             HHHHHhccccCcc-------------------------------------------------------cc-----ch---
Confidence            9999876421000                                                       00     00   


Q ss_pred             hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .+...+  ...+++.....+....|..+|+.||+++|+||.++|.    +++|++|||+.||||.++|+..+.||+++||
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  1123333444455667999999999999999999998    8999999999999999999999999999999


Q ss_pred             HHh
Q 008352          554 QSL  556 (569)
Q Consensus       554 ~~l  556 (569)
                      +++
T Consensus       179 ~~l  181 (182)
T PRK12537        179 ECM  181 (182)
T ss_pred             HHh
Confidence            876

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.2e-20  Score=189.26  Aligned_cols=174  Identities=15%  Similarity=0.223  Sum_probs=140.4

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352          315 SCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (569)
Q Consensus       315 ~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  393 (569)
                      ++..|+..+..| ..|++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+++|++..+ .|.+|++..+++.+
T Consensus        49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~  127 (233)
T PRK12538         49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC  127 (233)
T ss_pred             cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence            455666666555 4999999999999999999999999999999999999999999999987544 79999999999999


Q ss_pred             HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352          394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  473 (569)
Q Consensus       394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  473 (569)
                      .++++++.+. .                                                       ++. . .      
T Consensus       128 id~~Rk~~~~-~-------------------------------------------------------~~~-~-~------  143 (233)
T PRK12538        128 IDLRRKPRTE-N-------------------------------------------------------VDA-V-P------  143 (233)
T ss_pred             HHHHHhhccc-c-------------------------------------------------------ccc-c-c------
Confidence            9988764210 0                                                       000 0 0      


Q ss_pred             hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                       +. .+ ....+++.+...+....|..+|..||+++|+||.|+|.    +|+|++|||+.||+|.++|+++++||+++||
T Consensus       144 -~~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr  216 (233)
T PRK12538        144 -EV-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVAAVESLLKRGRQQLR  216 (233)
T ss_pred             -cc-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence             00 00 01134445555666778999999999999999999998    9999999999999999999999999999999


Q ss_pred             HHhhcCc
Q 008352          554 QSLGGKA  560 (569)
Q Consensus       554 ~~l~~~~  560 (569)
                      +.+...+
T Consensus       217 ~~l~~~~  223 (233)
T PRK12538        217 DLLRRHE  223 (233)
T ss_pred             HHHHHhh
Confidence            9887543

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.86  E-value=2.4e-20  Score=179.99  Aligned_cols=180  Identities=15%  Similarity=0.203  Sum_probs=140.6

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 008352          316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  394 (569)
Q Consensus       316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~  394 (569)
                      ++.|+..++.| ..+++.|+..|.+.|+.+++++.++..+.+|++||+++++|+++.+|++..  .|.+|++..+++.+.
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            34555555555 599999999999999999999999989999999999999999999999874  499999999999999


Q ss_pred             HHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008352          395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  474 (569)
Q Consensus       395 ~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~  474 (569)
                      ++++++.+....                                                  ....++.....++.    
T Consensus        85 d~~rk~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~----  110 (193)
T PRK11923         85 NHLVSRGRRPPD--------------------------------------------------SDVSSEDAEFYDGD----  110 (193)
T ss_pred             HHHHHhcCCCcc--------------------------------------------------ccccccchhhhccc----
Confidence            998765421000                                                  00000000000000    


Q ss_pred             hcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       475 d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ..+.  ....|++.+...+..+.+..+|..||+++|.||.++|.    +|+|++|||+.||+|..+|++...||+++||.
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  12256666677777889999999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhh
Q 008352          555 SLG  557 (569)
Q Consensus       555 ~l~  557 (569)
                      ++.
T Consensus       185 ~l~  187 (193)
T PRK11923        185 ALQ  187 (193)
T ss_pred             HHH
Confidence            885

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=2.1e-20  Score=179.53  Aligned_cols=173  Identities=15%  Similarity=0.157  Sum_probs=136.6

Q ss_pred             HHHHHHH-hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 008352          317 RDLKSEL-HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (569)
Q Consensus       317 ~~L~~~l-~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~  395 (569)
                      ..+...+ .++..+++.|+..|.++|+++|+++.++..+.+|++||+|+++|+++++|++.++ .|.+|++..+++.+.+
T Consensus        13 ~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d   91 (187)
T PRK12534         13 GRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAID   91 (187)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHH
Confidence            3344444 4455999999999999999999999999999999999999999999999998654 6889999999999999


Q ss_pred             HHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008352          396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE  475 (569)
Q Consensus       396 ~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d  475 (569)
                      +++++.+...                                                    ..+.+.         ..+
T Consensus        92 ~~R~~~~~~~----------------------------------------------------~~~~~~---------~~~  110 (187)
T PRK12534         92 HLRANAPQRR----------------------------------------------------NVALDD---------AGE  110 (187)
T ss_pred             HHHhcccccc----------------------------------------------------cccccc---------hhh
Confidence            9987541100                                                    000000         000


Q ss_pred             cccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          476 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       476 ~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      .. +. ..++++.....+....|..+|..||++++.|+.++|.    +++|++|||+.||+|..+|+++++||+++||+.
T Consensus       111 ~~-~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  184 (187)
T PRK12534        111 LR-AA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC  184 (187)
T ss_pred             hc-cc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence            00 00 1123444455566778999999999999999999998    899999999999999999999999999999998


Q ss_pred             hh
Q 008352          556 LG  557 (569)
Q Consensus       556 l~  557 (569)
                      +.
T Consensus       185 l~  186 (187)
T PRK12534        185 LE  186 (187)
T ss_pred             Hc
Confidence            74

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.86  E-value=1e-20  Score=182.35  Aligned_cols=173  Identities=20%  Similarity=0.290  Sum_probs=136.5

Q ss_pred             CCCHHHHHHHHhc----cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHH
Q 008352          313 GLSCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW  388 (569)
Q Consensus       313 g~~~~~L~~~l~~----G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~w  388 (569)
                      .++++.|+..++.    +..|++.|+..|.+.|+++|.+|.++..+.+|++||+++.+|+++++|++.  ..|.+|++.+
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            4567777777763    569999999999999999999999999999999999999999999999864  4799999999


Q ss_pred             HHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCC
Q 008352          389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWAD  468 (569)
Q Consensus       389 IRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d  468 (569)
                      +++.+.+++++..+....                          .                           .+...   
T Consensus        85 a~n~~~d~~R~~~~~~~~--------------------------~---------------------------~~~~~---  108 (188)
T PRK09640         85 TYNECITQYRKERRKRRL--------------------------M---------------------------DALSL---  108 (188)
T ss_pred             HHHHHHHHHHHhcccccC--------------------------c---------------------------chhhh---
Confidence            999999999864321000                          0                           00000   


Q ss_pred             CCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          469 QDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       469 ~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                            +...++.    ++.....+....|..+|+.||+++|+||.++|.    +++|++|||+.||||..+|+..+.||
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    001112234457899999999999999999998    89999999999999999999999999


Q ss_pred             HHHHHHHhh
Q 008352          549 LYRLKQSLG  557 (569)
Q Consensus       549 LkKLR~~l~  557 (569)
                      +++||+.+.
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=5.9e-20  Score=175.61  Aligned_cols=180  Identities=19%  Similarity=0.207  Sum_probs=138.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhc
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~----~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~  400 (569)
                      ++..|++.|+..|.+.|+.+|++|.+    +..+.+|++||+++.+|+++.+|++..+.+|.+|++..+++.+.+++++.
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            45699999999999999999999753    56789999999999999999999986666899999999999999998764


Q ss_pred             ccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCC-CCCCcchhhcccC
Q 008352          401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVW-ADQDTTFQEITAD  479 (569)
Q Consensus       401 ~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~-~d~~~~l~d~i~D  479 (569)
                      .+                 +.+       |.+                       ....+++.... ++....+.+.+.+
T Consensus        84 ~~-----------------~~~-------r~~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~~  116 (189)
T TIGR02984        84 LG-----------------AQK-------RDI-----------------------RREQSLDAGGRLDESSVRLAAQLAA  116 (189)
T ss_pred             HH-----------------HHh-------hhc-----------------------ccccCCCcccccCCcchhHHHHccC
Confidence            20                 000       000                       00112221110 1111123333333


Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          480 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       480 ~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                       ...+|++.+...+....|..+|..||+++|+||.++|+    +|++++|||+.||||.++|++.+.||+++||+.+
T Consensus       117 -~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l  188 (189)
T TIGR02984       117 -DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL  188 (189)
T ss_pred             -CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence             23356777777777788999999999999999999998    8999999999999999999999999999999876

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=5.4e-20  Score=177.32  Aligned_cols=177  Identities=19%  Similarity=0.262  Sum_probs=143.6

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      ++++.|+..+..| ..|++.|+..|.+.|+.++.++.++..+.+|++||+|+.+|+++++|++.  ..|.+|++..+++.
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            4566777766655 48999999999999999999999999999999999999999999999974  47999999999999


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  472 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  472 (569)
                      +.+++++..+..                                                        +..    +.   
T Consensus        85 ~~d~~r~~~~~~--------------------------------------------------------~~~----~~---  101 (189)
T PRK12515         85 ALSALRRRKHEE--------------------------------------------------------IDD----EA---  101 (189)
T ss_pred             HHHHHHccCCCC--------------------------------------------------------Ccc----cc---
Confidence            999987643100                                                        000    00   


Q ss_pred             hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                      . ....+ ...+++......+....+..+|+.||+++|+||.++|.    ++++++|||+.||+|..+|+.++.||+++|
T Consensus       102 ~-~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~l~Rar~~L  175 (189)
T PRK12515        102 A-AAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIPESTVKTRMFYARKKL  175 (189)
T ss_pred             c-cccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            0 00111 12245555566666778999999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhhcCch
Q 008352          553 KQSLGGKAS  561 (569)
Q Consensus       553 R~~l~~~~L  561 (569)
                      |+.+...+.
T Consensus       176 r~~l~~~~~  184 (189)
T PRK12515        176 AELLKAAGV  184 (189)
T ss_pred             HHHHHHhcc
Confidence            999876543

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=4.9e-20  Score=180.70  Aligned_cols=171  Identities=12%  Similarity=0.165  Sum_probs=133.1

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      .++..+++.|+..|.+.|+.++.++.++..+.+|++||+|+.+|+++..|++.++ .|.+|++.++++.+.++++++.+.
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            3556999999999999999999999999889999999999999999999998665 599999999999999999876421


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  483 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~  483 (569)
                      ...                         .                            .+     ++...+.+.+.+. ..
T Consensus       113 ~~~-------------------------~----------------------------~~-----~~~~~~~~~~~~~-~~  133 (206)
T PRK12526        113 KEQ-------------------------N----------------------------LG-----DDIWPIEQALAES-QS  133 (206)
T ss_pred             ccc-------------------------c----------------------------cc-----cccchhhhhcccc-cC
Confidence            100                         0                            00     0000000111111 11


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      .+. ..........|..+|..||+++|+||.++|+    +++|++|||+.||+|..+|+.+++||+++||+.+...
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 2233334457899999999999999999998    9999999999999999999999999999999988643

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=2.3e-20  Score=179.28  Aligned_cols=175  Identities=17%  Similarity=0.207  Sum_probs=138.9

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      .++..|++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+++++|++..+..|.||++..++|.+.++++++.+.
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            34569999999999999999999999999999999999999999999999875445799999999999999999876421


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  483 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~  483 (569)
                      ..                  ..                                    +. .   ..    +.... ..+
T Consensus        85 ~~------------------~~------------------------------------~~-~---~~----~~~~~-~~~  101 (185)
T PRK12542         85 ET------------------FL------------------------------------EE-Y---ER----ESIEA-VDE  101 (185)
T ss_pred             hh------------------hh------------------------------------hh-c---cc----cchhh-hhc
Confidence            00                  00                                    00 0   00    00000 001


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhh
Q 008352          484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG  563 (569)
Q Consensus       484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~  563 (569)
                      .+++.....+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|+..+.||+++||+.+.......
T Consensus       102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~  177 (185)
T PRK12542        102 NIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDE  177 (185)
T ss_pred             cHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            23333334444567999999999999999999998    89999999999999999999999999999999998877766


Q ss_pred             hh
Q 008352          564 YA  565 (569)
Q Consensus       564 yl  565 (569)
                      |+
T Consensus       178 ~~  179 (185)
T PRK12542        178 FK  179 (185)
T ss_pred             HH
Confidence            64

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=5.4e-20  Score=173.36  Aligned_cols=168  Identities=16%  Similarity=0.176  Sum_probs=138.7

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      .++..|++.|+..|.+.|+++|+++.++..+.+|++||++++||++++.|+  .+..|.+|++..+++.+.+++++..+.
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            345599999999999999999999999999999999999999999999998  345899999999999999998865421


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  483 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~  483 (569)
                      ...                                                     ..+ ..        .+...+....
T Consensus        87 ~~~-----------------------------------------------------~~~-~~--------~~~~~~~~~~  104 (179)
T PRK11924         87 KAV-----------------------------------------------------LSD-DA--------LEPEFAETAE  104 (179)
T ss_pred             ccc-----------------------------------------------------Ccc-cc--------cccccCCccC
Confidence            100                                                     000 00        0000000223


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      +|++.+...+....+..+|..||++++.||.++|.    ++++.+|||+.||+|+.+|++.+.||+++||+.+..+
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            67778888888899999999999999999999998    8999999999999999999999999999999988654

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.84  E-value=1e-19  Score=176.54  Aligned_cols=171  Identities=16%  Similarity=0.172  Sum_probs=138.4

Q ss_pred             CHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (569)
Q Consensus       315 ~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  393 (569)
                      ++..++..+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|++..  .|.+|++..+++.+
T Consensus        13 ~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~   90 (192)
T PRK09643         13 SDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNAC   90 (192)
T ss_pred             CHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHH
Confidence            4566666665554 99999999999999999999999999999999999999999999999753  59999999999999


Q ss_pred             HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352          394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  473 (569)
Q Consensus       394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  473 (569)
                      .+++++..+...                                                     .+++.    ..    
T Consensus        91 ~d~~Rk~~~~~~-----------------------------------------------------~~~~~----~~----  109 (192)
T PRK09643         91 LDRLRRAKARPT-----------------------------------------------------VPLDD----VY----  109 (192)
T ss_pred             HHHHHccccCCC-----------------------------------------------------CCccc----cc----
Confidence            999987542100                                                     00000    00    


Q ss_pred             hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                       +. .    ..+++.+...+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|+..+.||+++||
T Consensus       110 -~~-~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr  179 (192)
T PRK09643        110 -PV-A----QLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAEGTVKSRCARGRARLA  179 (192)
T ss_pred             -cc-c----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence             00 0    012233444555678999999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhhc
Q 008352          554 QSLGG  558 (569)
Q Consensus       554 ~~l~~  558 (569)
                      +.+..
T Consensus       180 ~~l~~  184 (192)
T PRK09643        180 ELLGY  184 (192)
T ss_pred             HHHHH
Confidence            98864

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

Probab=99.84  E-value=9.2e-20  Score=172.33  Aligned_cols=167  Identities=17%  Similarity=0.211  Sum_probs=132.3

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      |+++.++..+..| ..|++.++..|.+.|++++.++.++..+++|++||+++.+|+++++|++.  ..|.+|++..+++.
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            3455666666555 49999999999999999999999999999999999999999999999975  36999999999999


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  472 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  472 (569)
                      +.+++++..+..                                                       .++.....+    
T Consensus        79 ~~d~~R~~~~~~-------------------------------------------------------~~~~~~~~~----   99 (169)
T TIGR02954        79 CIDLLKKKKKVI-------------------------------------------------------PFDPNTSIE----   99 (169)
T ss_pred             HHHHHHhcCCcC-------------------------------------------------------ccccccccc----
Confidence            999988754210                                                       000000000    


Q ss_pred             hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                            +.   .++  ... +....+..+|..||+++|+||.++|.    +|+|.+|||+.||||..+|+....||+++|
T Consensus       100 ------~~---~~~--~~~-~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L  163 (169)
T TIGR02954       100 ------KG---ECE--THA-DSRLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVKTYLHRALKKL  163 (169)
T ss_pred             ------cc---hhh--hch-HHHHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                  00   000  001 11236889999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhh
Q 008352          553 KQSLG  557 (569)
Q Consensus       553 R~~l~  557 (569)
                      |+.+.
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.

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.84  E-value=6.8e-20  Score=173.93  Aligned_cols=172  Identities=13%  Similarity=0.189  Sum_probs=134.2

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          314 LSCRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       314 ~~~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      |++..+...+..| ..|++.|+..|.+.|+.+|+++.++..+.+|++||+|+++|++++.|++.  .+|.+|++..+++.
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            3455666655555 49999999999999999999999999999999999999999999999874  47999999999999


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  472 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  472 (569)
                      +.+++++..+....                           .+.+                       .+.         
T Consensus        81 ~~d~~r~~~~~~~~---------------------------~~~~-----------------------~~~---------  101 (176)
T PRK09638         81 YKDHLRKQKREKLR---------------------------LQRA-----------------------KEE---------  101 (176)
T ss_pred             HHHHHHHhccccch---------------------------hhhc-----------------------ccc---------
Confidence            99999875421100                           0000                       000         


Q ss_pred             hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                          ..+  .... +..........|..+|..||+++|+||.++|.    +|++++|||+.||+|..+|+..+.||+++|
T Consensus       102 ----~~~--~~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~~V~~~l~ra~~~l  170 (176)
T PRK09638        102 ----TLR--KEKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNIPEGTVKSRVHHGIKQL  170 (176)
T ss_pred             ----cCC--ccch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence                000  0000 11122234456889999999999999999998    899999999999999999999999999999


Q ss_pred             HHHhh
Q 008352          553 KQSLG  557 (569)
Q Consensus       553 R~~l~  557 (569)
                      |+.+.
T Consensus       171 ~~~l~  175 (176)
T PRK09638        171 RKEWG  175 (176)
T ss_pred             HHHhc
Confidence            99763

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

Probab=99.84  E-value=1.6e-19  Score=163.53  Aligned_cols=157  Identities=25%  Similarity=0.386  Sum_probs=131.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (569)
Q Consensus       329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~  408 (569)
                      |++.++..|.++|.++++++.+++.+.+|++|||++++|++++.|++.  .+|.+|+.+++++.+.++++++.+   .+.
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~~   76 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LRR   76 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CCc
Confidence            789999999999999999999999999999999999999999999998  689999999999999999988763   110


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352          409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  488 (569)
Q Consensus       409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~  488 (569)
                      ..                                                   .      ..    ... ......++..
T Consensus        77 ~~---------------------------------------------------~------~~----~~~-~~~~~~~~~~   94 (158)
T TIGR02937        77 EL---------------------------------------------------D------LL----EEL-LDSDPSPEEE   94 (158)
T ss_pred             ch---------------------------------------------------h------hh----hhc-ccccCCHHHH
Confidence            00                                                   0      00    000 0111245566


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      .........|..+|+.||++++.||.++|+    .|+|..|||+.+|+|+.+|+++..+++++||+.+
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            666777788999999999999999999987    7999999999999999999999999999999754

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.1e-19  Score=173.83  Aligned_cols=165  Identities=16%  Similarity=0.182  Sum_probs=133.1

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++..|++.|+..|.+.|+.++++|.++..+.+|++||+++.+|+++.+|++..  .|.+|++..+++.+.+++++..+..
T Consensus         4 ~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~   81 (179)
T PRK12543          4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRF   81 (179)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccc
Confidence            44589999999999999999999999999999999999999999999999864  5999999999999988876543100


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  484 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~  484 (569)
                      +                                                      .++... +     ..+   ......
T Consensus        82 ~------------------------------------------------------~~~~~~-~-----~~~---~~~~~~   98 (179)
T PRK12543         82 R------------------------------------------------------IFEKAE-E-----QRK---PVSIDF   98 (179)
T ss_pred             c------------------------------------------------------cccccc-c-----ccc---cccccC
Confidence            0                                                      000000 0     000   001113


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      |+. +...+....|..+|..||+++|+||.++|.    +++|++|||+.||||..+|+..+.||+++||+.+...
T Consensus        99 ~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~  168 (179)
T PRK12543         99 SED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE  168 (179)
T ss_pred             hHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            444 556667788999999999999999999998    9999999999999999999999999999999988754

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

Probab=99.84  E-value=8.1e-20  Score=169.05  Aligned_cols=160  Identities=18%  Similarity=0.204  Sum_probs=129.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (569)
Q Consensus       329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~  408 (569)
                      |+++|+..|.+.|+++++++.++..+.+|++||+++++|+++.+|++.  .+|.+|++.++++.+.+++++..+.-.   
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~---   76 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEK---   76 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhH---
Confidence            789999999999999999999998999999999999999999999874  479999999999999999887542100   


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352          409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  488 (569)
Q Consensus       409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~  488 (569)
                                     .         ...+                        .    ++..       .......+++.
T Consensus        77 ---------------~---------~~~~------------------------~----~~~~-------~~~~~~~~~~~   97 (161)
T TIGR02985        77 ---------------Y---------QEEI------------------------L----EIEV-------DELSENDPEEE   97 (161)
T ss_pred             ---------------H---------HHHH------------------------H----hhcc-------cccCCCCcHHH
Confidence                           0         0000                        0    0000       00011245566


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      +...+....|..++..||+++++||.++|.    +++|.+|||+.||+|+++|++++.+|+++||+.+
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            666777788999999999999999999998    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.

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.1e-19  Score=176.21  Aligned_cols=176  Identities=12%  Similarity=0.148  Sum_probs=134.0

Q ss_pred             HHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHH
Q 008352          319 LKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  397 (569)
Q Consensus       319 L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~I  397 (569)
                      ++..+..| ..+++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++..+ .|.+|++..++|.+.+++
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            45555544 5999999999999999999999999889999999999999999999997544 799999999999999999


Q ss_pred             HhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcc
Q 008352          398 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT  477 (569)
Q Consensus       398 r~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i  477 (569)
                      ++..+....                         .                           ..+... .+..  ....+
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 008352          478 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       478 ~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      .+  ...++..    ...+.+..+|..||+++|+||.++|.    +++|++|||+.||||.++|+.+++||+++||..+.
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 008352          558 GKA  560 (569)
Q Consensus       558 ~~~  560 (569)
                      ...
T Consensus       191 ~~~  193 (194)
T PRK12531        191 AES  193 (194)
T ss_pred             hcc
Confidence            654

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.83  E-value=2.1e-19  Score=170.28  Aligned_cols=165  Identities=14%  Similarity=0.133  Sum_probs=131.4

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      .+..+++.|+..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+..
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            35689999999999999999999999988999999999999999999997532 47999999999999999998654210


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  484 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~  484 (569)
                      .                                                     ...+      +..   +. ++.   .
T Consensus        85 ~-----------------------------------------------------~~~~------~~~---~~-~~~---~   98 (173)
T PRK09645         85 V-----------------------------------------------------EGGD------DVL---GV-PEQ---S   98 (173)
T ss_pred             c-----------------------------------------------------cccc------ccc---cC-CCC---C
Confidence            0                                                     0000      000   00 000   1


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      +++.+...+....|..+|+.||+++|+||.|+|.    +++|++|||+.||+|..+|+.+++||+++||+.+...+
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            2222333344557899999999999999999998    99999999999999999999999999999999987554

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=1.7e-19  Score=172.96  Aligned_cols=169  Identities=15%  Similarity=0.128  Sum_probs=130.1

Q ss_pred             HHHHHH-hccHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHH
Q 008352          318 DLKSEL-HSGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK  395 (569)
Q Consensus       318 ~L~~~l-~~G~~Are~LI~~nlrLV~sIArry~~-~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~  395 (569)
                      .++..+ .++..|++.|+..|.+.|+.++.++.+ ...+.+|++||+++.||+.++.|++.  ..|.+|++..++|.+.+
T Consensus        10 ~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d   87 (181)
T PRK12536         10 ALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMD   87 (181)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHH
Confidence            344444 455699999999999999999988764 57899999999999999999999975  46999999999999999


Q ss_pred             HHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhh
Q 008352          396 AIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQE  475 (569)
Q Consensus       396 ~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d  475 (569)
                      +++++.+....                                                   ..+++    +     ..+
T Consensus        88 ~~Rk~~~~~~~---------------------------------------------------~~~~~----~-----~~~  107 (181)
T PRK12536         88 FLRSRARREAL---------------------------------------------------HDPLD----D-----ESE  107 (181)
T ss_pred             HHHHHhccccc---------------------------------------------------cCCcc----c-----hhh
Confidence            99875421000                                                   00000    0     000


Q ss_pred             cccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          476 ITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       476 ~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      ...+.   .++.    .+....+..+|..||+++|.||.++|.    +++|++|||+.||||+.+|+..++||+++||+.
T Consensus       108 ~~~~~---~~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~  176 (181)
T PRK12536        108 LFATS---DDEA----AEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK  176 (181)
T ss_pred             hcCCC---Ccch----HHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            00011   1111    123446899999999999999999998    999999999999999999999999999999998


Q ss_pred             hhcC
Q 008352          556 LGGK  559 (569)
Q Consensus       556 l~~~  559 (569)
                      +...
T Consensus       177 l~~~  180 (181)
T PRK12536        177 IRGE  180 (181)
T ss_pred             hcCC
Confidence            7643

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=3.1e-19  Score=169.49  Aligned_cols=167  Identities=16%  Similarity=0.193  Sum_probs=131.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (569)
Q Consensus       328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP  407 (569)
                      ..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++..  +|.+|++..++|.+.++++++.+....+
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  7999999999999999998765311000


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  487 (569)
Q Consensus       408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee  487 (569)
                      ...                                                  .+.    +   ...+.........++.
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 008352          488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                       ....+..+.|..+|..||+++++||.++|.    ++++++|||+.||+|..+|+..+.||+++||+.+..
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             445556778999999999999999999998    999999999999999999999999999999998753

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

Probab=99.83  E-value=3.4e-19  Score=179.96  Aligned_cols=180  Identities=16%  Similarity=0.197  Sum_probs=141.3

Q ss_pred             CCCHHHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhhcCCCCCCchhhH
Q 008352          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFASY  384 (569)
Q Consensus       313 g~~~~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLir-------AiekFDp~kG~rFSTY  384 (569)
                      +.++..|+..+++|+ .|++.|+..|.+.|+.++.++.++..+++|++||.|+.+|+       .+.+|++.  ..|.||
T Consensus        23 ~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tW  100 (244)
T TIGR03001        23 HAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSW  100 (244)
T ss_pred             cccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhH
Confidence            346777888877766 99999999999999999999999999999999999999994       78889864  369999


Q ss_pred             HHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCC
Q 008352          385 AYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQP  464 (569)
Q Consensus       385 A~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~  464 (569)
                      ++.+++|.+.++++++.+...+                                                       +  
T Consensus       101 L~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~--  123 (244)
T TIGR03001       101 VRIVATRIALELQAQERRHSPV-------------------------------------------------------E--  123 (244)
T ss_pred             HHHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c--
Confidence            9999999999999865421000                                                       0  


Q ss_pred             CCCCCCcchhhcccCCCCCChhHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHH
Q 008352          465 VWADQDTTFQEITADTGVEIPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKER  540 (569)
Q Consensus       465 v~~d~~~~l~d~i~D~~~~~pee~l~~----~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrer  540 (569)
                        ++.  ...+. .+. ...|++.+..    .+..+.|..+|+.||+++|+||.|+|.    +++|++|||++||||.++
T Consensus       124 --~~~--~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~----eg~S~~EIA~~Lgis~~T  193 (244)
T TIGR03001       124 --EPT--ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV----DGLSMDRIGAMYQVHRST  193 (244)
T ss_pred             --ccc--ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHH
Confidence              000  00000 011 1134433332    235677999999999999999999998    999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhcCch
Q 008352          541 VRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       541 VRqie~RALkKLR~~l~~~~L  561 (569)
                      |+..+.||+++||+.+.+...
T Consensus       194 Vk~rl~RAr~~Lr~~l~~~~~  214 (244)
T TIGR03001       194 VSRWVAQARERLLERTRRRLA  214 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999876543

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=99.83  E-value=2.3e-19  Score=173.17  Aligned_cols=182  Identities=16%  Similarity=0.158  Sum_probs=137.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (569)
Q Consensus       329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~  408 (569)
                      +++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+++|++.  .+|.+|++..++|.+.++++++.+......
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            689999999999999999999999999999999999999999999865  369999999999999999987653211100


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352          409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  488 (569)
Q Consensus       409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~  488 (569)
                      ....                  .....++                       ++... . .+ ......++. ..+|++.
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 2356777


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      +...+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|++.+.||+++||+++...+.
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

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.83  E-value=3.4e-19  Score=170.68  Aligned_cols=164  Identities=16%  Similarity=0.180  Sum_probs=134.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (569)
Q Consensus       326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR  405 (569)
                      +..|++.|+..|.+.|+++|.++.++..+.+|++||+++.+|+++++|++.  ..|.+|++..+++.+.+++++..+-..
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            458999999999999999999999999999999999999999999999874  369999999999999999887431100


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352          406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  485 (569)
Q Consensus       406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p  485 (569)
                      .                                                     ..+.        ......  ....+|
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 008352          486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      ++.+...+....|..+|..||+++|+||.++|+    +|+|++|||+.||||.++|++++.||+++||+.+..
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            666666777788999999999999999999998    899999999999999999999999999999998754

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

Probab=99.83  E-value=2.1e-19  Score=167.43  Aligned_cols=158  Identities=18%  Similarity=0.218  Sum_probs=125.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (569)
Q Consensus       329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~  408 (569)
                      |++.++..|.+.|+.+|+++.++..+.||++||+++.+|+++++|++..  .|.+|++..+++.+.++++++.+.-.. .
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~   78 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F   78 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence            7899999999999999999999999999999999999999999999764  599999999999999999886521100 0


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352          409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  488 (569)
Q Consensus       409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~  488 (569)
                                               .++.                                    .+.+.+..  ++.+.
T Consensus        79 -------------------------~~~~------------------------------------~~~~~~~~--~~~~~   95 (159)
T TIGR02989        79 -------------------------DDEL------------------------------------LEALAAEA--EATEA   95 (159)
T ss_pred             -------------------------CHHH------------------------------------HHHHHhhc--ccchH
Confidence                                     0000                                    00000000  11112


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      ....+....|..+++.||++++.||.++|.    +|++.+|||+.||||..+|+...+||+++||+++
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            223334567899999999999999999998    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).

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=4.1e-19  Score=170.66  Aligned_cols=170  Identities=16%  Similarity=0.176  Sum_probs=130.8

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHH----hhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 008352          316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQ----YQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (569)
Q Consensus       316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArr----y~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR  390 (569)
                      ...|+..+..| ..|++.|+..|.+.|+.+|++    +.++..+.+|++||+++.+|++++.|++..  .|.+|++..++
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            34455555544 599999999999999999874    457788999999999999999999999753  59999999999


Q ss_pred             HHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 008352          391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD  470 (569)
Q Consensus       391 qaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~  470 (569)
                      +.+.+++++..+..                          .                          ....+      +.
T Consensus        86 n~~~d~~R~~~~~~--------------------------~--------------------------~~~~~------~~  107 (184)
T PRK12539         86 YKLIDHLRRTRASL--------------------------A--------------------------DVPID------DA  107 (184)
T ss_pred             HHHHHHHHHHhccc--------------------------c--------------------------ccChh------hh
Confidence            99999998753100                          0                          00000      00


Q ss_pred             cchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          471 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       471 ~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      .   ...       +.+.....+....|..+|..||+++|+||.++|.    +|++++|||+.||+|..+|+.++.||++
T Consensus       108 ~---~~~-------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~  173 (184)
T PRK12539        108 D---ELV-------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSESAVKVSVHRGLK  173 (184)
T ss_pred             c---ccc-------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            0   000       0011122234457899999999999999999998    8999999999999999999999999999


Q ss_pred             HHHHHhhcC
Q 008352          551 RLKQSLGGK  559 (569)
Q Consensus       551 KLR~~l~~~  559 (569)
                      +||+++...
T Consensus       174 ~Lr~~l~~~  182 (184)
T PRK12539        174 ALAALIGRE  182 (184)
T ss_pred             HHHHHHhhc
Confidence            999988643

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

Probab=99.82  E-value=5.4e-19  Score=168.76  Aligned_cols=171  Identities=19%  Similarity=0.265  Sum_probs=125.6

Q ss_pred             HHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhhcCCCCCCchhhHHHHHH
Q 008352          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFASYAYWWV  389 (569)
Q Consensus       317 ~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~-----~~EDLIQEG~IGLir-AiekFDp~kG~rFSTYA~~wI  389 (569)
                      ..|+..+..|+ .|++.|+..|.+.|+.+|++|.++..     +.+|++||+|+.+|+ ...+|++.  ..|.+|++.++
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             HHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCC
Q 008352          390 RQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ  469 (569)
Q Consensus       390 RqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~  469 (569)
                      +|.+.++++++.+..+.                      .                           .  ..+...    
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            99999998764310000                      0                           0  000000    


Q ss_pred             CcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          470 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       470 ~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                          .+..++.   .++.. ......+.+...|+.||+++|+||.|+|.    +|+|++|||+.||||..+|+.++.||+
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 008352          550 YRLKQSL  556 (569)
Q Consensus       550 kKLR~~l  556 (569)
                      ++||+.+
T Consensus       176 ~~Lr~~l  182 (183)
T TIGR02999       176 AWLADEL  182 (183)
T ss_pred             HHHHHHh
Confidence            9999876

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

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.81  E-value=7e-19  Score=169.65  Aligned_cols=170  Identities=16%  Similarity=0.105  Sum_probs=129.1

Q ss_pred             HHHHHHhc-cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHH
Q 008352          318 DLKSELHS-GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  396 (569)
Q Consensus       318 ~L~~~l~~-G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~  396 (569)
                      .|+..+.. +..|++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+.+++|++.  ..|.+|++..++|.+.++
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            34444444 459999999999999999995 67888899999999999999999999864  369999999999999999


Q ss_pred             HHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhc
Q 008352          397 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI  476 (569)
Q Consensus       397 Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~  476 (569)
                      +++..+..+.                                                     +.+.     .    .+.
T Consensus        90 ~Rk~~~~~~~-----------------------------------------------------~~~~-----~----~~~  107 (185)
T PRK09649         90 IRHVRSRPRT-----------------------------------------------------TRGA-----R----PEH  107 (185)
T ss_pred             HHHhcccccc-----------------------------------------------------cccc-----c----hhh
Confidence            9875311000                                                     0000     0    000


Q ss_pred             ccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          477 TADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       477 i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      ..+     ++......+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|+..+.||+++||+.+
T Consensus       108 ~~~-----~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~  178 (185)
T PRK09649        108 LID-----GDRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDALLADA  178 (185)
T ss_pred             ccC-----hhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            000     0000111122345788999999999999999998    9999999999999999999999999999999966


Q ss_pred             hcCch
Q 008352          557 GGKAS  561 (569)
Q Consensus       557 ~~~~L  561 (569)
                      ....+
T Consensus       179 ~~~~~  183 (185)
T PRK09649        179 EPDDL  183 (185)
T ss_pred             Ccccc
Confidence            55443

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.6e-18  Score=172.07  Aligned_cols=171  Identities=18%  Similarity=0.169  Sum_probs=136.5

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ....+++.|+..|.+.++.+++++.++..+.+|++||+|+.+|+.+++|++.   .|.+|++.+++|.+.++++++.+..
T Consensus        15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~   91 (216)
T PRK12533         15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAH   91 (216)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccc
Confidence            4468999999999999999999999999999999999999999999999853   4999999999999999988754210


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  484 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~  484 (569)
                      ..                                                     ........+  ..... . ++...+
T Consensus        92 ~~-----------------------------------------------------~~~~~~~~~--~~~~~-~-~~~~~~  114 (216)
T PRK12533         92 EV-----------------------------------------------------AAPDTLDDA--DSLDD-W-QPAGED  114 (216)
T ss_pred             cc-----------------------------------------------------ccccccccc--ccccc-c-ccCCCC
Confidence            00                                                     000000000  00000 0 111235


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      |++.+...+....|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|+++++||+++||+.+...
T Consensus       115 ~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~  185 (216)
T PRK12533        115 PLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA  185 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence            6677777777888999999999999999999998    8999999999999999999999999999999998643

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=9.2e-19  Score=167.68  Aligned_cols=166  Identities=9%  Similarity=0.032  Sum_probs=130.4

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352          324 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (569)
Q Consensus       324 ~~G~~Are~LI~~nlrLV~sIArry~~--~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~  401 (569)
                      .++..+++.|+..|.+.|+.++..+.+  +..+++|++||.|+.+|+..++|++.....|.||++..++|.+.++++++.
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            355699999999999999998766665  457899999999999999999998544457999999999999999887542


Q ss_pred             cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCC
Q 008352          402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG  481 (569)
Q Consensus       402 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~  481 (569)
                      +..                  ..                                    .+.         ..+. .+..
T Consensus        89 ~~~------------------~~------------------------------------~~~---------~~~~-~~~~  104 (178)
T PRK12529         89 LEL------------------AW------------------------------------LEA---------LATL-PEPL  104 (178)
T ss_pred             HHh------------------hh------------------------------------hhH---------hhhc-cCcC
Confidence            100                  00                                    000         0000 0011


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      ..+|++.+...+....|..+|..||+++|.||.|+|.    +|+|++|||+.||||.++|+.++.||+.+|++.+.
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            1245666666666678999999999999999999998    99999999999999999999999999999998753

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.2e-18  Score=166.80  Aligned_cols=166  Identities=19%  Similarity=0.249  Sum_probs=128.6

Q ss_pred             HHHHHh-ccHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHH
Q 008352          319 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTI  393 (569)
Q Consensus       319 L~~~l~-~G~~Are~LI~~nlrLV~sIArry~~~----g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI  393 (569)
                      ++..+. ++..|++.|+..|.+.|+.+|+++.++    ..+++|++||+++.+|+..++|+..  ..|.+|++..+++.+
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            334444 456999999999999999999998753    4689999999999999999999874  469999999999999


Q ss_pred             HHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcch
Q 008352          394 RKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTF  473 (569)
Q Consensus       394 ~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l  473 (569)
                      .++++++.+...+                                                     .++.         +
T Consensus        90 ~d~~Rr~~~~~~~-----------------------------------------------------~~~~---------~  107 (184)
T PRK12512         90 IDALRRRGRRVFV-----------------------------------------------------DIDD---------F  107 (184)
T ss_pred             HHHHHhhcccccC-----------------------------------------------------Cchh---------c
Confidence            9998865421100                                                     0000         0


Q ss_pred             hhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       474 ~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .+.+++..   +.    .....+.+..+|+.||+++|+||.++|.    +++|++|||+.||+|..+|+..+.||+++||
T Consensus       108 ~~~~~~~~---~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr  176 (184)
T PRK12512        108 AETLPAEP---AT----ETLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVRVALHRGLAALA  176 (184)
T ss_pred             cccccccc---hh----hHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence            00011100   00    1122346788999999999999999998    8999999999999999999999999999999


Q ss_pred             HHhhcC
Q 008352          554 QSLGGK  559 (569)
Q Consensus       554 ~~l~~~  559 (569)
                      ..+...
T Consensus       177 ~~l~~~  182 (184)
T PRK12512        177 AKFRSE  182 (184)
T ss_pred             HHhhcC
Confidence            988754

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=8.6e-19  Score=166.21  Aligned_cols=166  Identities=17%  Similarity=0.154  Sum_probs=128.0

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      .++..+++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++.  ..|.+|++..+++.+.+++++..+.
T Consensus         7 ~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~   83 (175)
T PRK12518          7 RGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQR   83 (175)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcc
Confidence            345699999999999999999999875 4689999999999999999999974  4699999999999999998864310


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  483 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~  483 (569)
                      -.                                                    .  .+... ....      ....   
T Consensus        84 ~~----------------------------------------------------~--~~~~~-~~~~------~~~~---   99 (175)
T PRK12518         84 PS----------------------------------------------------R--IQDDS-LNDQ------PSRP---   99 (175)
T ss_pred             cc----------------------------------------------------c--hhccc-cccc------ccCC---
Confidence            00                                                    0  00000 0000      0000   


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      .++......+....+..+|+.||+++|+||.++|+    +|+|++|||+.||+|..+|+..+.||+++||+.+...+
T Consensus       100 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~  172 (175)
T PRK12518        100 SDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG  172 (175)
T ss_pred             CCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence            11112222334456889999999999999999998    89999999999999999999999999999999987644

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

Probab=99.81  E-value=2.3e-18  Score=165.36  Aligned_cols=170  Identities=20%  Similarity=0.286  Sum_probs=135.8

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352          322 ELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (569)
Q Consensus       322 ~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~  401 (569)
                      ...++..++..++..|.+.++.+++++.++..+.+||+||+|+.+|+++..| .. +..|.||++.+++|.+.+++++..
T Consensus         9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~   86 (182)
T COG1595           9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRK   86 (182)
T ss_pred             HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhc
Confidence            3456669999999999999999999999998899999999999999999999 33 347999999999999999999765


Q ss_pred             cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCC
Q 008352          402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG  481 (569)
Q Consensus       402 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~  481 (569)
                      +....                                                      .+     +.+  ..+...+..
T Consensus        87 r~~~~------------------------------------------------------~~-----~~~--~~~~~~~~~  105 (182)
T COG1595          87 RRRAR------------------------------------------------------VE-----EAD--LLPEEADPA  105 (182)
T ss_pred             ccccc------------------------------------------------------cc-----ccc--ccccccCcc
Confidence            32211                                                      00     000  000000011


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      .+.. +.+...+....|..+|..||+++|++|.|+|+    +|+|++|||+.||||.++|+..++||+++||+.+...
T Consensus       106 ~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~  178 (182)
T COG1595         106 PDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA  178 (182)
T ss_pred             cccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            0011 24556677788999999999999999999999    9999999999999999999999999999999988754

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.81  E-value=8.5e-19  Score=164.13  Aligned_cols=157  Identities=13%  Similarity=0.044  Sum_probs=126.2

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  414 (569)
Q Consensus       335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l  414 (569)
                      +.|.+.|+.+|.++.++..+++|++||+|+.+|+++++|++.   .|.+|++..++|.+.++++++.+..+.        
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            578999999999999999999999999999999999999863   499999999999999999875421000        


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352          415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  494 (569)
Q Consensus       415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el  494 (569)
                                                                  ..+.    . ..   .+...  ....+++.+...+.
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  11245566666677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      ...|..+|+.||+++|+||.|+|.    +|+|++|||+.||+|..+|+.++.||+++||+.+...+
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            788999999999999999999998    99999999999999999999999999999999986543

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

Probab=99.81  E-value=6.2e-19  Score=170.52  Aligned_cols=172  Identities=18%  Similarity=0.200  Sum_probs=131.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (569)
Q Consensus       327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl  406 (569)
                      ..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+.+|++.  ..|.+|++..++|.+.++++++.+....
T Consensus        10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~   87 (193)
T TIGR02947        10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ   87 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence            48999999999999999999999998999999999999999999999864  4699999999999999999876421100


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  486 (569)
Q Consensus       407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe  486 (569)
                      .                         ..+++.           ..        .+.    ....    +  .......++
T Consensus        88 ~-------------------------~~~~~~-----------~~--------~~~----~~~~----~--~~~~~~~~e  113 (193)
T TIGR02947        88 S-------------------------DDDDIE-----------DW--------QLA----KAAS----H--TSNGLRSAE  113 (193)
T ss_pred             c-------------------------cchhhh-----------hh--------hhc----cccc----c--ccccccchh
Confidence            0                         000000           00        000    0000    0  000111233


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      ......+....|..+|..||+++|+||.|+|.    +++|++|||+.||||..+|+.++.||+++||+.+..
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            33334444567899999999999999999998    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.

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.1e-18  Score=168.83  Aligned_cols=162  Identities=20%  Similarity=0.191  Sum_probs=128.9

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++..++..|+..|.+.++.+|.++.++..+.+|++||.|+.+|+..++|+..  ..|.+|++..++|.+.++++++.+..
T Consensus         7 ~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~   84 (187)
T PRK12516          7 EGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREV   84 (187)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCc
Confidence            3468999999999999999999999999999999999999999999999865  35999999999999999998754210


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  484 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~  484 (569)
                      ..                                                      .+..        +.+....    .
T Consensus        85 ~~------------------------------------------------------~~~~--------~~~~~~~----~   98 (187)
T PRK12516         85 QD------------------------------------------------------TDGM--------FTEQLAV----H   98 (187)
T ss_pred             cc------------------------------------------------------cccc--------cccccCC----C
Confidence            00                                                      0000        0000000    0


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      ++.  ........|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|+.++.||+++||+.+...+
T Consensus        99 ~~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~  168 (187)
T PRK12516         99 PSQ--YGTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG  168 (187)
T ss_pred             cch--hhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            110  11122346889999999999999999998    99999999999999999999999999999999987654

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.80  E-value=1.9e-18  Score=162.88  Aligned_cols=158  Identities=15%  Similarity=0.107  Sum_probs=130.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (569)
Q Consensus       330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~  409 (569)
                      ++.|+..|.+.|+.+|+++.++..+.+|++||+++.+|++++.|++.   .|.+|++..+++.+.+++++..+...+   
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            67899999999999999999999999999999999999999999863   599999999999999999875421000   


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  489 (569)
Q Consensus       410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l  489 (569)
                                             ..+++                                     +.+.   ...+++.+
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 008352          490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      ...+....|..+|..||+++|+||.++|.    +|++++|||+.||+|.++|+..+.||+++||+.+....
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            66666778999999999999999999998    89999999999999999999999999999999987543

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

Probab=99.80  E-value=2.1e-18  Score=161.56  Aligned_cols=158  Identities=19%  Similarity=0.205  Sum_probs=128.0

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++..+++.|+..|.+.|+.+|.++.++..+.+|++||+|+.+|++.++|+.  ...|.+|++..+++.+.+++++..+. 
T Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~-   79 (162)
T TIGR02983         3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL-   79 (162)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-
Confidence            566999999999999999999999999999999999999999999999964  34799999999999999998865410 


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  484 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~  484 (569)
                      .+                                                      .+...            ++..   
T Consensus        80 ~~------------------------------------------------------~~~~~------------~~~~---   90 (162)
T TIGR02983        80 EL------------------------------------------------------PTREL------------PDAA---   90 (162)
T ss_pred             cc------------------------------------------------------ccccc------------Cccc---
Confidence            00                                                      00000            0000   


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      ++......+..+.|..+|..||+++|+||.|+|.    +|+|.+|||+.||+|.++|++.+.||+++||+.+..
T Consensus        91 ~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~  160 (162)
T TIGR02983        91 APDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRELLEE  160 (162)
T ss_pred             CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            0001122344567889999999999999999998    899999999999999999999999999999998754

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.80  E-value=1.9e-18  Score=164.23  Aligned_cols=162  Identities=14%  Similarity=0.099  Sum_probs=127.5

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (569)
Q Consensus       326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR  405 (569)
                      +..++..|+..|.+.|+.+|.++.++..+.+|++||+|+.+|+. ..|+..  ..|.+|++.+++|.+.++++++.+-  
T Consensus         8 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~--   82 (172)
T PRK12523          8 HSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALE--   82 (172)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHH--
Confidence            34999999999999999999999999999999999999999987 446543  3699999999999999999875310  


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352          406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  485 (569)
Q Consensus       406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p  485 (569)
                                      ....         .++                        .            . ........|
T Consensus        83 ----------------~~~~---------~~~------------------------~------------~-~~~~~~~~~  100 (172)
T PRK12523         83 ----------------QAYL---------AEL------------------------A------------L-VPEAEQPSP  100 (172)
T ss_pred             ----------------HHHH---------HHH------------------------h------------h-cccccCCCh
Confidence                            0000         000                        0            0 000001134


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      +......+....|..+|..||+++|+||.|+|.    +|+|++|||+.||+|.++|++++.||+++||..+..
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            444444444567999999999999999999998    999999999999999999999999999999998754

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.80  E-value=4.1e-18  Score=167.28  Aligned_cols=165  Identities=20%  Similarity=0.288  Sum_probs=135.7

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (569)
Q Consensus       326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR  405 (569)
                      +..+++.|+..|.+.++.++.++.++..+.+|++||+|+.+|+...+|++  + .|.+|++..+++.+.+++++..+ .+
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 69999999999999999987541 00


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352          406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  485 (569)
Q Consensus       406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p  485 (569)
                      .                                                    ..++     ++   + +.... ...+|
T Consensus       102 ~----------------------------------------------------~~~~-----~~---~-~~~~~-~~~~~  119 (203)
T PRK09647        102 M----------------------------------------------------EALP-----ED---Y-DRVPG-DEPNP  119 (203)
T ss_pred             c----------------------------------------------------cccc-----cc---c-cccCC-CCCCH
Confidence            0                                                    0000     00   0 00011 12245


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      +..+...+....|..+|..||+++|.||.|+|+    ++++++|||+.||||..+|++.+.||+++||+.+...+
T Consensus       120 ~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~  190 (203)
T PRK09647        120 EQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHA  190 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            566677777788999999999999999999998    99999999999999999999999999999999987654

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=4.4e-18  Score=159.64  Aligned_cols=157  Identities=15%  Similarity=0.099  Sum_probs=124.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (569)
Q Consensus       328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP  407 (569)
                      .|++.|+..|.+.|+.++.++.++..+.+|++||.|+.+|+..+.|++   ..|.+|++.++++.+.+++++..+.    
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~----   76 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLE----   76 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHH----
Confidence            689999999999999999999999999999999999999999988864   2699999999999999998864310    


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  487 (569)
Q Consensus       408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee  487 (569)
                                    ...         ..++                        +            + .++.....++.
T Consensus        77 --------------~~~---------~~~~------------------------~------------~-~~~~~~~~~~~   96 (161)
T PRK12528         77 --------------RAY---------LEAL------------------------A------------Q-LPERVAPSEEE   96 (161)
T ss_pred             --------------Hhh---------HHHh------------------------h------------c-cccccCCCHHH
Confidence                          000         0000                        0            0 00001112333


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      .....+....|..+|..||+++|+||.|+|.    +|+|++|||+.||+|.++|+..+.||+++||..
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

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=5.8e-18  Score=165.48  Aligned_cols=181  Identities=14%  Similarity=0.139  Sum_probs=130.8

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH
Q 008352          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  411 (569)
Q Consensus       332 ~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~  411 (569)
                      .++..|.+.|+.+|+++.++..+.+|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+.++++++.+...++..  
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            458889999999999999999999999999999999999999976  3599999999999999999876532111000  


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHH
Q 008352          412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  491 (569)
Q Consensus       412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~  491 (569)
                                            ..++.      .            ...++............+..++ ....+++....
T Consensus        88 ----------------------~~~~~------~------------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  126 (201)
T PRK12545         88 ----------------------DAELD------G------------EALLDRELFKDNGHWAAHAKPR-PWPKPETILQQ  126 (201)
T ss_pred             ----------------------ccccc------h------------hhhhhhhhhcccccccccccCc-CCCCHHHHHHH
Confidence                                  00000      0            0000000000000000000011 11245555555


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          492 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       492 ~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      .+....|..+|..||+++|+||.|+|+    +++|++|||+.||+|.++|+.++.||+++||+++...++
T Consensus       127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~  192 (201)
T PRK12545        127 QQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL  192 (201)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            666678899999999999999999998    999999999999999999999999999999999975443

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.79  E-value=9.4e-18  Score=166.80  Aligned_cols=117  Identities=18%  Similarity=0.273  Sum_probs=104.3

Q ss_pred             HhccHHHHHHHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhc
Q 008352          323 LHSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (569)
Q Consensus       323 l~~G~~Are~LI~~nlrLV~sIArry~~~g--~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~  400 (569)
                      ++.|+..+++||..|.|+|.++|.+|.++.  .+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++|+.
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            445665599999999999999999998764  589999999999999999999999999999999999999999999988


Q ss_pred             c---cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHH
Q 008352          401 S---RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLAR  439 (569)
Q Consensus       401 ~---r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~  439 (569)
                      .   +.+++|....+....+..+...+..+.++.|+.+||+.
T Consensus        84 ~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~  125 (218)
T TIGR02895        84 QKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILE  125 (218)
T ss_pred             ccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHH
Confidence            7   67899987666667777788888899999999999974

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).

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=6.7e-18  Score=159.38  Aligned_cols=159  Identities=17%  Similarity=0.164  Sum_probs=126.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (569)
Q Consensus       327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl  406 (569)
                      ...+..++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|++..  .|.+|++..++|.+.+++++..+... 
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~-   81 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQ-   81 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccccc-
Confidence            468999999999999999999999999999999999999999999998643  59999999999999999887542100 


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  486 (569)
Q Consensus       407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe  486 (569)
                                              .                             .+......         .+   ..++
T Consensus        82 ------------------------~-----------------------------~~~~~~~~---------~~---~~~~   96 (164)
T PRK12547         82 ------------------------D-----------------------------SDGVFTAR---------VA---VHPA   96 (164)
T ss_pred             ------------------------c-----------------------------cccccccc---------CC---CCch
Confidence                                    0                             00000000         00   0111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      .  ........+..+|..||+++|+||.|+|.    +|+|++|||+.||||.++|+..+.||+++||..+.-.
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  11222456889999999999999999998    8999999999999999999999999999999987543

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=6.8e-18  Score=163.49  Aligned_cols=180  Identities=18%  Similarity=0.166  Sum_probs=132.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352          331 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (569)
Q Consensus       331 e~LI~~nlrLV~sIArry~~~g~~-~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~  409 (569)
                      +..+..|.+.|+.+|+++.++..+ .+|++||+|+.+|+++++|++.  .+|.+|++..++|.+.++++++.+.......
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  4799999999999999999876531110000


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  489 (569)
Q Consensus       410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l  489 (569)
                      .                      ..+.+           ....      ...   ...+ .....+... ....+|+..+
T Consensus        86 ~----------------------~~~~~-----------~~~~------~~~---~~~~-~~~~~~~~~-~~~~~~e~~~  121 (195)
T PRK12532         86 L----------------------DDELL-----------DEAF------ESH---FSQN-GHWTPEGQP-QHWNTPEKSL  121 (195)
T ss_pred             c----------------------ccccc-----------chhh------hhh---hccc-cccccccCc-cccCCHHHHH
Confidence            0                      00000           0000      000   0000 000000000 1123577777


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      ...+....+..+|..||+++|+||.|+|.    +|+|++|||+.||+|..+|+.++.||+++||+++....
T Consensus       122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~  188 (195)
T PRK12532        122 NNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKW  188 (195)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            77777788999999999999999999998    89999999999999999999999999999999987554

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

Probab=99.78  E-value=6.2e-18  Score=163.58  Aligned_cols=178  Identities=12%  Similarity=0.138  Sum_probs=132.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  410 (569)
Q Consensus       331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~  410 (569)
                      .+.+..|.+.|+.+|+++.++..+.+|++||+|+.+|+..++|++.  .+|.+|++..++|.+.++++++.+....+. +
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             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHH
Q 008352          411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  490 (569)
Q Consensus       411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~  490 (569)
                                        .     .+.      .             .-.++... ...+....+..++ ....|+..+.
T Consensus        82 ------------------~-----~~~------~-------------~~~~~~~~-~~~~~~~~~~~~~-~~~~~e~~~~  117 (188)
T TIGR02943        82 ------------------D-----DEL------D-------------DEAFNALF-TQNGHWAQHGQPQ-HWNTPEKQLE  117 (188)
T ss_pred             ------------------c-----ccc------c-------------cchhhhhh-ccccchhcccccc-ccCCHHHHHH
Confidence                              0     000      0             00000000 0000000011111 1235667777


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       491 ~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      ..+....|..+|..||+++|+||.++|.    ++++++|||+.||+|.++|++++.||+++||+++...
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    8999999999999999999999999999999998654

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.

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=8.6e-18  Score=157.65  Aligned_cols=157  Identities=15%  Similarity=0.129  Sum_probs=124.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (569)
Q Consensus       326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR  405 (569)
                      ...+++.++..|.+.|+.++.++.++..+++|++||+++.+|+..++|++.   .|.||++..++|.+.+++++..+...
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            357999999999999999999999999999999999999999999999863   59999999999999999987642100


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352          406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  485 (569)
Q Consensus       406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p  485 (569)
                      +                          .                           .+       .  . .  .+.....+
T Consensus        80 ~--------------------------~---------------------------~~-------~--~-~--~~~~~~~~   94 (161)
T PRK12541         80 T--------------------------T---------------------------IE-------E--F-H--LPNVPSTE   94 (161)
T ss_pred             c--------------------------c---------------------------hh-------h--h-h--ccCCCCcH
Confidence            0                          0                           00       0  0 0  00000112


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      ++.....+. ..+..+|..||+++|.||.|+|.    +++|++|||+.||+|..+|++.+.||+++||+.
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            222223333 34567899999999999999998    899999999999999999999999999999975

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=7.9e-18  Score=162.87  Aligned_cols=176  Identities=16%  Similarity=0.116  Sum_probs=130.9

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  410 (569)
Q Consensus       331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~  410 (569)
                      +..|..|.+.++.+|.++.++..+++|++||.|+.+|+.+++|++.  .+|.+|++..++|.+.++++++.+...... .
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             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHH
Q 008352          411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  490 (569)
Q Consensus       411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~  490 (569)
                                        .     .+.                   .+....    +.......+.........++..+.
T Consensus        87 ------------------~-----~~~-------------------~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~  120 (189)
T PRK12530         87 ------------------I-----EED-------------------SPNSFF----DEKGHWKPEYYEPSEWQEVENTVY  120 (189)
T ss_pred             ------------------c-----ccc-------------------cchhhh----cccccccccccCCccccCHHHHHH
Confidence                              0     000                   000000    000000000000111235666677


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       491 ~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      ..+....|..+|+.||+++|+||.|+|.    +++|++|||+.||+|.++|+.++.||+++||+++...
T Consensus       121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~  185 (189)
T PRK12530        121 KEEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTSNLHVLLYRARLQLQACLSKN  185 (189)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            7777888999999999999999999998    8999999999999999999999999999999998644

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=1.1e-17  Score=164.65  Aligned_cols=180  Identities=18%  Similarity=0.215  Sum_probs=133.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (569)
Q Consensus       330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~  409 (569)
                      -..++..|.+.|+.+|+++.++....+|++||+|+.+|+.+.+|++.  .+|.+|++..++|.+.+++++..+....+..
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            36789999999999999999999999999999999999999999864  4699999999999999999876532111000


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  489 (569)
Q Consensus       410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l  489 (569)
                      .                  .  ....         ...+..+.              + ................|+..+
T Consensus        98 ~------------------~--~~~~---------~~~~~~~~--------------~-~~~~~~~~~~~~~~~~~e~~~  133 (206)
T PRK12544         98 L------------------R--DEEE---------EEDFEELF--------------D-ESGHWQKDERPQAWGNPEESL  133 (206)
T ss_pred             c------------------c--ccch---------hhHHHHhh--------------c-ccccccccccccccCCHHHHH
Confidence            0                  0  0000         00000000              0 000000000011123567777


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      ...+....+..+|..||+++|+||.|+|.    ++++++|||+.||+|..+|++.+.||+++||+.+...
T Consensus       134 ~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~  199 (206)
T PRK12544        134 EQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK  199 (206)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777778999999999999999999999    8999999999999999999999999999999998753

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.78  E-value=1.1e-17  Score=157.21  Aligned_cols=160  Identities=19%  Similarity=0.183  Sum_probs=129.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (569)
Q Consensus       327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl  406 (569)
                      +.+++.|+..|.+.|+.+|+++.++..+.+|++||+|+.+|++  .|+.  +..|.+|++..+++.+.+++++..+..+.
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  34799999999999999999875421100


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  486 (569)
Q Consensus       407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe  486 (569)
                      .                                                      +.      .....+.  + ....|+
T Consensus        78 ~------------------------------------------------------~~------~~~~~~~--~-~~~~~e   94 (166)
T PRK09639         78 I------------------------------------------------------LG------EFQWQEV--D-NEPSPE   94 (166)
T ss_pred             c------------------------------------------------------cc------hhhhhhc--c-CCCChH
Confidence            0                                                      00      0000000  1 122566


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      +.....+....|..+|..||+++|.||.++|     +|++++|||+.||+|..+|+..+.||+++||+.+..
T Consensus        95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~  161 (166)
T PRK09639         95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ  161 (166)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            6666667777899999999999999999999     489999999999999999999999999999998864

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.78  E-value=9.5e-18  Score=176.03  Aligned_cols=186  Identities=18%  Similarity=0.203  Sum_probs=135.3

Q ss_pred             HHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHH
Q 008352          318 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  396 (569)
Q Consensus       318 ~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~  396 (569)
                      +|+..+..| ..+++.|+..|.+.|+.+|.++.++..+.+|++||.|+.+|+.+++|++.  ..|.+|++..++|.+.++
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             HHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhc
Q 008352          397 IFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEI  476 (569)
Q Consensus       397 Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~  476 (569)
                      ++++.+... +.                  ..+ .+                         ..........+......+.
T Consensus        86 ~Rk~~~~~~-~~------------------~~~-~~-------------------------~~~~~~~~~~~~~~~~~~~  120 (339)
T PRK08241         86 LEGRARRPL-PT------------------DLG-AP-------------------------AADPVDELVERPEVPWLEP  120 (339)
T ss_pred             HHhhccccC-cc------------------ccC-CC-------------------------cCcccccccccccccccCC
Confidence            987542100 00                  000 00                         0000000000000000011


Q ss_pred             ccCC----CCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352          477 TADT----GVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  551 (569)
Q Consensus       477 i~D~----~~~~pee~l~~~e-l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK  551 (569)
                      +.+.    ...+|++.+...+ ....|..+|..||+++|+||.|+|.    +++|++|||++||+|..+|++++.||+++
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 4556899999999999999999998    99999999999999999999999999999


Q ss_pred             HHH
Q 008352          552 LKQ  554 (569)
Q Consensus       552 LR~  554 (569)
                      ||+
T Consensus       197 Lr~  199 (339)
T PRK08241        197 LAE  199 (339)
T ss_pred             Hhh
Confidence            998

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=1.1e-17  Score=163.10  Aligned_cols=169  Identities=17%  Similarity=0.103  Sum_probs=129.1

Q ss_pred             HHHHHh-ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHH
Q 008352          319 LKSELH-SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI  397 (569)
Q Consensus       319 L~~~l~-~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~I  397 (569)
                      |+..+. ++..+++.|+..|.+.++.+++ +.++..+.+|++||.|+.+|+..++|++.  ..|.+|++..++|.+.+++
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            444444 4459999999999999999975 67888899999999999999999999864  3699999999999999999


Q ss_pred             HhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcc
Q 008352          398 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEIT  477 (569)
Q Consensus       398 r~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i  477 (569)
                      +++.+..+.                                                     ..+ .. .    ...+  
T Consensus        92 Rk~~~~~~~-----------------------------------------------------~~~-~~-~----~~~~--  110 (196)
T PRK12535         92 RHDMARPRK-----------------------------------------------------SAT-EY-E----DAAA--  110 (196)
T ss_pred             HhhccCCCc-----------------------------------------------------ccc-cc-c----cccc--
Confidence            875421100                                                     000 00 0    0000  


Q ss_pred             cCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          478 ADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       478 ~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                        . ...++.... .+....|..+|+.||+++|+||.|+|.    +++|++|||+.||+|.++|+..+.||+++||+.+.
T Consensus       111 --~-~~~~~~~~~-~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~  182 (196)
T PRK12535        111 --T-TASNETTGS-WSEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTIRSRVARARADLIAATA  182 (196)
T ss_pred             --c-cCCcchhHH-HHHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence              0 011111111 122346889999999999999999998    89999999999999999999999999999999886


Q ss_pred             cC
Q 008352          558 GK  559 (569)
Q Consensus       558 ~~  559 (569)
                      ..
T Consensus       183 ~~  184 (196)
T PRK12535        183 TG  184 (196)
T ss_pred             cc
Confidence            54

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

Probab=99.78  E-value=1.2e-17  Score=173.82  Aligned_cols=183  Identities=17%  Similarity=0.184  Sum_probs=134.4

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++..+++.|+..|.+.|+++|.++.++..+.+|++||.|+.+|+.+++|++.  ..|.+|++..++|.+.++++++.+..
T Consensus         2 gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~   79 (324)
T TIGR02960         2 VDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRP   79 (324)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCc
Confidence            3458999999999999999999999999999999999999999999999864  46999999999999999998754210


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhccc------
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA------  478 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~------  478 (569)
                      ....                  ...  .                        ........ ..+......+.+.      
T Consensus        80 ~~~~------------------~~~--~------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~  114 (324)
T TIGR02960        80 RPVG------------------LGA--P------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDL  114 (324)
T ss_pred             Cccc------------------cCC--C------------------------CCcccccc-cccccccccCCCCcccccc
Confidence            0000                  000  0                        00000000 0000000000000      


Q ss_pred             -CCCCCChhHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          479 -DTGVEIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       479 -D~~~~~pee~l~~~e-l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                       .....+|++.+...+ +...+..+|..||+++|+||.|+|.    +++|++|||+.||+|.++|++++.||+++||+++
T Consensus       115 ~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  190 (324)
T TIGR02960       115 DDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----LGWRAAETAELLGTSTASVNSALQRARATLDEVG  190 (324)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence             011224565555444 4567889999999999999999998    8999999999999999999999999999999988


Q ss_pred             hc
Q 008352          557 GG  558 (569)
Q Consensus       557 ~~  558 (569)
                      ..
T Consensus       191 ~~  192 (324)
T TIGR02960       191 PS  192 (324)
T ss_pred             cc
Confidence            74

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.77  E-value=2.1e-17  Score=154.96  Aligned_cols=159  Identities=14%  Similarity=0.214  Sum_probs=125.4

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH
Q 008352          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  411 (569)
Q Consensus       332 ~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~  411 (569)
                      .++..|.+.++++|.++.++..+.+|++||+++.+|+....|++.   .|.+|++..+++.+.++++++.+....     
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             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHH
Q 008352          412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  491 (569)
Q Consensus       412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~  491 (569)
                                                                      .      ..+.... +. .+. ..+++..+..
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 1245555566


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          492 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       492 ~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      .+..+.+..+|+.||+++|.||.++|.    +++|++|||+.||+|.++|+..+.||+++||+.+...
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            666778999999999999999999998    8999999999999999999999999999999988653

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.77  E-value=5.6e-18  Score=157.01  Aligned_cols=152  Identities=19%  Similarity=0.216  Sum_probs=122.6

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  414 (569)
Q Consensus       335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l  414 (569)
                      ..|.+.|+.++.++.++..+.+|++||+++.+|+.+++|++   .+|.+|++..+++.+.++++++.+....        
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~--------   70 (154)
T TIGR02950         2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTI--------   70 (154)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccc--------
Confidence            57899999999999999889999999999999999999997   3799999999999999998865421000        


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352          415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  494 (569)
Q Consensus       415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el  494 (569)
                                         ..+.                                   +.+... +....|++.+...+.
T Consensus        71 -------------------~~~~-----------------------------------~~~~~~-~~~~~~~~~~~~~~~   95 (154)
T TIGR02950        71 -------------------DDDA-----------------------------------IGDLEQ-HPVESPEHHLLIKIE   95 (154)
T ss_pred             -------------------cHhh-----------------------------------hhhccc-cccCChhHHHHHHHH
Confidence                               0000                                   000000 011245555666666


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      ...|..+|..||+++++||.++|+    +|+|++|||+.||+|..+|++...||+++||+.+
T Consensus        96 ~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l  153 (154)
T TIGR02950        96 QEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL  153 (154)
T ss_pred             HHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            678999999999999999999998    8999999999999999999999999999999865

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=2.1e-17  Score=159.37  Aligned_cols=160  Identities=18%  Similarity=0.222  Sum_probs=126.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (569)
Q Consensus       328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP  407 (569)
                      .++..++..|.+.|+++|.++.++..+++|++||.|+.+|+..++|++..  .|.+|++..++|.+.++++++.+.... 
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  599999999999999998875421000 


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  487 (569)
Q Consensus       408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee  487 (569)
                                                                           .+.        ...+.. +.   .++.
T Consensus        82 -----------------------------------------------------~~~--------~~~~~~-~~---~~~~   96 (182)
T PRK12540         82 -----------------------------------------------------ADG--------SYAKTL-KS---QPGQ   96 (182)
T ss_pred             -----------------------------------------------------ccc--------cccccc-cC---CCch
Confidence                                                                 000        000000 00   1111


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      ..  ......|..+|+.||+++|+||.|+|.    +++|++|||+.||+|..+|++.+.||+++||+.+.....
T Consensus        97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~  164 (182)
T PRK12540         97 NA--HLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA  164 (182)
T ss_pred             HH--HHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            11  112346899999999999999999998    999999999999999999999999999999999986553

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.76  E-value=1.9e-17  Score=155.04  Aligned_cols=155  Identities=12%  Similarity=0.098  Sum_probs=124.3

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  414 (569)
Q Consensus       335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l  414 (569)
                      ..|.+.++.++.++.++..+.+|++||+|+.+|+..+.|++   .+|.||++..+++.+.++++++.+...         
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            56888999999999999889999999999999999999875   279999999999999999886531000         


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352          415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  494 (569)
Q Consensus       415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el  494 (569)
                                                                  .+++. . .+.     .   .....+|++.+..++.
T Consensus        70 --------------------------------------------~~~~~-~-~~~-----~---~~~~~~~~~~~~~~~~   95 (159)
T PRK12527         70 --------------------------------------------EPLEV-L-DEE-----E---RLHSPSPQTRLDLGQR   95 (159)
T ss_pred             --------------------------------------------cchhh-h-hcc-----c---cccCCCHHHHHHHHHH
Confidence                                                        00000 0 000     0   0011246666667777


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      ...|..+|..||+++++||.|+|+    +++|++|||+.||+|.++|+..+.||+++||+.+...
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    9999999999999999999999999999999988643

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.75  E-value=4.5e-17  Score=156.82  Aligned_cols=154  Identities=21%  Similarity=0.194  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (569)
Q Consensus       330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~  409 (569)
                      ++.|++.|.+.|+.+|.++.++..+++|++||.++.+|+.+..|++.  .+|.+|++..+++.+.++++++.+...++  
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  47999999999999999998764210000  


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  489 (569)
Q Consensus       410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l  489 (569)
                                                                               .+      +...+    .+++..
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 008352          490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      ...+....+..+|+.||+++|.||.++|.    +|++.+|||+.||+|..+|+.++.||+++||+.+..
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    899999999999999999999999999999998763

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.75  E-value=3.9e-17  Score=155.49  Aligned_cols=164  Identities=15%  Similarity=0.070  Sum_probs=127.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (569)
Q Consensus       326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR  405 (569)
                      +..|++.++..|.+.++.++.++.++..+.+||+||.|+.+|+. ..|++-.  .|.+|++..+++.+.++++++.+.. 
T Consensus         8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~-   83 (172)
T PRK09651          8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEK-   83 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence            35899999999999999999999999999999999999999998 3565432  5899999999999999988643100 


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352          406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  485 (569)
Q Consensus       406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p  485 (569)
                                       .    .     ...+                        +            + +.+....+|
T Consensus        84 -----------------~----~-----~~~~------------------------~------------~-~~~~~~~~~  100 (172)
T PRK09651         84 -----------------A----Y-----LEML------------------------A------------L-MPEGGAPSP  100 (172)
T ss_pred             -----------------h----h-----hhHH------------------------h------------h-ccccCCCCh
Confidence                             0    0     0000                        0            0 000011133


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      +......+....|..+|..||+++|+||.++|+    +++|++|||+.||+|.++|+..+.||+++|+......|
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            444444455567999999999999999999998    99999999999999999999999999999998764433

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=3.6e-17  Score=158.41  Aligned_cols=161  Identities=19%  Similarity=0.155  Sum_probs=125.8

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       324 ~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      ..+..+++.++..|.+.|+.+|+++.++..+++|++||.|+.+|+.++.|++.  ..|.+|++..+++.+.+.++++.+.
T Consensus        19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~   96 (188)
T PRK12517         19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD   96 (188)
T ss_pred             hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC
Confidence            45679999999999999999999999999999999999999999999999865  3699999999998765554332100


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVE  483 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~  483 (569)
                                                                            ....+       .    +...+....
T Consensus        97 ------------------------------------------------------~~~~~-------~----~~~~~~~~~  111 (188)
T PRK12517         97 ------------------------------------------------------LVDIE-------D----DSIEDDASH  111 (188)
T ss_pred             ------------------------------------------------------ccCcc-------c----ccccCcccc
Confidence                                                                  00000       0    000111111


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      .++..    ...+.|..+|..||+++|.||.++|+    ++++++|||+.||||..+|+.++.||+++||+.+...
T Consensus       112 ~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  179 (188)
T PRK12517        112 SSEEE----MEQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP  179 (188)
T ss_pred             ChhHH----HHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            23322    22356889999999999999999998    9999999999999999999999999999999998643

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.74  E-value=7.3e-17  Score=153.47  Aligned_cols=148  Identities=21%  Similarity=0.220  Sum_probs=120.9

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHH
Q 008352          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLL  414 (569)
Q Consensus       335 ~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l  414 (569)
                      ..|.+.++.++.++.++..+++|++||+++.+|+++++|++.  .+|.+|++..+++.+.+++++..+...++       
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            468899999999999999999999999999999999999864  57999999999999999998765211000       


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHH
Q 008352          415 SKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLM  494 (569)
Q Consensus       415 ~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el  494 (569)
                                                                     +     +       ....   ..+++.....+.
T Consensus        73 -----------------------------------------------~-----~-------~~~~---~~~~~~~~~~e~   90 (170)
T TIGR02959        73 -----------------------------------------------E-----S-------LLAA---DSAREETFVKEL   90 (170)
T ss_pred             -----------------------------------------------h-----h-------hccc---CCccHHHHHHHH
Confidence                                                           0     0       0000   011222334445


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      ...|..+|..||+++|.||.++|.    ++++++|||+.||+|..+|++.+.||+++||..+.
T Consensus        91 ~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  149 (170)
T TIGR02959        91 SQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE  149 (170)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999999998    89999999999999999999999999999999885

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.74  E-value=8.9e-17  Score=155.96  Aligned_cols=156  Identities=19%  Similarity=0.200  Sum_probs=121.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (569)
Q Consensus       328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP  407 (569)
                      .+++.|+. |.+.|+++|+++.++..+.+|++||.|+.+|+.+..|+..  ..|.+|++..++|.+.+++++..+...  
T Consensus         8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~--   82 (188)
T PRK12546          8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVP--   82 (188)
T ss_pred             hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccccc--
Confidence            56666766 7799999999999999999999999999999999999864  469999999999999999887542100  


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  487 (569)
Q Consensus       408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee  487 (569)
                                                                          ..+.        ...+...+..  ..+ 
T Consensus        83 ----------------------------------------------------~~~~--------~~~~~~~~~~--~~~-   99 (188)
T PRK12546         83 ----------------------------------------------------DPEG--------VHAASLAVKP--AHD-   99 (188)
T ss_pred             ----------------------------------------------------Cccc--------ccccccccCC--cch-
Confidence                                                                0000        0000000000  011 


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                         .......+..+|..||+++|+||.|+|.    +++|.+|||+.||||..+|+..+.||+++||+.+..
T Consensus       100 ---~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~  163 (188)
T PRK12546        100 ---GRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL  163 (188)
T ss_pred             ---hHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence               1122346889999999999999999998    899999999999999999999999999999998864

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.74  E-value=6.7e-17  Score=155.94  Aligned_cols=157  Identities=13%  Similarity=0.166  Sum_probs=122.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (569)
Q Consensus       330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~  409 (569)
                      .+..+..+++.|+.+|.++.++..+.+|++||.|+.+|+.+..|++.  .+|.+|++..+++.+.++++++.+....   
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~---   80 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARR---   80 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccc---
Confidence            45557789999999999999999999999999999999999999864  3699999999999999999876421100   


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  489 (569)
Q Consensus       410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l  489 (569)
                                              .+++                                    .+. .+.....+.   
T Consensus        81 ------------------------~~~~------------------------------------~~~-~~~~~~~~~---   96 (182)
T PRK12511         81 ------------------------ADEL------------------------------------AVL-ADASLPAAQ---   96 (182)
T ss_pred             ------------------------ccch------------------------------------hhc-cccCCCcch---
Confidence                                    0000                                    000 000000111   


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      ........|..+|..||+++|+||.|+|.    +++|++|||+.||||.++|+..+.||+++||..+...
T Consensus        97 ~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~  162 (182)
T PRK12511         97 EHAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGT  162 (182)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence            11223456889999999999999999998    8999999999999999999999999999999988744

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=2.1e-16  Score=149.81  Aligned_cols=160  Identities=14%  Similarity=0.116  Sum_probs=126.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 008352          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL  406 (569)
Q Consensus       327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRl  406 (569)
                      ..++.+++..|.+.++++|.++.++..+.+|++||.|+.+|+..+.++.   ..|.+|++..++|.+.+++++...    
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   369999999999999998875320    


Q ss_pred             chhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChh
Q 008352          407 PENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPD  486 (569)
Q Consensus       407 P~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pe  486 (569)
                              .+      ...         ..+                        +            + .+......|+
T Consensus        81 --------~~------~~~---------~~~------------------------~------------~-~~~~~~~~~~  100 (168)
T PRK12525         81 --------ER------AYL---------QSL------------------------A------------E-APEAVQPSPE  100 (168)
T ss_pred             --------HH------HHH---------HHH------------------------h------------c-ccccccCChH
Confidence                    00      000         000                        0            0 0000112455


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          487 ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       487 e~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      +.....+....|..+|..||+++|+||.|+|.    +++|++|||+.||+|..+|+..+.+|+++||..+.
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            55556666788999999999999999999998    99999999999999999999999999999998763

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.70  E-value=3.4e-16  Score=146.13  Aligned_cols=156  Identities=17%  Similarity=0.183  Sum_probs=113.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcC
Q 008352          350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGN  429 (569)
Q Consensus       350 ~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~g  429 (569)
                      ++..+++|++||+|+.+|+.... ++  +..|.+|++..++|.+.++++++.+..+...                     
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            34467899999999999999886 33  3579999999999999999987542100000                     


Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCC--CCChhHHHHHHHHHHHHHHHHhcCCH
Q 008352          430 HSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTG--VEIPDISVQKQLMRQHVRNLLTLLNP  507 (569)
Q Consensus       430 r~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~--~~~pee~l~~~el~e~L~~aL~~L~~  507 (569)
                                                 ...++.... ++++....+.+.+..  ...|++.+...+....|..+|..||+
T Consensus        58 ---------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~  109 (161)
T PRK09047         58 ---------------------------LFSSFSDDD-DDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA  109 (161)
T ss_pred             ---------------------------ccccccccc-ccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence                                       000000000 000111111122211  23577777777788889999999999


Q ss_pred             HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       508 rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      ++|+||.|+|+    +|+|++|||+.||||..+|+.++.||+++||+++...++
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    999999999999999999999999999999999876553

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.69  E-value=5.1e-16  Score=160.26  Aligned_cols=160  Identities=16%  Similarity=0.110  Sum_probs=123.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (569)
Q Consensus       328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP  407 (569)
                      .....++..|.+.++.+|+++.++..+.||++||.|+. |.....|+.   ..|.+|++..++|.+.+++++..+.-   
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~---   76 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRR---   76 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccc---
Confidence            34678999999999999999999999999999999999 666677762   47999999999999999998653100   


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  487 (569)
Q Consensus       408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee  487 (569)
                                             .                           .... ..       +.+...+.. ..|++
T Consensus        77 -----------------------~---------------------------~~~~-~~-------~~e~~~~~~-~~~~~   97 (293)
T PRK09636         77 -----------------------E---------------------------TYVG-PW-------LPEPVVEEL-DDPLE   97 (293)
T ss_pred             -----------------------c---------------------------cccC-Cc-------CCcCCCCCC-CChHH
Confidence                                   0                           0000 00       000000111 12333


Q ss_pred             H-HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          488 S-VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       488 ~-l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      . ....++...+..+|+.|||++|.||.|+|.    ++++++|||+.||+|..+|+++++||+++||+.+.
T Consensus        98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~  164 (293)
T PRK09636         98 AVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRARKHVRAARP  164 (293)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence            3 334455667899999999999999999998    89999999999999999999999999999999765

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.66  E-value=2.7e-15  Score=150.36  Aligned_cols=158  Identities=18%  Similarity=0.175  Sum_probs=122.6

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 008352          319 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  398 (569)
Q Consensus       319 L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir  398 (569)
                      |.+.+..+..+++.+++.| +.+++++.++.++..+.+||+||.|+.+|+.   |+..  ..|.+|++..++|.+.++++
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            4444555668888888877 7899999999999999999999999999986   5543  25999999999999999988


Q ss_pred             hcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhccc
Q 008352          399 QHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITA  478 (569)
Q Consensus       399 ~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~  478 (569)
                      ++.+.-.                               +                       .+     +  ..      
T Consensus        83 k~k~~~~-------------------------------~-----------------------~~-----~--~~------   95 (228)
T PRK06704         83 SKSVHEK-------------------------------I-----------------------RD-----Q--IT------   95 (228)
T ss_pred             ccccccc-------------------------------c-----------------------cc-----c--cc------
Confidence            7541000                               0                       00     0  00      


Q ss_pred             CCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          479 DTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       479 D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                         ...+....  .+..+.+..+|+.||+++|.||.|+|.    +++|++|||+.||+|.++|+..+.||+++||+.+..
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  123456889999999999999999998    899999999999999999999999999999998865

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

Probab=99.65  E-value=3e-15  Score=153.91  Aligned_cols=156  Identities=22%  Similarity=0.150  Sum_probs=118.9

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHH
Q 008352          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY  411 (569)
Q Consensus       332 ~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~  411 (569)
                      +++..|.+.++.+|+++.++..+.||++||+++.+++.  .|+..  ..|.+|++.+++|.+.+++++..+--       
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~-------   69 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARR-------   69 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcc-------
Confidence            36889999999999999999999999999999997765  45432  36999999999999999998643100       


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHH
Q 008352          412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK  491 (569)
Q Consensus       412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~  491 (569)
                                         .                           . ...+.       +.+...+. ...|++.+..
T Consensus        70 -------------------~---------------------------~-~~~~~-------~~e~~~~~-~~~~~~~~~~   94 (281)
T TIGR02957        70 -------------------E---------------------------V-YVGPW-------LPEPLLTT-SADPAESVEL   94 (281)
T ss_pred             -------------------c---------------------------c-cCCCC-------CCcccCCC-CCChHHHHHH
Confidence                               0                           0 00000       00000001 1234444433


Q ss_pred             -HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          492 -QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       492 -~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                       +.+...+..+|+.|||+||.||.|+|.    .++|++|||+.||+|..+|+++++||+++||+...
T Consensus        95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~  157 (281)
T TIGR02957        95 AESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP  157 (281)
T ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence             345567889999999999999999998    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=99.64  E-value=5.7e-15  Score=152.87  Aligned_cols=161  Identities=17%  Similarity=0.135  Sum_probs=123.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 008352          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLP  407 (569)
Q Consensus       328 ~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP  407 (569)
                      ..+..++..|.+.++++|+++.++..+.||++||.|+.+|++...+ .   ..|.+|++...+|.+.+++++..+.-   
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr---   77 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRR---   77 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccC---
Confidence            5678999999999999999999999999999999999999987543 1   35999999999999999998643100   


Q ss_pred             hhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhH
Q 008352          408 ENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDI  487 (569)
Q Consensus       408 ~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee  487 (569)
                                             ..                         ....+.  +..     .+...+  ..+|++
T Consensus        78 -----------------------~~-------------------------~~~~~~--~~~-----~~~~~~--~~~~~~  100 (290)
T PRK09635         78 -----------------------ER-------------------------PQDIAA--WHD-----GDASVS--SVDPAD  100 (290)
T ss_pred             -----------------------cC-------------------------cccccc--cCc-----cccCCC--CCCcHH
Confidence                                   00                         000000  000     000001  112333


Q ss_pred             -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          488 -SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       488 -~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                       ....++....+..+|..|||++|.||.|+|.    .+++++|||+.||+|..+|+++++||+++||+..
T Consensus       101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~  166 (290)
T PRK09635        101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAHRARRKINESR  166 (290)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence             3445556678999999999999999999998    8999999999999999999999999999999864

>PRK09191 two-component response regulator; Provisional

Probab=99.52  E-value=8.5e-14  Score=138.90  Aligned_cols=136  Identities=17%  Similarity=0.132  Sum_probs=110.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecch
Q 008352          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPE  408 (569)
Q Consensus       329 Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~  408 (569)
                      ++..|+..|.+.|+++|.++.++..+.+|++||+|+.+|+....|++.  ..|.+|++.++++.....    .       
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~----~-------   68 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA----G-------   68 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc----c-------
Confidence            578999999999999999999999999999999999999999999875  358999988765321000    0       


Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352          409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  488 (569)
Q Consensus       409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~  488 (569)
                                                                              . .+.         ..  ..+.. 
T Consensus        69 --------------------------------------------------------~-~~~---------~~--~~~~~-   79 (261)
T PRK09191         69 --------------------------------------------------------A-NDP---------EP--GSPFE-   79 (261)
T ss_pred             --------------------------------------------------------c-cCC---------CC--CCCch-
Confidence                                                                    0 000         00  01111 


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       489 l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                             ..+..+|+.||+++|+||.|+|.    +++|++|||+.||+|.++|+.+..+|+++||..+.
T Consensus        80 -------~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~  137 (261)
T PRK09191         80 -------ARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA  137 (261)
T ss_pred             -------HHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence                   16888999999999999999998    99999999999999999999999999999998765

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.52  E-value=2.1e-13  Score=125.52  Aligned_cols=136  Identities=12%  Similarity=0.141  Sum_probs=99.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhh-----cCCCCCCchhhHHHHHHHHHHHHHHHhcccce
Q 008352          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTI  404 (569)
Q Consensus       330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiek-----FDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~I  404 (569)
                      ++.++..|.++++.+|++|...    +| +||.++.+|..+.+     |++.  ..|.||++..++|.+.++++++.+..
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            4679999999999999999652    34 49999999999875     5543  46999999999999999998653100


Q ss_pred             ecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCC
Q 008352          405 RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEI  484 (569)
Q Consensus       405 RlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~  484 (569)
                      +.                 . .       ..++                               .+         ... .
T Consensus        74 ~~-----------------~-~-------~~~~-------------------------------~~---------~~~-~   87 (142)
T TIGR03209        74 KI-----------------I-Y-------NSEI-------------------------------TD---------IKL-S   87 (142)
T ss_pred             hh-----------------h-h-------hhhh-------------------------------hc---------ccc-c
Confidence            00                 0 0       0000                               00         000 1


Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHH
Q 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR  542 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVR  542 (569)
                      +.+.+...+....|..+|+.||+++|+||.|+|.    +++|++|||+.||+|.++|+
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            1122333444557889999999999999999998    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.

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.45  E-value=5.3e-12  Score=127.33  Aligned_cols=88  Identities=20%  Similarity=0.354  Sum_probs=77.9

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~--~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      .+.++..++.| ..|++.|+..|.++|+++|.++.++..  +.+|++|||++++|+++++|++++|..|.+|+..+|++.
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            34555566555 489999999999999999999998765  589999999999999999999998889999999999999


Q ss_pred             HHHHHHhcccc
Q 008352          393 IRKAIFQHSRT  403 (569)
Q Consensus       393 I~~~Ir~~~r~  403 (569)
                      +.+++++..+.
T Consensus        85 ~iDylRk~~~~   95 (237)
T PRK08311         85 LIDYFRKESKH   95 (237)
T ss_pred             HHHHHHHhhcc
Confidence            99999987654

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.38  E-value=3.2e-11  Score=116.85  Aligned_cols=174  Identities=20%  Similarity=0.309  Sum_probs=118.2

Q ss_pred             HHHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCC---CCCHHH--HHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHH
Q 008352          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVR  390 (569)
Q Consensus       317 ~~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~---g~~~ED--LIQEG~IGLirAiekFDp~kG~rFSTYA~~wIR  390 (569)
                      .+|+..++.|+ .|.+.|+..|++-++.+|+++...   +.+.+|  |++|.|+.+++.-...+.+....|..|+...++
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            34555565555 999999999999999999987633   344555  477778777763333233333468889999999


Q ss_pred             HHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC
Q 008352          391 QTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD  470 (569)
Q Consensus       391 qaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~  470 (569)
                      +.+.++++++.+..                      .+|..                         ...+|+...     
T Consensus        85 r~lid~~R~~~a~K----------------------Rg~~~-------------------------~~~~l~~~~-----  112 (185)
T PF07638_consen   85 RKLIDHARRRQAQK----------------------RGGDQ-------------------------VRVELDERA-----  112 (185)
T ss_pred             HHHHHHHHHHHHHh----------------------cCCCC-------------------------cccchhhhh-----
Confidence            88888887654211                      11100                         011122111     


Q ss_pred             cchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          471 TTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       471 ~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                             .+...+.|+..+.   +.+.+..+.. |+|++++||.++|.    .|+|.+|||+.||||..+|+.....|..
T Consensus       113 -------~~~~~~~~~~~~~---l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~~lgiS~~tV~r~l~~aR~  177 (185)
T PF07638_consen  113 -------DSGDEPSPEELLE---LEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAERLGISERTVRRRLRRARA  177 (185)
T ss_pred             -------ccccCCCHHHHHH---HHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                   0111124444332   3344555555 99999999999998    8999999999999999999999999999


Q ss_pred             HHHHHhh
Q 008352          551 RLKQSLG  557 (569)
Q Consensus       551 KLR~~l~  557 (569)
                      +|+..+.
T Consensus       178 ~l~~~l~  184 (185)
T PF07638_consen  178 WLRRELR  184 (185)
T ss_pred             HHHHHhc
Confidence            9998764

>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.25  E-value=1.9e-11  Score=98.54  Aligned_cols=70  Identities=23%  Similarity=0.432  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccc
Q 008352          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSR  402 (569)
Q Consensus       333 LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r  402 (569)
                      |++.|.++|++++++|.+++.+.+|++||++++||+++++||+++|..|.+|++..+++.+.++++++.|
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r   70 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR   70 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence            6899999999999999999999999999999999999999999999899999999999999999998764

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.23  E-value=2.4e-11  Score=93.33  Aligned_cols=50  Identities=36%  Similarity=0.628  Sum_probs=46.3

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          501 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       501 aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +|+.||++|++||.++|+    +++|++|||+.||+|+++|++++.+|++|||+
T Consensus         1 Al~~L~~~er~vi~~~y~----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen    1 ALDQLPPREREVIRLRYF----EGLTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             HHCTS-HHHHHHHHHHHT----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             ChhhCCHHHHHHHHHHhc----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            588999999999999998    99999999999999999999999999999985

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.04  E-value=6e-10  Score=92.86  Aligned_cols=77  Identities=30%  Similarity=0.491  Sum_probs=66.1

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHH
Q 008352          412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDIS  488 (569)
Q Consensus       412 ~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~  488 (569)
                      +.+++|.++++.|.+++||.||.+|||+.|||++++|..++...+.+.||+.+++.+++.++.+++.|+...+|++.
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            36789999999999999999999999999999999999999999999999999998888899999999988788764

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=98.93  E-value=3.1e-09  Score=82.58  Aligned_cols=54  Identities=30%  Similarity=0.440  Sum_probs=46.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          495 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       495 ~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                      ++.|..+|..||+++|.||.++|.    +|+|++|||+.+|+|.++|++.+.+|+++|
T Consensus         1 r~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L   54 (54)
T PF08281_consen    1 REALQQALAQLPERQREIFLLRYF----QGMSYAEIAEILGISESTVKRRLRRARKKL   54 (54)
T ss_dssp             HHHHHHHHHCS-HHHHHHHHHHHT----S---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHH----HCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence            357899999999999999999999    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=91.36  Aligned_cols=71  Identities=18%  Similarity=0.285  Sum_probs=62.4

Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      +.+.....+....|..+|+.||+++|+||.++|+    +|+|++|||+.||+|..+|++++.||+++|+..+...
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            3334445556678999999999999999999998    8999999999999999999999999999999988644

>PRK00118 putative DNA-binding protein; Validated

Probab=98.43  E-value=1e-06  Score=78.27  Aligned_cols=62  Identities=21%  Similarity=0.135  Sum_probs=55.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      ..+.-+...||+++++|+.++|.    +++|..|||+.+|+|+.+|+.++.||+++||+++..-++
T Consensus         9 ~l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~   70 (104)
T PRK00118          9 LLFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL   70 (104)
T ss_pred             HHHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            34455668999999999999998    999999999999999999999999999999999876553

>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=98.29  E-value=2.4e-06  Score=64.17  Aligned_cols=54  Identities=37%  Similarity=0.589  Sum_probs=49.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      +.+..++..|++.++.++.++|.    +++|..+||+.+|+|..+|+++..++..+||
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            35778899999999999999997    8899999999999999999999999998874

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.18  E-value=3.8e-06  Score=78.15  Aligned_cols=57  Identities=19%  Similarity=0.269  Sum_probs=49.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhh
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY  564 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~y  564 (569)
                      ..|+++|++||.+++     +|+|++|||+.||+|+.+|++++++|+++|+.......+-.+
T Consensus         5 ~~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~   61 (137)
T TIGR00721         5 TFLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKF   61 (137)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHH
Confidence            359999999999975     799999999999999999999999999999986555444443

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=98.13  E-value=5.8e-06  Score=77.30  Aligned_cols=51  Identities=24%  Similarity=0.399  Sum_probs=46.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      ..|+++|++||.+++     +++|++|||+.||+|+.+|+.++++|+++||+....
T Consensus         5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t   55 (141)
T PRK03975          5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARET   55 (141)
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999965     799999999999999999999999999999987654

>PRK04217 hypothetical protein; Provisional

Probab=98.10  E-value=6.3e-06  Score=74.01  Aligned_cols=55  Identities=20%  Similarity=0.136  Sum_probs=50.9

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      ..|++.|++||.++|.    +++|++|||+.||||+.+|++++.+|+++|++.+.....
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            5799999999999998    899999999999999999999999999999999876544

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.04  E-value=1.2e-06  Score=63.65  Aligned_cols=34  Identities=41%  Similarity=0.464  Sum_probs=30.1

Q ss_pred             CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH
Q 008352          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR  287 (569)
Q Consensus       254 ~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~  287 (569)
                      +|+++.||++|+++||||++||++|+++|+.+..
T Consensus         1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~   34 (37)
T PF00140_consen    1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE   34 (37)
T ss_dssp             HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence            3789999999999999999999999999998654

2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=97.97  E-value=3.3e-05  Score=71.55  Aligned_cols=62  Identities=18%  Similarity=0.264  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      ...+.|..+|+.|++.+|.||.++|+  .+..+|..+||..||+|+.+|.++..+|+.+|+..+
T Consensus        71 ~~~~~I~~~l~~Ld~~er~II~~rY~--~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l  132 (134)
T TIGR01636        71 RNRDAIENCLNEADEQTRVIIQELYM--KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL  132 (134)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc--cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            45677899999999999999999996  223469999999999999999999999999999865

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>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=97.95  E-value=3.9e-05  Score=67.85  Aligned_cols=58  Identities=28%  Similarity=0.350  Sum_probs=45.3

Q ss_pred             HHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          497 HVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       497 ~L~~aL-~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      .|.+.. .-|+++|++++.++|.    +++|+.|||+.+||||..|...++||.++|...=..
T Consensus         9 ~L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k   67 (101)
T PF04297_consen    9 LLFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK   67 (101)
T ss_dssp             HHHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            344444 4499999999999998    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=97.94  E-value=0.0017  Score=74.40  Aligned_cols=34  Identities=32%  Similarity=0.493  Sum_probs=31.7

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI  286 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~  286 (569)
                      .+||+++||++||+.||||+|+|+++|++|..+.
T Consensus       102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~  135 (619)
T PRK05658        102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE  135 (619)
T ss_pred             CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence            6799999999999999999999999999998754

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.81  E-value=4.3e-05  Score=58.38  Aligned_cols=46  Identities=26%  Similarity=0.400  Sum_probs=41.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|+.|+.+.+     .+++.+|||+.+|+|+.+|+++..+++++|+
T Consensus         2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~   47 (58)
T smart00421        2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLG   47 (58)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            468999999997743     6899999999999999999999999998886

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=97.67  E-value=0.0001  Score=58.19  Aligned_cols=46  Identities=24%  Similarity=0.335  Sum_probs=41.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|.+|+.+..     .|++.+|||+.+|||..+|+....++++||.
T Consensus         2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~   47 (58)
T PF00196_consen    2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLG   47 (58)
T ss_dssp             GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred             CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence            479999999999987     6999999999999999999999999999985

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.63  E-value=0.00014  Score=55.72  Aligned_cols=45  Identities=29%  Similarity=0.487  Sum_probs=40.4

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      |+++|++|+.+.+     .++|.+|||+.+|+|+.+|+...++++++|+.
T Consensus         1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~   45 (57)
T cd06170           1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGV   45 (57)
T ss_pred             CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            6899999998854     68999999999999999999999999888864

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=97.59  E-value=0.00033  Score=61.76  Aligned_cols=55  Identities=22%  Similarity=0.439  Sum_probs=49.7

Q ss_pred             HHHHHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          494 MRQHVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       494 l~e~L~~aL~~L~-~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                      .+..+..+++.|+ +.+|.||.++|.    .+++..+|++.||+|+.++-.+.++|++.|
T Consensus        44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi----~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L   99 (100)
T PF07374_consen   44 EKLEIRRAINKLEDPDERLILRMRYI----NKLTWEQIAEELNISRRTYYRIHKKALKEL   99 (100)
T ss_pred             HHHHHHHHHHHccChhHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            3456788888886 799999999998    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.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.57  E-value=0.00017  Score=60.19  Aligned_cols=47  Identities=19%  Similarity=0.213  Sum_probs=41.9

Q ss_pred             HHHHHHhcCCHHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          497 HVRNLLTLLNPKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       497 ~L~~aL~~L~~rER~VL~LR-ygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .+.+-|+.||++.+.++.|. |.    +++|++|||+.||||..+|+.++++
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            46677899999999999994 55    8999999999999999999998875

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

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

Probab=97.51  E-value=0.00035  Score=54.86  Aligned_cols=48  Identities=27%  Similarity=0.428  Sum_probs=42.0

Q ss_pred             CCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       505 L~~rER~VL~LRygL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                      |+++|++||..-|-.+  + ...-|+.|||+.||||+.++.+++.+|.+||
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            7899999998866433  3 3688999999999999999999999999987

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

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.43  E-value=0.00022  Score=62.24  Aligned_cols=50  Identities=22%  Similarity=0.240  Sum_probs=43.4

Q ss_pred             HHHHHHH-hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHH
Q 008352          496 QHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLE  545 (569)
Q Consensus       496 e~L~~aL-~~L~~rER~VL~LRygL~d---~e~~Tl~EIAe~LGISrerVRqie  545 (569)
                      +.+..+| ..|+|+|+.+|.+||++.+   ..++|++|||+.+|||+.+|.+..
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            3566667 5599999999999999997   679999999999999999998654

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=97.33  E-value=0.00044  Score=66.85  Aligned_cols=47  Identities=23%  Similarity=0.352  Sum_probs=43.8

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ..|+++|++|+.+.-     +|+|.+|||+.||+|..||+....++++||.-
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     79999999999999999999999999999964

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.31  E-value=0.0004  Score=68.62  Aligned_cols=46  Identities=11%  Similarity=0.237  Sum_probs=43.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .|++||++||.+.-     +|+|.+|||+.||||..||+....+.++||.-
T Consensus       137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v  182 (207)
T PRK15411        137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT  182 (207)
T ss_pred             cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            49999999999986     79999999999999999999999999999963

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.26  E-value=0.00048  Score=67.26  Aligned_cols=46  Identities=22%  Similarity=0.291  Sum_probs=43.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|++||++|+.+.-     +|+|.+|||+.||||..||+....+.++||-
T Consensus       149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~  194 (216)
T PRK10840        149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG  194 (216)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            469999999999986     6999999999999999999999999999994

>PRK13870 transcriptional regulator TraR; Provisional

Probab=97.26  E-value=0.00047  Score=69.69  Aligned_cols=46  Identities=26%  Similarity=0.364  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .|++||++||.+--     +|+|..|||.+||||..||...+++|++||-.
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     79999999999999999999999999999943

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.24  E-value=0.00053  Score=68.41  Aligned_cols=50  Identities=8%  Similarity=-0.050  Sum_probs=46.5

Q ss_pred             HHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          499 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       499 ~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .+++..|+++|++|+.+.-     +|+|.+|||+.|++|..||+....+.++||.
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=97.24  E-value=0.00054  Score=69.96  Aligned_cols=48  Identities=21%  Similarity=0.261  Sum_probs=44.4

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +..|+++|++|+.+..     +|+|.+|||++||||..||+....++++||.-
T Consensus       188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v  235 (247)
T TIGR03020       188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV  235 (247)
T ss_pred             ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            4579999999999965     79999999999999999999999999999964

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.24  E-value=0.00052  Score=69.08  Aligned_cols=48  Identities=19%  Similarity=0.267  Sum_probs=44.4

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ...|+++|++||.+..     +|+|.+|||++||||..||+..+.+|++||+.
T Consensus       169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~  216 (232)
T TIGR03541       169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGV  216 (232)
T ss_pred             hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            3579999999999964     79999999999999999999999999999974

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.22  E-value=0.00059  Score=67.68  Aligned_cols=46  Identities=20%  Similarity=0.342  Sum_probs=43.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|++||++||.+..     +|+|.+|||+.||||..||+....+.++||.
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

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=97.18  E-value=0.00068  Score=68.71  Aligned_cols=45  Identities=16%  Similarity=0.258  Sum_probs=43.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .|++||++||.+-.     +|+|..|||++||||..||+..+.++++||-
T Consensus       179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~  223 (240)
T PRK10188        179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFN  223 (240)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            69999999999986     7999999999999999999999999999995

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=97.16  E-value=0.00072  Score=67.46  Aligned_cols=48  Identities=17%  Similarity=0.127  Sum_probs=44.4

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +..|+++|++|+.+.+     +|+|.+|||+.||+|..||+....++++||.-
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     69999999999999999999999999999964

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=97.11  E-value=0.0012  Score=58.97  Aligned_cols=53  Identities=19%  Similarity=0.164  Sum_probs=48.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      .|+..|-+.|+|.+.    +++|++|.|+.||||+.|+..++..|.+|+-..|....
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            588889999999998    99999999999999999999999999999999886544

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=97.06  E-value=0.00094  Score=66.35  Aligned_cols=46  Identities=30%  Similarity=0.371  Sum_probs=43.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|++||++|+++--     +|+|.+|||+.|++|..||+....++++||.
T Consensus       147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~  192 (211)
T COG2197         147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLG  192 (211)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence            469999999999875     7999999999999999999999999999995

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=97.01  E-value=0.0025  Score=62.32  Aligned_cols=59  Identities=17%  Similarity=0.260  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          493 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       493 el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      .....+...+.+|++|||+|+..--     .|+..++||..||||.-||...-.+.++||+..-
T Consensus       131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~S  189 (202)
T COG4566         131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARS  189 (202)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhcc
Confidence            3456788999999999999999877     6999999999999999999999999999998643

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=96.97  E-value=0.0025  Score=50.35  Aligned_cols=48  Identities=33%  Similarity=0.432  Sum_probs=43.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      ..|+++|.+|+.+.-     .|++..|||..+|+|..+|+....++.+||.-.
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            368999999998876     579999999999999999999999999999643

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=96.90  E-value=0.0012  Score=49.54  Aligned_cols=41  Identities=24%  Similarity=0.339  Sum_probs=24.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      ..|++.||..|...+-    +|+|..+||+.||+|+.||...++|
T Consensus         3 ~~Lt~~eR~~I~~l~~----~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALLE----QGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHHC----S---HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHHH----cCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            4689999999988776    8999999999999999999988776

>PRK09483 response regulator; Provisional

Probab=96.87  E-value=0.0018  Score=62.02  Aligned_cols=46  Identities=22%  Similarity=0.300  Sum_probs=42.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|++|+.+..     +|+|.+|||+.|++|..||+....+.++||-
T Consensus       147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~  192 (217)
T PRK09483        147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN  192 (217)
T ss_pred             cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            469999999998764     7899999999999999999999999999994

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.79  E-value=0.0084  Score=55.06  Aligned_cols=63  Identities=21%  Similarity=0.231  Sum_probs=53.9

Q ss_pred             HHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          493 LMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       493 el~e~L~~aL-~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      .....+..++ +.|++.+|+||..+|. . .++++..+|+..+|+|+.+...+.++|+.++-..+.
T Consensus        67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~  130 (132)
T TIGR01637        67 QEARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG  130 (132)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence            3445677777 9999999999999997 2 137899999999999999999999999999987654

This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.71  E-value=0.0032  Score=58.81  Aligned_cols=46  Identities=22%  Similarity=0.358  Sum_probs=42.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|++||.+. .    ++++.+|||+.+++|..||+....++++||.
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    7899999999999999999999999999995

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.65  E-value=0.0041  Score=61.85  Aligned_cols=53  Identities=23%  Similarity=0.350  Sum_probs=45.9

Q ss_pred             cCCHHHHHHHHHHhccc--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          504 LLNPKERCIVRLRFGIE--D-GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~--d-~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      .|+++|++||+.-|-.+  | ....+++|||+.||||+.++.+++.+|.+||=..+
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~  210 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY  210 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            69999999999876543  3 36789999999999999999999999999996543

>PRK01381 Trp operon repressor; Provisional

Probab=96.48  E-value=0.003  Score=55.62  Aligned_cols=49  Identities=27%  Similarity=0.316  Sum_probs=41.0

Q ss_pred             HHHHHHHHhc-CCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHH
Q 008352          495 RQHVRNLLTL-LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQ  543 (569)
Q Consensus       495 ~e~L~~aL~~-L~~rER~VL~LRygL~d---~e~~Tl~EIAe~LGISrerVRq  543 (569)
                      .+.+..+|.. |+|+|+..|..||++..   ..++|+.||++.+|||..+|.+
T Consensus        22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR   74 (99)
T PRK01381         22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR   74 (99)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence            3456666655 99999999999999886   4579999999999999988863

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.48  E-value=0.005  Score=58.32  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=42.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|++|+.+..     ++++.++||+.+++|..||+....++++||.
T Consensus       154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~  199 (216)
T PRK10651        154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMK  199 (216)
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence            459999999999865     7899999999999999999999999999995

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.44  E-value=0.0084  Score=55.72  Aligned_cols=53  Identities=13%  Similarity=0.190  Sum_probs=46.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          497 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       497 ~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .+...+..|+++|++|+.+.+     .+++.++||+.+|+|..+|+....++++||+.
T Consensus       134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~  186 (202)
T PRK09390        134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQA  186 (202)
T ss_pred             HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence            355667889999999999744     57999999999999999999999999999964

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=96.41  E-value=0.0027  Score=57.95  Aligned_cols=48  Identities=25%  Similarity=0.359  Sum_probs=44.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      -|+++|-.||.||-     +|+|.+|||++||-|+..|+-++++|+.++.+.-
T Consensus         8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar   55 (143)
T COG1356           8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR   55 (143)
T ss_pred             eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence            48899999999997     7999999999999999999999999999998753

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.21  E-value=0.019  Score=50.59  Aligned_cols=48  Identities=25%  Similarity=0.328  Sum_probs=44.0

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .-|+.+|+..+.++|.    .++|+.|||+.++|||..|...++|.-+.|-.
T Consensus        16 sLLT~KQ~~Y~~lyy~----dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~   63 (105)
T COG2739          16 SLLTKKQKNYLELYYL----DDLSLSEIAEEFNVSRQAIYDNIKRTEKILED   63 (105)
T ss_pred             HHHhHHHHHHHHHHHH----hhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence            4589999999999998    89999999999999999999999998877754

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=96.20  E-value=0.013  Score=51.09  Aligned_cols=52  Identities=19%  Similarity=0.148  Sum_probs=47.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  559 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  559 (569)
                      .|+..|-+.|+|...    ++++++|-|.+||||+.|+-..+..|++|+-.++...
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

>PRK15320 transcriptional activator SprB; Provisional

Probab=95.98  E-value=0.013  Score=57.75  Aligned_cols=48  Identities=19%  Similarity=0.267  Sum_probs=43.8

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      --.|+++|.+|+.+--     +|+|.+|||+.|++|..||+....+.+.||.-
T Consensus       162 ~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA  209 (251)
T PRK15320        162 PPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM  209 (251)
T ss_pred             CCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence            3678999999999876     79999999999999999999999999999853

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

Probab=95.97  E-value=0.16  Score=53.85  Aligned_cols=159  Identities=18%  Similarity=0.143  Sum_probs=96.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  410 (569)
Q Consensus       331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~  410 (569)
                      +..+..-.+-++.---+|+++=.-.||.+||.|+..++.-.+=-|-+  .-..|.+..-|+.-++.++++.+.-..|.  
T Consensus         8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~--   83 (415)
T COG4941           8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPP--   83 (415)
T ss_pred             HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCCh--
Confidence            33444444444444455666656679999999986555443332222  24677777788888888777653222111  


Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHH
Q 008352          411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQ  490 (569)
Q Consensus       411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~  490 (569)
                                               |+.                    ++      . ++.+..+.      +.+++...
T Consensus        84 -------------------------el~--------------------~~------~-e~~e~~~a------~~~~d~~i  105 (415)
T COG4941          84 -------------------------ELL--------------------LS------D-EDEEMEEA------EALDDEHI  105 (415)
T ss_pred             -------------------------hhc--------------------cc------c-cchhhhcc------cccccccc
Confidence                                     110                    00      0 00000000      00111111


Q ss_pred             HHHHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          491 KQLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       491 ~~el~e~L~~aL-~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      .++....|.-|. -.|++.+|--|.||..    .|+|..|||..|=|+..++-|.+.||.++++..
T Consensus       106 ~Dd~LRLiFvccHPal~~~~riALtLR~v----~GLs~~eIArAFLv~e~am~QRivRAK~ri~~a  167 (415)
T COG4941         106 RDDRLRLIFVCCHPALPPEQRIALTLRLV----GGLSTAEIARAFLVPEAAMAQRIVRAKARIREA  167 (415)
T ss_pred             chhhHHhhhhhcCCCCChhhHHHHHHHHH----cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence            112222333333 5699999999999998    799999999999999999999999999999974

>PRK10403 transcriptional regulator NarP; Provisional

Probab=95.92  E-value=0.014  Score=55.01  Aligned_cols=46  Identities=15%  Similarity=0.230  Sum_probs=42.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|.+|+.+..     +++|.+|||+.+|+|..||+....++++||.
T Consensus       152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~  197 (215)
T PRK10403        152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLN  197 (215)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence            459999999998765     6899999999999999999999999999984

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=95.50  E-value=0.028  Score=53.25  Aligned_cols=47  Identities=21%  Similarity=0.320  Sum_probs=42.8

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      +..|+++|++|+.+..     .+.+.+|||+.+++|..||+....+.++||.
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            3569999999999877     6889999999999999999999999999994

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.50  E-value=0.021  Score=53.72  Aligned_cols=46  Identities=20%  Similarity=0.255  Sum_probs=42.4

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|++|+.+..     ++++.++||+.+|+|..+|+....+.++||.
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            469999999999866     5799999999999999999999999999985

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.47  E-value=0.029  Score=53.02  Aligned_cols=45  Identities=24%  Similarity=0.242  Sum_probs=40.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .|+++|..|+.+..     +++|.+|||+.+++|..||+....++++||.
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            48999999988654     6799999999999999999999999999995

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.24  E-value=0.035  Score=63.63  Aligned_cols=55  Identities=13%  Similarity=0.070  Sum_probs=45.6

Q ss_pred             HhcCCHHHHHHHHHHhccc---CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          502 LTLLNPKERCIVRLRFGIE---DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~---d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      ...|+++|+++|..-|..+   -..+-|.+|||+.||||+.|+.+++.+|.+||=..+
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            4689999999999988721   113349999999999999999999999999996543

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.24  E-value=0.03  Score=66.21  Aligned_cols=46  Identities=11%  Similarity=0.172  Sum_probs=43.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|++|+.+..     +|+|.+|||+.|+||..||+..+++.++||.
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            349999999999976     7999999999999999999999999999995

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=95.05  E-value=0.03  Score=39.56  Aligned_cols=27  Identities=30%  Similarity=0.643  Sum_probs=19.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ++|.+|||+.+|+|+|+|.    |++++|++
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            4799999999999999998    55566654

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein

Probab=94.81  E-value=0.12  Score=42.17  Aligned_cols=56  Identities=18%  Similarity=0.287  Sum_probs=44.8

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhh----C--CCCCHHHHHHHHHHHHHHhhhhcC
Q 008352          319 LKSELHSGNSSREKLINANLRLVVHVAKQYQ----G--RGISLHDLLQEGSMGLMKSVEKFK  374 (569)
Q Consensus       319 L~~~l~~G~~Are~LI~~nlrLV~sIArry~----~--~g~~~EDLIQEG~IGLirAiekFD  374 (569)
                      +..+..|+..|.++++..|.+++.+.+.+-.    +  ++.--+|+-|+-...|++++-+|+
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            3444556669999999999999999998722    2  233349999999999999999996

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

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=94.64  E-value=0.07  Score=46.26  Aligned_cols=38  Identities=13%  Similarity=0.239  Sum_probs=31.5

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  545 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie  545 (569)
                      +..|++| ..|+.+.-     .|+|..|||+.+|||+.||..+.
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            3458899 77877754     57999999999999999999843

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

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

Probab=94.56  E-value=0.1  Score=39.37  Aligned_cols=42  Identities=17%  Similarity=0.226  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      |++.++.||..-+-   ..+.|..|||+.+|+|..+|++++++-.
T Consensus         1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L~   42 (48)
T PF13412_consen    1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKLE   42 (48)
T ss_dssp             --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            57788888876553   3569999999999999999997766543

...

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=94.51  E-value=0.093  Score=40.82  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=42.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      .|+..++-++.+.|.   -.+.++++||..+|||+.+|.++.+..+.-|...+
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            578888888887664   26899999999999999999999999988876643

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=94.38  E-value=0.2  Score=46.52  Aligned_cols=56  Identities=16%  Similarity=0.315  Sum_probs=46.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352          494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  551 (569)
Q Consensus       494 l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK  551 (569)
                      ..+.|...++.|.+.++.||.+||+  ...++|..+||..|+|+..+++.....-...
T Consensus        71 ~k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~~  126 (130)
T PF05263_consen   71 QKEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKND  126 (130)
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHHH
Confidence            3466788889999999999999998  3346999999999999999998776554443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=94.25  E-value=0.039  Score=41.79  Aligned_cols=32  Identities=28%  Similarity=0.361  Sum_probs=22.8

Q ss_pred             HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       512 VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      ||.+..     +|+|..+||+.||||+.+|+++.++-
T Consensus        10 ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~   41 (50)
T PF13384_consen   10 IIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY   41 (50)
T ss_dssp             HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred             HHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence            555554     58999999999999999999987663

>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=94.14  E-value=0.075  Score=43.39  Aligned_cols=44  Identities=18%  Similarity=0.405  Sum_probs=29.6

Q ss_pred             hcCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 008352          503 TLLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLS-KERVRQLES  546 (569)
Q Consensus       503 ~~L~~rER~VL~L--RygL~d~e~~Tl~EIAe~LGIS-rerVRqie~  546 (569)
                      ..|+++|++||..  .|.-..|-+-|..|||+.||++ ..+|.+.+.
T Consensus         2 ~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen    2 KELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             ----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            5799999999987  3333356788999999999997 999987654

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=94.08  E-value=0.07  Score=56.52  Aligned_cols=36  Identities=22%  Similarity=0.344  Sum_probs=33.0

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      +|-.|+|.    +++|..|||++|||||.+|.+++.+|++
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            46778888    9999999999999999999999999976

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=93.50  E-value=0.44  Score=43.74  Aligned_cols=53  Identities=19%  Similarity=0.137  Sum_probs=48.2

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      |..-.+.+-.+|.++|.    .++|...||..+++|...||+...+|-.-+..++.-
T Consensus        60 L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~  112 (125)
T PF06530_consen   60 LKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSM  112 (125)
T ss_pred             HHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHH
Confidence            45578999999999999    899999999999999999999999999999887643

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

>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=93.46  E-value=0.17  Score=33.77  Aligned_cols=36  Identities=19%  Similarity=0.335  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL  544 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqi  544 (569)
                      +++.++..+...|.    .+.+..+||+.+|+|+.+|..+
T Consensus         6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence            45555655555554    5779999999999999999865

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

>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=93.41  E-value=0.1  Score=39.26  Aligned_cols=33  Identities=24%  Similarity=0.296  Sum_probs=23.9

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          509 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       509 ER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      ..+|+.|+-     +|+|..+||+.+|||+.||..++.
T Consensus        11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence            345666664     679999999999999999998753

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 ....

>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=93.14  E-value=0.18  Score=41.65  Aligned_cols=36  Identities=31%  Similarity=0.632  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHH
Q 008352          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  322 (569)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~  322 (569)
                      ++.+++.+|+..+||+||.+|.|+.+|++.+.+...
T Consensus         5 ~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~   40 (78)
T PF04539_consen    5 KIERARRELEQELGREPTDEEIAEELGISVEEVREL   40 (78)
T ss_dssp             HHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHH
Confidence            466788999999999999999999999998877543

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 ....

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=92.78  E-value=1.6  Score=49.18  Aligned_cols=130  Identities=17%  Similarity=0.282  Sum_probs=70.5

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHH-HHHH
Q 008352          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQE-GSMG  365 (569)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQE-G~IG  365 (569)
                      ++.+++.+|...+|++||.+|.|..+|++.+.+.....                   ++    ...+++++.+.+ +...
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-------------------~~----~~~~SLD~~i~~d~~~~  415 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK-------------------YN----REPISLDKTIGKEGDSQ  415 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-------------------hc----CCCcccccccccCCccc
Confidence            35567788888999999999999999998877643211                   01    112222222211 1111


Q ss_pred             HHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCH
Q 008352          366 LMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITV  445 (569)
Q Consensus       366 LirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~  445 (569)
                      +...+.  |+........+.....+..+..++.      .||..-...+..      .+.-..+.+-|..|||..+||+.
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            222221  1111122333344445555555553      233322222211      11111246789999999999999


Q ss_pred             HHHHHHHH
Q 008352          446 EKLERLIF  453 (569)
Q Consensus       446 e~v~~ll~  453 (569)
                      ++|+++..
T Consensus       482 ERVRQIe~  489 (509)
T PRK05901        482 ERIRQIES  489 (509)
T ss_pred             HHHHHHHH
Confidence            99999854

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

Probab=92.67  E-value=1.5  Score=44.03  Aligned_cols=33  Identities=33%  Similarity=0.579  Sum_probs=28.1

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (569)
Q Consensus       288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~  320 (569)
                      +.++...+...+|++||.+|.|...|++.+.+.
T Consensus        89 ~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~  121 (238)
T TIGR02393        89 LIKAERQLTQELGREPTDEELAERMGMPAEKVR  121 (238)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            445667788889999999999999999987774

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=92.53  E-value=1.7  Score=46.89  Aligned_cols=129  Identities=19%  Similarity=0.278  Sum_probs=71.6

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH-HHHH
Q 008352          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG-SMGL  366 (569)
Q Consensus       288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG-~IGL  366 (569)
                      +.+...+|...+|++||.+|.|...|++.+.+...+..                   +..    .+++++.+.++ -..|
T Consensus       218 ~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~-------------------~~~----~~SLd~~~~~~~~~~l  274 (367)
T PRK09210        218 LIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI-------------------AQE----PVSLETPIGEEDDSHL  274 (367)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------hcC----CCCcCCCCCCCCcchh
Confidence            45567778888999999999999999998777543211                   111    11111111110 0111


Q ss_pred             HHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHH
Q 008352          367 MKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVE  446 (569)
Q Consensus       367 irAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e  446 (569)
                      ...+.  |..............++..+.++|.      .+|..-...+..      .+.-..|.+-|.+|||+.+|++.+
T Consensus       275 ~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~l------rygl~~~~~~tl~EIa~~lgvs~e  340 (367)
T PRK09210        275 GDFIE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLRL------RFGLDDGRTRTLEEVGKVFGVTRE  340 (367)
T ss_pred             hhhcc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHHH------HhccCCCCCccHHHHHHHHCCCHH
Confidence            11111  2111223444455566666666664      234322222211      111123467899999999999999


Q ss_pred             HHHHHHH
Q 008352          447 KLERLIF  453 (569)
Q Consensus       447 ~v~~ll~  453 (569)
                      +|+++..
T Consensus       341 rVrQi~~  347 (367)
T PRK09210        341 RIRQIEA  347 (367)
T ss_pred             HHHHHHH
Confidence            9998854

>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=92.27  E-value=0.38  Score=35.88  Aligned_cols=40  Identities=35%  Similarity=0.460  Sum_probs=27.5

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      |++-.+.||..--.  | ...|+.+||+.+|+|..+|.+++.+
T Consensus         1 lD~~D~~Il~~Lq~--d-~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    1 LDELDRKILRLLQE--D-GRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--c-CCccHHHHHHHHCcCHHHHHHHHHH
Confidence            34556677766443  2 5789999999999999999987764

...

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=92.25  E-value=2.4  Score=45.20  Aligned_cols=34  Identities=32%  Similarity=0.460  Sum_probs=28.9

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (569)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~  320 (569)
                      ++.+++.+|...+|++||.+|.|..+|++.+.+.
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~  207 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIA  207 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            4556777888899999999999999999987764

>PHA00675 hypothetical protein

Probab=92.22  E-value=0.26  Score=41.53  Aligned_cols=40  Identities=18%  Similarity=0.089  Sum_probs=31.5

Q ss_pred             hcCCHHHHHHHHHHh-cccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRF-GIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       503 ~~L~~rER~VL~LRy-gL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      ..|++.+-+.|+.++ -    .+.|+.+||+.||||+.+|.+|..
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

>PF13730 HTH_36: Helix-turn-helix domain

Probab=92.14  E-value=0.49  Score=36.44  Aligned_cols=47  Identities=19%  Similarity=0.289  Sum_probs=34.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCC---CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPK---SLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~---Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .|++.++.|+..-..+.++.+.   |.+.||+.+|+|+.||+    ++++.|.+
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            5888888887765544332222   89999999999999998    45555543

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=91.83  E-value=0.32  Score=48.34  Aligned_cols=48  Identities=15%  Similarity=0.070  Sum_probs=36.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  551 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK  551 (569)
                      .|+++|.+++.....=..++|+|.+|||+.||+|..||+....++...
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            488999877644331112378999999999999999999999887543

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=91.58  E-value=0.48  Score=42.96  Aligned_cols=49  Identities=20%  Similarity=0.310  Sum_probs=41.8

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +..|++.+..-|....-    ..=+++|+++.||||-.|||.++.+.+.+|.-
T Consensus        31 ~~~L~~E~~~Fi~~Fi~----~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   31 FARLSPEQLEFIKLFIK----NRGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hhcCCHHHHHHHHHHHH----hcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            57899988887766554    33499999999999999999999999999975

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

Probab=91.37  E-value=5.7  Score=40.86  Aligned_cols=147  Identities=18%  Similarity=0.195  Sum_probs=80.2

Q ss_pred             HHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHhccHHHHHHHHH
Q 008352          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (569)
Q Consensus       256 ~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~~G~~Are~LI~  335 (569)
                      .+..||++-.  +.--+.--.+++.+      +..+..+|+..+|++||..|.|+..|++.+++...+          ..
T Consensus        88 ei~d~LR~~~--~v~vpR~~~~~~~~------i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~----------~~  149 (247)
T COG1191          88 EILDYLRKND--SVKVPRSLRELGRR------IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEAL----------LA  149 (247)
T ss_pred             HHHHHHHhCC--CccCcHHHHHHHHH------HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHH----------HH
Confidence            4566888877  11122333444444      445778899999999999999999999988775433          22


Q ss_pred             HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHH
Q 008352          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS  415 (569)
Q Consensus       336 ~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~  415 (569)
                      .|.....++--.....+...              +   +...+..+..+-.|-..+.+..++..      +|..-...  
T Consensus       150 ~~~~~~~sld~~~~~~~d~~--------------~---~~~~~~~~~~~~~~~~~~~l~~ai~~------L~EREk~V--  204 (247)
T COG1191         150 INGSQLLSLDEDVLKDDDDD--------------V---DDQIENPDDGVEKEELLEILKEAIEP------LPEREKLV--  204 (247)
T ss_pred             hccccccchhhhhccccccc--------------h---hhccccchhHHHHHHHHHHHHHHHHc------cCHHHHHH--
Confidence            22222222222221111110              1   11122234445555555666655541      22211100  


Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIF  453 (569)
Q Consensus       416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~  453 (569)
                              +.....-+-|..|||+.||++..+|.++..
T Consensus       205 --------l~l~y~eelt~kEI~~~LgISes~VSql~k  234 (247)
T COG1191         205 --------LVLRYKEELTQKEIAEVLGISESRVSRLHK  234 (247)
T ss_pred             --------HHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence                    111112256789999999999999988754

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=91.27  E-value=0.27  Score=52.29  Aligned_cols=37  Identities=22%  Similarity=0.258  Sum_probs=32.4

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  551 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK  551 (569)
                      ++-.++|.    +++|..|||++||||+.+|+.++.+|+++
T Consensus        17 ~~A~lYY~----~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~   53 (321)
T COG2390          17 RAAWLYYV----EGLTQSEIAERLGISRATVSRLLAKAREE   53 (321)
T ss_pred             HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            35667887    99999999999999999999999988753

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=90.90  E-value=4.9  Score=44.32  Aligned_cols=37  Identities=22%  Similarity=0.399  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHH
Q 008352          416 KVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLI  452 (569)
Q Consensus       416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll  452 (569)
                      .+.+.+..+..++|+.||.+|.|..+|+++..++..+
T Consensus       112 ~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l  148 (415)
T PRK07598        112 RLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL  148 (415)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence            3455667888999999999999988887766666554

>PF13518 HTH_28: Helix-turn-helix domain

Probab=90.79  E-value=0.43  Score=36.03  Aligned_cols=28  Identities=25%  Similarity=0.336  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      ++.|+.+||+.+|||+.+|+++..+-..
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~~y~~   38 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIKRYRE   38 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence            4569999999999999999988766543

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=90.57  E-value=0.29  Score=57.45  Aligned_cols=45  Identities=18%  Similarity=0.100  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      -|+.||++|+.+.|     .|+|.+|||+.+.||-.||+....+...||.
T Consensus       831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLg  875 (894)
T COG2909         831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLG  875 (894)
T ss_pred             CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            38999999999999     6999999999999999999999999999995

>smart00351 PAX Paired Box domain

Probab=90.32  E-value=0.7  Score=42.31  Aligned_cols=42  Identities=14%  Similarity=0.051  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      ++..+|.=|...|-    ++.+..+||+.||||+.+|..+.++...
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            45545554445554    6889999999999999999999988643

>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=90.21  E-value=0.57  Score=37.46  Aligned_cols=26  Identities=19%  Similarity=0.331  Sum_probs=23.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      +|++..|||+.||+++.+|.....+-
T Consensus        12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   12 QGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            79999999999999999999987763

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>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=90.08  E-value=0.62  Score=36.42  Aligned_cols=44  Identities=23%  Similarity=0.270  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      .|++.+..||..-+.- ++.+.|..|||+.+|+++.+|.+++++-
T Consensus         2 glt~~q~~vL~~l~~~-~~~~~t~~~la~~l~~~~~~vs~~v~~L   45 (62)
T PF12802_consen    2 GLTPSQFRVLMALARH-PGEELTQSELAERLGISKSTVSRIVKRL   45 (62)
T ss_dssp             TSTHHHHHHHHHHHHS-TTSGEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4778888888776652 2234899999999999999998766543

...

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

Probab=89.99  E-value=4.3  Score=43.58  Aligned_cols=33  Identities=24%  Similarity=0.326  Sum_probs=29.5

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDL  285 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~  285 (569)
                      ....+..|+..+...|+||++||.+|+.+++.+
T Consensus        65 ~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g   97 (342)
T COG0568          65 PAGRLSFYIRAIEAAPLLTPEEEKALARRLKRG   97 (342)
T ss_pred             hhhhHHHHHHHHhhhcccChHHHHHHHHHHHcC
Confidence            345678899999999999999999999999987

>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=89.99  E-value=0.38  Score=37.59  Aligned_cols=40  Identities=20%  Similarity=0.305  Sum_probs=26.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|+..|+.=|.-+|-    .|.+..+||..|||++.||+.+...
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            466666654444454    6779999999999999999999876

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=89.69  E-value=0.59  Score=35.98  Aligned_cols=39  Identities=21%  Similarity=0.417  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          508 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       508 rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      |++.||.+-+  ..+.+.|.+|||+.||||+.||+..++..
T Consensus         1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~L   39 (55)
T PF08279_consen    1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKEL   39 (55)
T ss_dssp             HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred             CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence            4556666542  23356999999999999999998665543

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 ....

>PHA02591 hypothetical protein; Provisional

Probab=88.98  E-value=0.76  Score=38.90  Aligned_cols=24  Identities=21%  Similarity=0.436  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .|+|.++||+.||+|.++||+...
T Consensus        58 qGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         58 KGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHh
Confidence            689999999999999999999865

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=88.92  E-value=17  Score=38.39  Aligned_cols=178  Identities=12%  Similarity=0.132  Sum_probs=92.8

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhH
Q 008352          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENI  410 (569)
Q Consensus       331 e~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~  410 (569)
                      ++-+...+..+..++.+.     .+.+-+.|....+++.+..-..-+|.....++.-.|.-+++    .           
T Consensus       119 er~l~~a~~~I~~~~~~L-----~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR----~-----------  178 (310)
T PRK00423        119 ERNLAFALSELDRIASQL-----GLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR----R-----------  178 (310)
T ss_pred             hHHHHHHHHHHHHHHHHc-----CCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH----H-----------
Confidence            334444556666666655     23366777777888877666667786665555544443332    1           


Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh-hcccCCCCCChhHHH
Q 008352          411 YTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ-EITADTGVEIPDISV  489 (569)
Q Consensus       411 ~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~-d~i~D~~~~~pee~l  489 (569)
                                       .+-+-|..||+..++++..++..........+.++.+..  +-..+. .+...-..  +....
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                             233567888999999998888765443322222222211  111111 11111111  11111


Q ss_pred             HHHHHHHHHHHHHh-cC----CHH--HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          490 QKQLMRQHVRNLLT-LL----NPK--ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       490 ~~~el~e~L~~aL~-~L----~~r--ER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                      .  .....+..+.+ .|    +|.  =--+|.+-.-+. |.+.|++|||...||+..+|++..+.-.+.|
T Consensus       238 ~--~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l  304 (310)
T PRK00423        238 K--KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKL  304 (310)
T ss_pred             H--HHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence            1  11122222221 11    111  111222221122 3789999999999999999998777666654

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=88.87  E-value=0.59  Score=44.63  Aligned_cols=50  Identities=14%  Similarity=0.050  Sum_probs=43.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS-----KERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGIS-----rerVRqie~RALkKLR~  554 (569)
                      .|+++|.+|+.+-.. +.|.++|.+||++.++.+     ..+|+....+.++||..
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (228)
T PRK11083        154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA  208 (228)
T ss_pred             ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence            599999999988764 445689999999999986     78999999999999974

>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=88.87  E-value=0.75  Score=37.16  Aligned_cols=25  Identities=24%  Similarity=0.481  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      ..+++.+||+.||||..+||....+
T Consensus        21 g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   21 GKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHhhh
Confidence            6899999999999999999987554

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 [].

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=88.74  E-value=0.88  Score=39.24  Aligned_cols=45  Identities=29%  Similarity=0.339  Sum_probs=34.4

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh--CCCHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF--GLSKERVRQLESRAL  549 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L--GISrerVRqie~RAL  549 (569)
                      ++.||+..+++..+|.-   ....|+.|+|+.|  .||++.|..+..+..
T Consensus        35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~   81 (85)
T PF02650_consen   35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKLK   81 (85)
T ss_dssp             GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHHH
Confidence            57899999999999875   3789999999999  999999987766543

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=88.11  E-value=1.2  Score=33.47  Aligned_cols=37  Identities=27%  Similarity=0.390  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      |.-.+|+.+-..    .+++..||++.+|+|+.+|++.++.
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            334455555444    6899999999999999999987654

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 ....

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=87.83  E-value=3.8  Score=41.88  Aligned_cols=33  Identities=24%  Similarity=0.395  Sum_probs=26.6

Q ss_pred             HHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352          289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (569)
Q Consensus       289 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~  321 (569)
                      ......|...+|++|+.+|.|+..|++.+.+..
T Consensus       113 ~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~  145 (257)
T PRK05911        113 ADAMDSLRQSLGKEPTDGELCEYLNISQQELSG  145 (257)
T ss_pred             HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence            345556777889999999999999998877643

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=87.72  E-value=1.5  Score=44.76  Aligned_cols=33  Identities=30%  Similarity=0.510  Sum_probs=28.3

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (569)
Q Consensus       288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~  320 (569)
                      +.++..+|...+|++||.+|.|+..|++.+++.
T Consensus       115 ~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~  147 (256)
T PRK07408        115 AKKVRQELRQELGRQPTDQEIAQALDISLEEWQ  147 (256)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHH
Confidence            455677888899999999999999999987764

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=87.70  E-value=0.81  Score=36.69  Aligned_cols=42  Identities=17%  Similarity=0.368  Sum_probs=29.6

Q ss_pred             CCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       505 L~~rER~VL~LRygL~-d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      |++....-|...|.|. ++..-+..+||+.||||+.+|...++
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~   44 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLK   44 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHH
Confidence            4455555555555554 55789999999999999999986543

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 ....

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=87.52  E-value=0.81  Score=44.25  Aligned_cols=50  Identities=18%  Similarity=0.120  Sum_probs=44.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  554 (569)
                      .|+++|++|+.+... +.|++.|.++|++.+.     ++..+|+....+.++||..
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

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=87.10  E-value=2.2  Score=41.27  Aligned_cols=64  Identities=13%  Similarity=0.130  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 008352          335 NANLRLVVHVAKQYQGRGIS---LHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  398 (569)
Q Consensus       335 ~~nlrLV~sIArry~~~g~~---~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir  398 (569)
                      .+-+..+..++++|.-+|..   -+|.|.+|.-.+++.+..||+++...+-.|.+..+-++..+-|.
T Consensus        44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~  110 (179)
T PHA02547         44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIK  110 (179)
T ss_pred             HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHH
Confidence            33455555666665444554   48999999999999999999999877777777766666555444

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=86.97  E-value=2.1  Score=33.90  Aligned_cols=36  Identities=28%  Similarity=0.374  Sum_probs=27.4

Q ss_pred             HHHHHHHHHH-hcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          507 PKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       507 ~rER~VL~LR-ygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      |.-+.||.+- -.    .++|..|||+.+|++..+|++.++
T Consensus        10 p~R~~Il~~L~~~----~~~t~~ela~~l~~~~~t~s~hL~   46 (61)
T PF12840_consen   10 PTRLRILRLLASN----GPMTVSELAEELGISQSTVSYHLK   46 (61)
T ss_dssp             HHHHHHHHHHHHC----STBEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHhcC----CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            5556666665 33    899999999999999999986554

...

>cd00131 PAX Paired Box domain

Probab=86.75  E-value=1.7  Score=40.11  Aligned_cols=41  Identities=12%  Similarity=0.017  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      |+...|.-|...|.    +|++..+||+.||||+.+|..+.++-.
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            44444443334454    789999999999999999999888755

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=86.55  E-value=9.7  Score=41.44  Aligned_cols=34  Identities=32%  Similarity=0.584  Sum_probs=28.4

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (569)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~  320 (569)
                      ++.+....|...+|+.||.+|.|+.+|++.+.+.
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            4555677788889999999999999999987664

>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=86.27  E-value=1.6  Score=37.16  Aligned_cols=42  Identities=24%  Similarity=0.400  Sum_probs=34.4

Q ss_pred             cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLSKERVRQLE  545 (569)
Q Consensus       504 ~L~~rER~VL~LRyg--L~d~e~~Tl~EIAe~LGISrerVRqie  545 (569)
                      .|++++++||..---  ...|++-.-++||+.+|+|..|||...
T Consensus         1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M   44 (78)
T PF03444_consen    1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEM   44 (78)
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHH
Confidence            388999998876322  346789999999999999999999764

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

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=86.20  E-value=1.1  Score=42.65  Aligned_cols=49  Identities=16%  Similarity=0.180  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK  553 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR  553 (569)
                      .|+++|.+|+.+..- +.|..+|.++|++.+.     ++..+|+....+.++||.
T Consensus       149 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~  202 (219)
T PRK10336        149 TLKPKEFALLELLMR-NAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG  202 (219)
T ss_pred             ecCHHHHHHHHHHHh-CCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence            499999999987652 3446699999999996     999999999999999985

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=86.16  E-value=1.2  Score=42.31  Aligned_cols=49  Identities=18%  Similarity=0.233  Sum_probs=41.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK  553 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR  553 (569)
                      .|+++|.+|+.+... +.|...|.++|++.+.     +|..+|.....+.++||.
T Consensus       148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~  201 (221)
T PRK15479        148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ  201 (221)
T ss_pred             ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence            599999999987643 3346679999999986     999999999999999995

>PRK12423 LexA repressor; Provisional

Probab=85.77  E-value=1.4  Score=43.47  Aligned_cols=47  Identities=30%  Similarity=0.513  Sum_probs=35.3

Q ss_pred             cCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRyg--L~d~e~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~  554 (569)
                      .|++++++|+..---  ..+|-+.|..|||+.|| +|+.+|+    ++|++|++
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            489999999876332  22334679999999999 5999999    46666665

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=85.75  E-value=2.9  Score=41.60  Aligned_cols=32  Identities=38%  Similarity=0.579  Sum_probs=26.0

Q ss_pred             HHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352          290 KEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (569)
Q Consensus       290 ~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~  321 (569)
                      +....+...+|+.||.+|.|+..|++.+.+..
T Consensus       101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~  132 (231)
T TIGR02885       101 YMKEELSKELGREPTINELAEALGVSPEEIVM  132 (231)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence            34566777889999999999999998877643

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=85.73  E-value=15  Score=37.61  Aligned_cols=35  Identities=29%  Similarity=0.532  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (569)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~  321 (569)
                      ++.+....|+..+|++||.+|.|...|++.+.+..
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~  153 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNS  153 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHH
Confidence            34556677888899999999999999998776643

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=85.59  E-value=1.5  Score=34.89  Aligned_cols=42  Identities=19%  Similarity=0.315  Sum_probs=26.6

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      |+..|..||..-.  ..+.+++..+|++.+|+++.+|...+++.
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L   42 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKL   42 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4566666766554  23479999999999999999998555443

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=85.54  E-value=11  Score=38.88  Aligned_cols=34  Identities=26%  Similarity=0.524  Sum_probs=28.2

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (569)
Q Consensus       288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~  321 (569)
                      +.+...+|...+|++||.+|.|+..|++.+++..
T Consensus       129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~  162 (264)
T PRK07122        129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE  162 (264)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            4456677888899999999999999999877754

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=85.39  E-value=1.9  Score=37.61  Aligned_cols=42  Identities=29%  Similarity=0.260  Sum_probs=32.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      |++.++.||.....  + ...|..+||+.+|+|+.+|+....+-.
T Consensus         1 ld~~D~~il~~L~~--~-~~~~~~~la~~l~~s~~tv~~~l~~L~   42 (108)
T smart00344        1 LDEIDRKILEELQK--D-ARISLAELAKKVGLSPSTVHNRVKRLE   42 (108)
T ss_pred             CCHHHHHHHHHHHH--h-CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            46777888876543  2 468999999999999999997665543

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PRK05949 RNA polymerase sigma factor; Validated

Probab=85.34  E-value=12  Score=39.81  Aligned_cols=34  Identities=26%  Similarity=0.448  Sum_probs=27.7

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (569)
Q Consensus       288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~  321 (569)
                      +.+....+...+|++|+.+|.|+.+|++.+.+..
T Consensus       180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~  213 (327)
T PRK05949        180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIRE  213 (327)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            4455667778889999999999999999876643

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=85.23  E-value=0.65  Score=44.18  Aligned_cols=50  Identities=16%  Similarity=0.114  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEV-----GNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EI-----Ae~LGISrerVRqie~RALkKLR~  554 (569)
                      .|+++|.+|+.+-.. +.|+++|.++|     |+.++++..+|+....+.++||..
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 34467898888     788999999999999999999963

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.

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=84.71  E-value=2.2  Score=32.32  Aligned_cols=33  Identities=27%  Similarity=0.405  Sum_probs=26.3

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      .|+.+..     +..|.++||+.+|||-.+|+.+..+.
T Consensus        19 ~i~~~~~-----~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   19 YILKLLR-----ESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHHHHh-----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            4555544     34699999999999999999998764

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=84.36  E-value=12  Score=38.01  Aligned_cols=34  Identities=26%  Similarity=0.317  Sum_probs=27.7

Q ss_pred             HHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHH
Q 008352          289 EKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  322 (569)
Q Consensus       289 e~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~  322 (569)
                      .+...++...+|++||.+|.|+..|++.+.+...
T Consensus       123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~  156 (254)
T TIGR02850       123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA  156 (254)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            3455677788899999999999999998877543

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.

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=84.03  E-value=2.2  Score=34.85  Aligned_cols=23  Identities=17%  Similarity=0.299  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q 008352          524 PKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       524 ~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      +.|..|||+.+||++.+|++++.
T Consensus        22 ~~ta~eLa~~lgl~~~~v~r~L~   44 (68)
T smart00550       22 TSTALQLAKNLGLPKKEVNRVLY   44 (68)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHH
Confidence            59999999999999998886544

Helix-turn-helix-containing domain. Also known as Zab.

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=83.89  E-value=2  Score=36.06  Aligned_cols=45  Identities=29%  Similarity=0.341  Sum_probs=29.8

Q ss_pred             HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH-----HHHHHHHHHhhcCc
Q 008352          512 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES-----RALYRLKQSLGGKA  560 (569)
Q Consensus       512 VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~-----RALkKLR~~l~~~~  560 (569)
                      |..++--    .++|..|+|+.+|+|+.+|.++++     -.+.+|...+..-+
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     23566666555443

>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=83.86  E-value=1.4  Score=33.76  Aligned_cols=33  Identities=36%  Similarity=0.477  Sum_probs=24.3

Q ss_pred             HHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          514 RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       514 ~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .+.+.-..+.++|+.|||+.+|+++.+|..++.
T Consensus         8 iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~   40 (52)
T PF09339_consen    8 ILEALAESGGPLTLSEIARALGLPKSTVHRLLQ   40 (52)
T ss_dssp             HHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444455778999999999999999987654

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.

>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=83.85  E-value=1.4  Score=38.23  Aligned_cols=46  Identities=26%  Similarity=0.345  Sum_probs=32.4

Q ss_pred             cCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d---~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      -++|.|+.-|..|+-+-.   .+++|+.||++.+|+|..||.+ .+|+|+
T Consensus        26 L~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk   74 (87)
T PF01371_consen   26 LCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLK   74 (87)
T ss_dssp             HSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHH
Confidence            367777766665554332   1689999999999999999874 344444

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 ....

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=83.83  E-value=1.1  Score=44.16  Aligned_cols=39  Identities=18%  Similarity=0.232  Sum_probs=28.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .|+++  +|+.+.-  .+..|+|.+|||+.||||+.||+....
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            35564  5665542  122479999999999999999998875

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=83.59  E-value=11  Score=34.02  Aligned_cols=23  Identities=17%  Similarity=0.277  Sum_probs=20.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLE  545 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie  545 (569)
                      .+.|+.|||+.||||..+|...+
T Consensus        70 pd~tl~Ela~~l~Vs~~ti~~~L   92 (119)
T PF01710_consen   70 PDATLRELAERLGVSPSTIWRAL   92 (119)
T ss_pred             CCcCHHHHHHHcCCCHHHHHHHH
Confidence            78999999999999999987443

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 [].

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

Probab=83.53  E-value=19  Score=37.60  Aligned_cols=35  Identities=26%  Similarity=0.496  Sum_probs=28.2

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (569)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~  321 (569)
                      ++.+.+..+...+|++||..|.|..+|++.+.+..
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~  196 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE  196 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34455667778899999999999999999877753

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).

>PF12728 HTH_17: Helix-turn-helix domain

Probab=83.34  E-value=1.3  Score=33.67  Aligned_cols=24  Identities=17%  Similarity=0.376  Sum_probs=21.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          525 KSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       525 ~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      +|.+|+|+.||||+.+|+++..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g   25 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQG   25 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            689999999999999999988643

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=83.26  E-value=31  Score=36.00  Aligned_cols=84  Identities=23%  Similarity=0.320  Sum_probs=46.5

Q ss_pred             CCCHHHHHHHhC--CCHHHHHHHHHhcCC--CcccCCCCCCCCCcchh-hcccCCCCCChhHH--HHHHHHHHHHHHHHh
Q 008352          431 SPDKEDLARRVG--ITVEKLERLIFITRM--PLSMQQPVWADQDTTFQ-EITADTGVEIPDIS--VQKQLMRQHVRNLLT  503 (569)
Q Consensus       431 ~Pt~eEIA~~lg--is~e~v~~ll~~~~~--~~SLD~~v~~d~~~~l~-d~i~D~~~~~pee~--l~~~el~e~L~~aL~  503 (569)
                      .+++++||+.++  |+.++|++.+.....  -+-.+.    ++.-... ..+.. ..+.+...  -...++.+.-.++|+
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----DGFYKQTDKAVST-GDEVIPLAVRQYQKQMIDLAKEALD  211 (271)
T ss_pred             CCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC----CCcEEeecceeec-CCccchHHHHHHHHHHHHHHHHHHH
Confidence            567889999999  999999988763321  111111    1101011 11111 11122221  122344455677889


Q ss_pred             cCCHHHHHHHHHHhcc
Q 008352          504 LLNPKERCIVRLRFGI  519 (569)
Q Consensus       504 ~L~~rER~VL~LRygL  519 (569)
                      ..|+.+|.+=.+-+++
T Consensus       212 ~~p~~eR~~S~lT~~i  227 (271)
T TIGR02147       212 ALPPSERDVSTVTFGI  227 (271)
T ss_pred             hCCccccccceeeEec
Confidence            9999999977766664

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.

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=83.23  E-value=4.6  Score=35.11  Aligned_cols=49  Identities=18%  Similarity=0.244  Sum_probs=36.2

Q ss_pred             HhcCCHHHHHHHHHH----hccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLR----FGIE-DGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       502 L~~L~~rER~VL~LR----ygL~-d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ...+++++..||...    ||.. ...+.|..|||+.+|+++++|.    |++++|.+
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            467899999877643    3322 2368999999999999999987    55556554

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>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=83.06  E-value=1.2  Score=35.83  Aligned_cols=40  Identities=18%  Similarity=0.239  Sum_probs=30.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .|++.|..|+..-.  . ..+.|..|||+.+|+++.+|+..++
T Consensus         5 gLs~~E~~vy~~Ll--~-~~~~t~~eIa~~l~i~~~~v~~~L~   44 (68)
T PF01978_consen    5 GLSENEAKVYLALL--K-NGPATAEEIAEELGISRSTVYRALK   44 (68)
T ss_dssp             CHHHHHHHHHHHHH--H-HCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHH--H-cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            46777888775532  1 1589999999999999999985443

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=82.99  E-value=2  Score=32.72  Aligned_cols=30  Identities=37%  Similarity=0.508  Sum_probs=23.4

Q ss_pred             CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          521 DGKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       521 d~e~~-Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .|+.. |..|||+.+|+|+.+|++    ++++|.+
T Consensus        16 ~~~~l~s~~~la~~~~vs~~tv~~----~l~~L~~   46 (60)
T smart00345       16 PGDKLPSERELAAQLGVSRTTVRE----ALSRLEA   46 (60)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence            34556 899999999999999984    5555554

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=82.91  E-value=1.3  Score=33.83  Aligned_cols=22  Identities=18%  Similarity=0.356  Sum_probs=20.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q 008352          526 SLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       526 Tl~EIAe~LGISrerVRqie~R  547 (569)
                      |++|||+..|||..||+..++.
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~   22 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNG   22 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTT
T ss_pred             CHHHHHHHHCcCHHHHHHHHhC
Confidence            7899999999999999988764

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=82.63  E-value=1.8  Score=41.64  Aligned_cols=50  Identities=14%  Similarity=0.087  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEV--GNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EI--Ae~LGISrerVRqie~RALkKLR~  554 (569)
                      .|+++|.+||.+..- +.|..+|.++|  +..++++..+|+....+.++||..
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            499999999988662 22355699999  888999999999999999999973

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=82.52  E-value=4.8  Score=37.30  Aligned_cols=53  Identities=21%  Similarity=0.290  Sum_probs=41.3

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +.+..++-.|++.+-+|+..-.  ..+.++|..|||+.+|++++||.    ||+++|=.
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            3566778899999999887654  12368999999999999999986    66666643

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=82.49  E-value=2.7  Score=35.02  Aligned_cols=52  Identities=19%  Similarity=0.247  Sum_probs=35.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhc-ccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          495 RQHVRNLLTLLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       495 ~e~L~~aL~~L~~rER~VL~LRyg-L~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .+.|......|++.|+.|..+-.- ..+-..+|..|||+..|||..+|-+..+
T Consensus         4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~k   56 (77)
T PF01418_consen    4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCK   56 (77)
T ss_dssp             HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHH
Confidence            456777889999999998765332 0012579999999999999999986543

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.

>TIGR00498 lexA SOS regulatory protein LexA

Probab=82.39  E-value=2.1  Score=41.79  Aligned_cols=44  Identities=18%  Similarity=0.279  Sum_probs=34.3

Q ss_pred             hcCCHHHHHHHHHHhc--ccCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLS-KERVRQLES  546 (569)
Q Consensus       503 ~~L~~rER~VL~LRyg--L~d~e~~Tl~EIAe~LGIS-rerVRqie~  546 (569)
                      ..|+++|++||.+-.-  ..++.+.|..|||+.+|++ +.+|+.++.
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~   48 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLK   48 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHH
Confidence            3589999999987552  2245678999999999998 999985443

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.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=82.36  E-value=2.8  Score=39.47  Aligned_cols=41  Identities=15%  Similarity=0.276  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.++.||..--.  | ...|+.|||+.+|+|+.+|+.+.++
T Consensus         6 ~lD~~D~~Il~~Lq~--d-~R~s~~eiA~~lglS~~tV~~Ri~r   46 (153)
T PRK11179          6 QIDNLDRGILEALME--N-ARTPYAELAKQFGVSPGTIHVRVEK   46 (153)
T ss_pred             ccCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            377888888876543  2 5789999999999999999976654

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=82.28  E-value=19  Score=38.15  Aligned_cols=34  Identities=26%  Similarity=0.522  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHH
Q 008352          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK  320 (569)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~  320 (569)
                      ++.+....+...+|+.||.+|.|..+|++.+.+.
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~  202 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR  202 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            3556677788889999999999999999876664

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=82.28  E-value=21  Score=28.41  Aligned_cols=74  Identities=22%  Similarity=0.255  Sum_probs=45.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHH
Q 008352          431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKER  510 (569)
Q Consensus       431 ~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER  510 (569)
                      +++.++||+.+|++...+..++.....                         .++.+.+..    ..+           .
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f~~~~~-------------------------~s~~~~~~~----~r~-----------~   40 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFKKETG-------------------------TTPKQYLRD----RRL-----------E   40 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHhC-------------------------cCHHHHHHH----HHH-----------H
Confidence            368899999999999999887653210                         012111111    011           1


Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCC-CHHHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGL-SKERVRQLESRA  548 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGI-SrerVRqie~RA  548 (569)
                      .++.+..   . .+.++.+||..+|+ +.....+..++.
T Consensus        41 ~a~~~l~---~-~~~~~~~ia~~~g~~s~~~f~r~Fk~~   75 (84)
T smart00342       41 RARRLLR---D-TDLSVTEIALRVGFSSQSYFSRAFKKL   75 (84)
T ss_pred             HHHHHHH---c-CCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence            2222222   1 36899999999999 988887766543

>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=82.27  E-value=2.6  Score=32.71  Aligned_cols=42  Identities=24%  Similarity=0.384  Sum_probs=29.9

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      |+..|-.||..-+-   ..+.|..|||+.+|+++.+|.++.++-.
T Consensus         1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L~   42 (59)
T PF01047_consen    1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRLE   42 (59)
T ss_dssp             STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence            45566666666543   2569999999999999999987665543

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 ....

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=82.26  E-value=26  Score=36.61  Aligned_cols=25  Identities=20%  Similarity=0.337  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHh
Q 008352          430 HSPDKEDLARRVGITVEKLERLIFI  454 (569)
Q Consensus       430 r~Pt~eEIA~~lgis~e~v~~ll~~  454 (569)
                      ..-|.+|||+.+|++.++|.++...
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~  268 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEAR  268 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4678999999999999999988653

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=82.14  E-value=2.5  Score=39.71  Aligned_cols=27  Identities=26%  Similarity=0.208  Sum_probs=24.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      +|+|.+|||++||||..+|...+++-.
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

>CHL00148 orf27 Ycf27; Reviewed

Probab=82.03  E-value=1.8  Score=41.85  Aligned_cols=50  Identities=18%  Similarity=0.115  Sum_probs=42.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-------GLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L-------GISrerVRqie~RALkKLR~  554 (569)
                      .|+++|.+|+.+... +.|+++|.+||++.+       +++..+|..+..+.++||..
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 345789999999999       48999999999999999974

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=81.49  E-value=3.6  Score=32.10  Aligned_cols=39  Identities=21%  Similarity=0.242  Sum_probs=25.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .|++-||--|....-    .|+++.|||..+|-|+..|+..++
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            467777776666555    589999999999999999997653

>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=81.36  E-value=4.7  Score=32.90  Aligned_cols=38  Identities=29%  Similarity=0.503  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 008352          416 KVLEAKRLYIQEGNHSPDKEDLARRVGIT-VEKLERLIF  453 (569)
Q Consensus       416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgis-~e~v~~ll~  453 (569)
                      +|-.....+..+.|..||..|||+.+|+. ...|...+.
T Consensus        10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen   10 EVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             HHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            34444556677889999999999999997 888887765

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.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=81.27  E-value=24  Score=35.77  Aligned_cols=34  Identities=24%  Similarity=0.375  Sum_probs=27.5

Q ss_pred             HHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHH
Q 008352          288 LEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS  321 (569)
Q Consensus       288 le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~  321 (569)
                      +++....+...+|++|+..++|+..|++.+.+..
T Consensus       111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~  144 (251)
T PRK07670        111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEA  144 (251)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHH
Confidence            3445566777889999999999999999877754

>TIGR01764 excise DNA binding domain, excisionase family

Probab=81.18  E-value=1.8  Score=31.70  Aligned_cols=24  Identities=25%  Similarity=0.407  Sum_probs=21.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          525 KSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       525 ~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      +|.+|+|+.||||+.+|+++.+..
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            589999999999999999988654

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>PRK00215 LexA repressor; Validated

Probab=80.55  E-value=3  Score=40.89  Aligned_cols=45  Identities=24%  Similarity=0.304  Sum_probs=34.5

Q ss_pred             cCCHHHHHHHHHHh--cccCCCCCCHHHHHHHhCC-CHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRF--GIEDGKPKSLSEVGNIFGL-SKERVRQLESRA  548 (569)
Q Consensus       504 ~L~~rER~VL~LRy--gL~d~e~~Tl~EIAe~LGI-SrerVRqie~RA  548 (569)
                      .|+++|++||.+-.  ....+.+.|+.|||+.+|+ ++.+|..++.+-
T Consensus         1 ~lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L   48 (205)
T PRK00215          1 MLTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKAL   48 (205)
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence            37889999987543  2334578899999999999 999998765543

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=80.51  E-value=2  Score=31.22  Aligned_cols=25  Identities=16%  Similarity=0.300  Sum_probs=22.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          525 KSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       525 ~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      +|..|+|+.+|||+.+|+.......
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~   25 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGK   25 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence            5889999999999999999988754

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=80.36  E-value=6.9  Score=36.91  Aligned_cols=61  Identities=20%  Similarity=0.351  Sum_probs=34.8

Q ss_pred             HHHHHhcCCHHHHHHHHHH----hcccCCCCCCHHHHHHHhCCCHHHHHHHHH--HHHHHHHHHhhc
Q 008352          498 VRNLLTLLNPKERCIVRLR----FGIEDGKPKSLSEVGNIFGLSKERVRQLES--RALYRLKQSLGG  558 (569)
Q Consensus       498 L~~aL~~L~~rER~VL~LR----ygL~d~e~~Tl~EIAe~LGISrerVRqie~--RALkKLR~~l~~  558 (569)
                      +..+=..|++.|+....+.    |-..+|+.+|+.|||+.+||++.+.-++..  ++.....+.+..
T Consensus         4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~   70 (142)
T PF13022_consen    4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELAD   70 (142)
T ss_dssp             HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHH
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHH
Confidence            4455578999988843332    212234789999999999999999998874  334444444333

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=80.22  E-value=2.9  Score=40.89  Aligned_cols=34  Identities=26%  Similarity=0.293  Sum_probs=27.4

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          509 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       509 ER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      ++.|..++-     +|+|..+||+.||||+.||.++.+.
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            345666543     5799999999999999999988763

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	569
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		3e-45
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		3e-45
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		4e-45
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		7e-44
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		6e-43
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		6e-43
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		6e-43
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		2e-26
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		3e-26
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		1e-20
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		1e-17
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		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		7e-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		9e-07
1ku3_A	73	Crystal Structure Of Thermus Aquaticus Rna Polymera		1e-06
1tlh_B	81	T4 Asia Bound To Sigma70 Region 4 Length = 81		2e-06
3t72_q	99	Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna		3e-06
3n97_A	72	Rna Polymerase Alpha C-Terminal Domain (E. Coli) An		3e-06
2p7v_B	68	Crystal Structure Of The Escherichia Coli Regulator		2e-05

>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: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 431
           KF+ + G +F++YA WW+RQ I ++I   +RTIR+P ++   ++K+    R  +QE    
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 432 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 491
           P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+D+   +   DT +E+P  S   
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT 537
Query: 492 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 551
           + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +
Sbjct: 538 ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 597
Query: 552 LK 553
           L+
Sbjct: 598 LR 599

>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: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 311 AIGLS------------CRDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISL 355
            +G +             ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S 
Sbjct: 59  ILGTARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSF 118
Query: 356 HDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLS 415
            DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +RTIR+P ++   ++
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETIN 178
Query: 416 KVLEAKRLYIQEGNHSPDKEDLARRV--GITVEKLERLIFITRMPLSMQQPVWADQDTTF 473
           K+    R   QE    P  E++A  +  G   +++E  + I + P+S++ P+  ++D+ +
Sbjct: 179 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFY 238
Query: 474 QEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 533
            +   D  +  P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  
Sbjct: 239 GDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAY 298
Query: 534 FGLSKERVRQLESRALYRLK 553
           FG+++ER+RQ+E++AL +LK
Sbjct: 299 FGVTRERIRQIENKALRKLK 318

>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: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS 431
           KF+ + G +F++YA WW+RQ I ++I   +RTIR+P ++   ++K+    R  +QE    
Sbjct: 418 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRE 477
Query: 432 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQK 491
           P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+D+   +   DT +E+P  S   
Sbjct: 478 PTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATT 537
Query: 492 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 551
           + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +
Sbjct: 538 ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRK 597
Query: 552 LK 553
           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 = 7e-44,   Method: Compositional matrix adjust.
 Identities = 106/335 (31%), Positives = 188/335 (56%), Gaps = 38/335 (11%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 93  SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 149
Query: 311 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 340
            +G +                            ++LK  LH    G ++R+ LI ANLRL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 341 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400
           VV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI--TVEKLERLIFITRMP 458
           +RTIR+P ++   ++K+    R   QE    P  E++A  +G     +++E  + I + P
Sbjct: 270 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 329
Query: 459 LSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFG 518
           +S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+ L+ +E  +++LR G
Sbjct: 330 VSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKG 389
Query: 519 IEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           + 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 = 6e-43,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 443
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 444 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 503
             +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
            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 = 6e-43,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 443
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 444 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 503
             +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
            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 =  172 bits (435), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 149/230 (64%), Gaps = 2/230 (0%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYA 385
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 386 YWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGI-- 443
            WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A  +G   
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 444 TVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLT 503
             +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 379
Query: 504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
            L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK
Sbjct: 380 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 429

>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase Sigma Subunit Fragment Containing Regions 1.2 To 3.1 Length = 241

Iteration: 1
 Score =  117 bits (292), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 60/150 (40%), Positives = 97/150 (64%), Gaps = 5/150 (3%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 92  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 151
Query: 374 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 433
           + +   +F++YA WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P 
Sbjct: 152 EYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPS 211
Query: 434 KEDLARRV--GITVEKLERLIFITRMPLSM 461
            E++A  +  G   +++E  + I + P+S+
Sbjct: 212 YEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241

>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2 Complexed With -10 Promoter Element Ssdna Oligo (Tacaat) Length = 245

Iteration: 1
 Score =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 130/243 (53%), Gaps = 38/243 (15%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 6   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 62
Query: 311 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 340
            +G +                            ++LK  LH    G ++R+ LI ANLRL
Sbjct: 63  ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 122
Query: 341 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH 400
           VV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   
Sbjct: 123 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 182
Query: 401 SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRV--GITVEKLERLIFITRMP 458
           +RTIR+P ++   ++K+    R   QE    P  E++A  +  G   +++E  + I + P
Sbjct: 183 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 242
Query: 459 LSM 461
           +S+
Sbjct: 243 VSL 245

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 45/89 (50%), Positives = 65/89 (73%), Gaps = 3/89 (3%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 91  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 374 KPQAGCRFASYAYWWVRQTIRKAIFQHSR 402
           + + G  F++YA WW+RQ I +AI   +R
Sbjct: 151 EYKRGFAFSTYATWWIRQAINRAIADQAR 179

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 87.8 bits (216), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 34/74 (45%), Positives = 58/74 (78%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 389 VRQTIRKAIFQHSR 402
           +RQ I ++I   +R
Sbjct: 326 IRQAITRSIADQAR 339

>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti- Sigma Factor Spoiiab With The Sporulation Sigma Factor Sigmaf Length = 243

Iteration: 1
 Score = 77.0 bits (188), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 117/229 (51%), Gaps = 18/229 (7%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWW 388
           +R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF      +F++YA   
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88
Query: 389 VRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKL 448
           +   I++   +   T+++  ++  + +K+ +AK    +    +P   ++A  +GI+ E +
Sbjct: 89  IIGEIQR-FLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 449 ERLIFITRMPLSMQQPVW---ADQDTTFQEIT-ADTGVEIPDISVQKQLMRQHVRNLLTL 504
                  R+P S+ + V+    D  T   +I  AD       I+++K +           
Sbjct: 148 VLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASWFDKIALKKAIEE--------- 198
Query: 505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           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: 491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550
           + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +AL 
Sbjct: 5   RMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALR 64
Query: 551 RLKQ 554
           +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 = 7e-11,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 48/61 (78%)
Query: 494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           M++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 554 Q 554
Sbjct: 61  H 61

>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 62

Iteration: 1
 Score = 65.5 bits (158), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 48/61 (78%)
Query: 494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           M++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 554 Q 554
Sbjct: 61  H 61

>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma Complex, Sigma-28FLGM Length = 239

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 66/248 (26%), Positives = 123/248 (49%), Gaps = 31/248 (12%)
Query: 324 HSGNSSREKLINANLRLVVHVA---KQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
           +S    RE+LI   L LV  +A   K++    + + DL+  G +GL+K+V+    +   R
Sbjct: 8   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67
Query: 381 FASYAYWWVRQTIRKAIFQH-------SRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPD 433
               A  +++  I+ AI+ +       SR +R  E     + +V+E  +   ++    P 
Sbjct: 68  ----AEAYIKLRIKGAIYDYLRSLDFGSRQVREKER---RIKEVVEKLK---EKLGREPT 117
Query: 434 KEDLARRVGITVEKLERLIFITRMP--LSMQQPVWADQDTTFQE-ITADTGVEIPDISVQ 490
            E++A+ +GI+ E+L + +        LS+++ V+ D    + E I + T VE     V 
Sbjct: 118 DEEVAKELGISTEELFKTLDKINFSYILSLEE-VFRDFARDYSELIPSSTNVE---EEVI 173
Query: 491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 550
           K+ + + V+  ++ L  +E+ +++L F  E+   K   EV  I   S  RV QL+++AL 
Sbjct: 174 KRELTEKVKEAVSKLPEREKLVIQLIF-YEELPAK---EVAKILETSVSRVSQLKAKALE 229
Query: 551 RLKQSLGG 558
           RL++ L  
Sbjct: 230 RLREMLSN 237

>pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With Sigma-Region4 Of Thermus Aquaticus Bound To Dna Length = 73

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 40/52 (76%)
Query: 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           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: 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           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: 488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 2   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 61
Query: 548 ALYRLKQ 554
           AL +L+ 
Sbjct: 62  ALRKLRH 68

>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna Transcription Activation Sub-Complex Length = 99

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 3   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62
Query: 548 ALYRLKQ 554
           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: 502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
           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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 38/55 (69%)
Query: 500 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
           ++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	569
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	3e-65
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	3e-64
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	2e-63
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	3e-57
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	7e-46
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	1e-38
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	1e-22
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	5e-17
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	2e-16
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	1e-14
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	3e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-13
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	3e-09

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Length = 423

 Score =  218 bits (556), Expect = 3e-65
 Identities = 101/339 (29%), Positives = 180/339 (53%), Gaps = 32/339 (9%)

Query: 248 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQ---------------------DLI 286
                 +DP+R +L       LLT +EE EL  +++                     +++
Sbjct: 72  IPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVV 131

Query: 287 RLEKEKSKL--QSQFGREPTLIEWAKAIGLSCRDLKSEL-------HSGNSSREKLINAN 337
           R +   S         +E    +  + I    + L  E          G ++R+ LI AN
Sbjct: 132 RAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEAN 191

Query: 338 LRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAI 397
           LRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI
Sbjct: 192 LRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAI 251

Query: 398 FQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR--VGITVEKLERLIFIT 455
              +RTIR+P ++   ++K+    R   QE    P  E++A     G   +++E  + I 
Sbjct: 252 ADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIA 311

Query: 456 RMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRL 515
           + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +   L+ L+ +E  +++L
Sbjct: 312 QEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKL 371

Query: 516 RFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
           R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 372 RKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKY 410

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Length = 438

 Score =  215 bits (549), Expect = 3e-64
 Identities = 92/294 (31%), Positives = 163/294 (55%), Gaps = 6/294 (2%)

Query: 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322
           G +   +        L       I   KEK   ++    +  L    K +    +     
Sbjct: 136 GLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKEL----KRYLHI 191

Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
              G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F+
Sbjct: 192 AREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 251

Query: 383 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR-- 440
           +YA WW+RQ I +AI   +RTIR+P ++   ++K+    R   QE    P  E++A    
Sbjct: 252 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMG 311

Query: 441 VGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRN 500
            G   +++E  + I + P+S++ P+  ++D+ + +   D  +  P  +  + L+ + +  
Sbjct: 312 PGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEK 371

Query: 501 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
            L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 372 ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 425

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 613

 Score =  217 bits (555), Expect = 2e-63
 Identities = 115/504 (22%), Positives = 226/504 (44%), Gaps = 37/504 (7%)

Query: 74  PLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM 133
            LL    E   ++   D  N    +     +    L +    +E +     DL       
Sbjct: 109 ELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDP 168

Query: 134 KRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTD 193
              ED + + T        E+  D E  D      +           + +P+L   +F +
Sbjct: 169 NAEEDLAPTATHVGSELSQEDLDDDEDED-----EEDGDDDSADDDNSIDPELAREKFAE 223

Query: 194 ISLTSSLGYPLEEVKQFSQPRFLERRSK----------KRKVSKPQVTNHETYNSRKASV 243
           +     +     + K  S     E   K            K     V +      R  + 
Sbjct: 224 LRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQ 283

Query: 244 KKKLSE------GFDRNDPLRLFL-------WGPETRKLLTADEEFELIAQIQDLIRLEK 290
           ++ + +         + + + LF        W      +     E  L    +++ R  +
Sbjct: 284 ERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEK-LHDVSEEVHRALQ 342

Query: 291 EKSKLQSQFGREPT-LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQ 349
           +  +++ + G     + +  + + +     +        ++++++ ANLRLV+ +AK+Y 
Sbjct: 343 KLQQIEEETGLTIEQVKDINRRMSIGEAKARR-------AKKEMVEANLRLVISIAKKYT 395

Query: 350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN 409
            RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I   +RTIR+P +
Sbjct: 396 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 455

Query: 410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQ 469
           +   ++K+    R  +QE    P  E+LA R+ +  +K+ +++ I + P+SM+ P+  D+
Sbjct: 456 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDE 515

Query: 470 DTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSE 529
           D+   +   DT +E+P  S   + +R    ++L  L  +E  ++R+RFGI+     +L E
Sbjct: 516 DSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEE 575

Query: 530 VGNIFGLSKERVRQLESRALYRLK 553
           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 =  191 bits (487), Expect = 3e-57
 Identities = 59/238 (24%), Positives = 117/238 (49%), Gaps = 11/238 (4%)

Query: 317 RDLKSELHSGNSS-REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 375
           ++L      G+   R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF  
Sbjct: 16  KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDL 75

Query: 376 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKE 435
               +F++YA   +   I++ +     T+++  ++  + +K+ +AK    +    +P   
Sbjct: 76  SYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVT 134

Query: 436 DLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMR 495
           ++A  +GI+ E +       R+P S+ + V+ +          D    I D        +
Sbjct: 135 EIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPIT--LLDQ---IADADEASWFDK 189

Query: 496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
             ++  +  L+ +ER IV LR+     K ++ SEV +  G+S+ ++ +LE + L  +K
Sbjct: 190 IALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK 243

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Length = 239

 Score =  160 bits (408), Expect = 7e-46
 Identities = 53/238 (22%), Positives = 108/238 (45%), Gaps = 15/238 (6%)

Query: 324 HSGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 8   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67

Query: 381 FASYAYWWVRQTIRKAIFQHSRTI-RLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLAR 439
             +Y    ++     AI+ + R++      +     ++ E      ++    P  E++A+
Sbjct: 68  AEAYIKLRIKG----AIYDYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAK 123

Query: 440 RVGITVEKLERLIFITRMPLSMQ-QPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHV 498
            +GI+ E+L + +        +  + V+ D    + E+   +     +  V K+ + + V
Sbjct: 124 ELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSS--TNVEEEVIKRELTEKV 181

Query: 499 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 556
           +  ++ L  +E+ +++L F  E        EV  I   S  RV QL+++AL RL++ L
Sbjct: 182 KEAVSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLREML 235

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 1ku2_A 3lev_A* 3les_A* Length = 245

 Score =  141 bits (356), Expect = 1e-38
 Identities = 71/242 (29%), Positives = 122/242 (50%), Gaps = 36/242 (14%)

Query: 254 NDPLRLFLWGPETRK--LLTADEEFELIAQI------------------QDLIRLEKEKS 293
           +DP+R +L   E  +  LLT +EE +L  ++                  + +  + + K 
Sbjct: 6   SDPVRQYLH--EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKI 63

Query: 294 KLQSQFGREPTLIEWAKAIGLS------------CRDLKSELHSGNSSREKLINANLRLV 341
              ++  + P L E      +              +        G ++R+ LI ANLRLV
Sbjct: 64  LGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLV 123

Query: 342 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS 401
           V +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +
Sbjct: 124 VSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQA 183

Query: 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARR--VGITVEKLERLIFITRMPL 459
           RTIR+P ++   ++K+    R   QE    P  E++A     G   +++E  + I + P+
Sbjct: 184 RTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV 243

Query: 460 SM 461
           S+
Sbjct: 244 SL 245

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Length = 339

 Score = 98.4 bits (245), Expect = 1e-22
 Identities = 40/123 (32%), Positives = 69/123 (56%), Gaps = 10/123 (8%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK-------LINANLR 339
           +L     ++     +   L +  +  GL+   +K      +    K       ++ ANLR
Sbjct: 220 KLHDVSEEVHRALQK---LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLR 276

Query: 340 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQ 399
           LV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA WW+RQ I ++I  
Sbjct: 277 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAD 336

Query: 400 HSR 402
            +R
Sbjct: 337 QAR 339

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Length = 87

 Score = 75.5 bits (186), Expect = 5e-17
 Identities = 28/66 (42%), Positives = 48/66 (72%)

Query: 488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547
              + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +
Sbjct: 2   EAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVK 61

Query: 548 ALYRLK 553
           AL +L+
Sbjct: 62  ALRKLR 67

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B Length = 99

 Score = 74.0 bits (182), Expect = 2e-16
 Identities = 23/66 (34%), Positives = 42/66 (63%)

Query: 488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 547
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 3   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62

Query: 548 ALYRLK 553
           AL +L+
Sbjct: 63  ALRKLR 68

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Length = 68

 Score = 67.7 bits (166), Expect = 1e-14
 Identities = 21/54 (38%), Positives = 38/54 (70%)

Query: 500 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +L+
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLR 54

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Length = 73

 Score = 67.0 bits (164), Expect = 3e-14
 Identities = 22/59 (37%), Positives = 42/59 (71%)

Query: 496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
           + +   L+ L+ +E  ++++R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 60

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 73.3 bits (179), Expect = 1e-13
 Identities = 95/565 (16%), Positives = 175/565 (30%), Gaps = 152/565 (26%)

Query: 38  MHNEQSAPAVASVPTSSVARHFPTSVL---LQEQRDEYRPLLH-MFKEDKTSQATSDSRN 93
           ++N+            +V+R  P   L   L E R     L+  +    KT  A     +
Sbjct: 119 LYND-----NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLS 173

Query: 94  IETEAFF--------VEEKNSGD--LDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVS- 142
            + +           ++  NS +  L+ L Q L +Q    P+  + S      +    S 
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEML-QKLLYQID--PNWTSRSDHSSNIKLRIHSI 230

Query: 143 ---LTMQSLSNDTEES------V-DAEPFDAVALARKALSASKEAASLAENPKLNGAEFT 192
              L     S   E        V +A+ ++A  L+ K L  ++    + +   L+ A  T
Sbjct: 231 QAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK-QVTD--FLSAATTT 287

Query: 193 DISLT-SSLGYPLEEVKQ-FSQPRFLERRSKK--RKVSK--PQVTNHETYNSRKASVKKK 246
            ISL   S+    +EVK      ++L+ R +   R+V    P+           + + + 
Sbjct: 288 HISLDHHSMTLTPDEVKSLLL--KYLDCRPQDLPREVLTTNPRRL---------SIIAES 336

Query: 247 LSEGFDRNDPLRLFLWGPETRKL---LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 303
           + +G    D  +       T  +   L   E  E       L       + + +      
Sbjct: 337 IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS-AHIPTI----- 390

Query: 304 TL-IEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEG 362
            L + W   I      + ++LH     +  L+           KQ +   IS+  +  E 
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLH-----KYSLVE----------KQPKESTISIPSIYLEL 435

Query: 363 SMGLMKS-------VEKFK-PQAGCRFA-------SYAYWWVRQTIRKAIFQHSRTIRLP 407
            + L          V+ +  P+              Y Y          I  H + I  P
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH--------IGHHLKNIEHP 487

Query: 408 ENIYTLLSKV------LEAK-RLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLS 460
           E   TL   V      LE K R      N S    +        ++  +   +I      
Sbjct: 488 ER-MTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTL----QQLKFYKP--YIC----- 535

Query: 461 MQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIE 520
                  D D  ++ +       +  I      + +   NL+     K   ++R+    E
Sbjct: 536 -------DNDPKYERL-------VNAI---LDFLPKIEENLI---CSKYTDLLRIALMAE 575

Query: 521 DGKPKSLSEVGNIFGLSKERVRQLE 545
           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 = 55.2 bits (133), Expect = 3e-09
 Identities = 27/205 (13%), Positives = 69/205 (33%), Gaps = 49/205 (23%)

Query: 352 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIY 411
           G    DL+QEG +GL+K+++ +       F+S+A+  +R+ +  AI + +    +  N  
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDET-KSSFSSFAFLCIRREMISAIRKANTQKHMVLNEA 59

Query: 412 TLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT 471
              + +LE    +  EG++  + +                                    
Sbjct: 60  LKTNAILEDSAYFDDEGHNINNYK------------------------------------ 83

Query: 472 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVG 531
                   +     +  + K+ + +  +      +  E+ ++        G   S  E+ 
Sbjct: 84  -------SSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLI---RG--YSYREIA 131

Query: 532 NIFGLSKERVRQLESRALYRLKQSL 556
            I   + + +     R   + ++ +
Sbjct: 132 TILSKNLKSIDNTIQRIRKKSEEWI 156

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	569
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	100.0
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.97
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.89
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.89
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.86
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.71
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.64
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.56
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.53
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.33
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.3
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.29
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.26
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	99.0
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	98.96
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.86
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.84
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.73
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.69
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.52
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.49
3c57_A	95	Two component transcriptional regulatory protein;	98.47
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.46
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	97.97
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.91
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.86
2q0o_A	236	Probable transcriptional activator protein TRAR; h	97.46
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	97.45
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	97.28
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	97.17
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.9
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.53
1yio_A	208	Response regulatory protein; transcription regulat	96.47
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.3
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.16
3c3w_A	225	Two component transcriptional regulatory protein;	95.87
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	95.15
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	94.92
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	94.3
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	93.43
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	93.22
2oqr_A	230	Sensory transduction protein REGX3; response regul	93.03
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	93.03
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	92.85
2gwr_A	238	DNA-binding response regulator MTRA; two-component	92.7
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	91.96
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	91.72
1ys7_A	233	Transcriptional regulatory protein PRRA; response	91.55
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	91.21
1u78_A	141	TC3 transposase, transposable element TC3 transpos	90.97
3r0j_A	250	Possible two component system response transcript	90.78
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	90.74
3q9s_A	249	DNA-binding response regulator; DNA binding protei	90.74
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	90.42
2hqr_A	223	Putative transcriptional regulator; phosporylation	89.93
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	88.57
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	88.55
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	88.51
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	88.4
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	88.15
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	87.36
3r0a_A	123	Putative transcriptional regulator; structural gen	87.35
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	86.92
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	86.78
1y0u_A	96	Arsenical resistance operon repressor, putative; s	86.77
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	86.24
3nqo_A	189	MARR-family transcriptional regulator; structural	86.21
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	85.81
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	85.02
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	84.96
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	84.73
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	84.61
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	84.49
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	84.4
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	84.34
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	84.04
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	84.0
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	83.91
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	83.54
2w25_A	150	Probable transcriptional regulatory protein; trans	83.5
2gxg_A	146	146AA long hypothetical transcriptional regulator;	83.37
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	83.21
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	82.93
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	82.87
3sqn_A	485	Conserved domain protein; structural genomics, PSI	82.49
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	82.48
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	82.48
1sfx_A	109	Conserved hypothetical protein AF2008; structural	82.37
2k27_A	159	Paired box protein PAX-8; paired domain, solution	82.3
3frw_A	107	Putative Trp repressor protein; structural genomic	82.11
3jth_A	98	Transcription activator HLYU; transcription factor	82.07
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	82.01
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	81.9
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	81.42
3iwf_A	107	Transcription regulator RPIR family; transcription	81.41
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	81.36
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	81.26
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	80.71
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	80.61
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	80.44
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	80.38
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	80.34
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	80.29
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	80.27
1ku9_A	152	Hypothetical protein MJ223; putative transcription	80.03
1u78_A	141	TC3 transposase, transposable element TC3 transpos	80.01

>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=9e-55  Score=468.44  Aligned_cols=315  Identities=31%  Similarity=0.569  Sum_probs=284.2

Q ss_pred             CCCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHhhhhCCCCcHHHHHH---
Q 008352          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAK---  310 (569)
Q Consensus       252 ~~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~------------------~l~~~~g~~pt~~ewA~---  310 (569)
                      ...|+++.||++|+++||||+|||++|+++|+.+..++....                  ......|+.|+..+|+.   
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            356899999999999999999999999999998754332211                  11223567788888743   


Q ss_pred             ---------HcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCch
Q 008352          311 ---------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF  381 (569)
Q Consensus       311 ---------a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rF  381 (569)
                               +.|++...|+..+++|..|+++||.+|+++|++||++|.++|.+++|||||||||||+|+++|||.+|++|
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                     23566788889998999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCCc
Q 008352          382 ASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPL  459 (569)
Q Consensus       382 STYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~~~  459 (569)
                      +|||+||||+.|.++|++++|.||+|.|+...+++++++.+.+.+.+||.|+.++||+.+|  +++++|..++.....++
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             ccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHH
Q 008352          460 SMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE  539 (569)
Q Consensus       460 SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISre  539 (569)
                      |+|.+++++++..+.+++.+....+|++.+...++...|..+|+.||++||.||.+||||+||+++|++|||+.||||++
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            99999887766677888877665678888888888999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH-HHhhcCchhhhhh
Q 008352          540 RVRQLESRALYRLK-QSLGGKASYGYAD  566 (569)
Q Consensus       540 rVRqie~RALkKLR-~~l~~~~L~~yld  566 (569)
                      ||||+++||++||| +.+....|++|++
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=6.7e-55  Score=469.14  Aligned_cols=311  Identities=33%  Similarity=0.589  Sum_probs=276.1

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh---------------------hhCCCCcHHH----
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS---------------------QFGREPTLIE----  307 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~~---------------------~~g~~pt~~e----  307 (569)
                      ..|+++.||++|+++|+||+|||++|+++|+.+..+..   .|..                     ..++.|+..+    
T Consensus        77 ~~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~---~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (423)
T 2a6h_F           77 TSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIK---KLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDP  153 (423)
T ss_dssp             THHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHH---HHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTT
T ss_pred             CCcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHH---HHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhh
Confidence            56899999999999999999999999999998654332   2222                     2234555433    


Q ss_pred             -----HHH---HcCCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCC
Q 008352          308 -----WAK---AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGC  379 (569)
Q Consensus       308 -----wA~---a~g~~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~  379 (569)
                           |+.   ++++++..|+..+++|..|+++||.+|+++|++||++|.++|.+++|||||||+|||+|+++|||.+|+
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   346678889999988899999999999999999999999999999999999999999999999999999


Q ss_pred             chhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--CCHHHHHHHHHhcCC
Q 008352          380 RFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRM  457 (569)
Q Consensus       380 rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~  457 (569)
                      +|+|||+||||+.|.++|++++|+||+|.|+...+++++++.+.+.+.+||.|+.++||+.+|  +++++|..++.....
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             CcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCC
Q 008352          458 PLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS  537 (569)
Q Consensus       458 ~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGIS  537 (569)
                      ++|+|.+++++++..+.+++++....+|++.+...++...|..+|+.||++||.||.+||||+||+++|++|||+.||||
T Consensus       314 ~~Sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~L~~aL~~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS  393 (423)
T 2a6h_F          314 PVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVT  393 (423)
T ss_dssp             CEESSCBCSSSSSCBGGGSSCCSSSCCHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTCC-----CHHHHSSSSC
T ss_pred             CcccccccCCCCccchhhhhccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcC
Confidence            99999999877777788888877666888888888889999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHH-HHhhcCchhhhhh
Q 008352          538 KERVRQLESRALYRLK-QSLGGKASYGYAD  566 (569)
Q Consensus       538 rerVRqie~RALkKLR-~~l~~~~L~~yld  566 (569)
                      ++||||++.+|++||| +.+....|++|++
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=5.2e-42  Score=384.36  Aligned_cols=251  Identities=34%  Similarity=0.671  Sum_probs=236.9

Q ss_pred             HHHHHHHHhccH-HH---HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHH
Q 008352          316 CRDLKSELHSGN-SS---REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQ  391 (569)
Q Consensus       316 ~~~L~~~l~~G~-~A---re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRq  391 (569)
                      ...|+.+++.|+ .|   ++.||..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+||++|||||
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            456777777666 66   99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCc
Q 008352          392 TIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDT  471 (569)
Q Consensus       392 aI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~  471 (569)
                      .|.++++++.+.+|+|.|+...+++++++.+.+.+++||.||.+|||+.+|+++++++.++.....++|++.+++++++.
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            99999999999999999999999999999999999999999999999999999999999999999999999999887777


Q ss_pred             chhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 008352          472 TFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  551 (569)
Q Consensus       472 ~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkK  551 (569)
                      .+.+++.+....+|++.+...++...|..+|..||+++|.||.||||+++++++|++|||+.||||++||+++++||+++
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            88888888777789998888888889999999999999999999999998899999999999999999999999999999


Q ss_pred             HHHHhhcCchhhhhh
Q 008352          552 LKQSLGGKASYGYAD  566 (569)
Q Consensus       552 LR~~l~~~~L~~yld  566 (569)
                      ||+++....++.|+|
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=2.9e-36  Score=302.60  Aligned_cols=209  Identities=33%  Similarity=0.577  Sum_probs=132.0

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHH-HHHHHHHHh--h-----------------------hhCCCCcHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR-LEKEKSKLQ--S-----------------------QFGREPTLI  306 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~-le~~~~~l~--~-----------------------~~g~~pt~~  306 (569)
                      .+|+++.||++|+++||||++||++|+++|+.++. .+.+.....  .                       ..+.+|+..
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            57899999999999999999999999999999765 222221100  0                       024789999


Q ss_pred             HHHHHcCCC----HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchh
Q 008352          307 EWAKAIGLS----CRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA  382 (569)
Q Consensus       307 ewA~a~g~~----~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFS  382 (569)
                      +||++.|++    ...|...+++|+.|++.||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+
T Consensus        85 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~  164 (245)
T 3ugo_A           85 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS  164 (245)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHH
T ss_pred             HHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHH
Confidence            999998885    3456677888899999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCCcc
Q 008352          383 SYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLS  460 (569)
Q Consensus       383 TYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~~~S  460 (569)
                      ||++||||++|.++++++.+.+++|.++...++++.++.+.+...+++.||.+|||+.||  +++++|...+...+..+|
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  999999999988877776


Q ss_pred             c
Q 008352          461 M  461 (569)
Q Consensus       461 L  461 (569)
                      |
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=100.00  E-value=6.3e-32  Score=262.97  Aligned_cols=222  Identities=22%  Similarity=0.304  Sum_probs=192.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccc
Q 008352          327 NSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       327 ~~Are~LI~~nlrLV~sIArry~---~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~  403 (569)
                      ..|++.|+..|.++|+++|++|.   +++.+++||+|||+++||+++++||+.+|.+|.||+++||++.+.++++++.  
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            35899999999999999999998   6789999999999999999999999999999999999999999999999876  


Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CCcccCCCCCCCCCcchhhcccCCC
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITR--MPLSMQQPVWADQDTTFQEITADTG  481 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~--~~~SLD~~v~~d~~~~l~d~i~D~~  481 (569)
                       +.|.+.....++++++...+....|+.|+.+++|+.+|++++++..++....  ...|++.++.++++.. .++ +++ 
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             4678888889999999999999999999999999999999999988775432  2345554432222122 233 222 


Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Q 008352          482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  558 (569)
Q Consensus       482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  558 (569)
                      ..+|++.+...+....|..+|..||+++|.||.++|+    +++|++|||+.||||.++|++++++|+++||+.+..
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            3367888888888889999999999999999999998    899999999999999999999999999999998754

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

Probab=99.97  E-value=1.3e-31  Score=260.55  Aligned_cols=216  Identities=26%  Similarity=0.440  Sum_probs=52.7

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (569)
Q Consensus       326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR  405 (569)
                      +..|++.|+..|.++|+++|++|.++..+++||+|||+++||+++++||+.+|.+|.||+++|+++.+.++++++. .++
T Consensus        26 d~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~~d~~r~~~-~~~  104 (243)
T 1l0o_C           26 DQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVK  104 (243)
T ss_dssp             --------------------------------------------------------------------------CC-CCT
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-Ccc
Confidence            3489999999999999999999999999999999999999999999999998889999999999999999999987 789


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCC--cchhhcccCCCCC
Q 008352          406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQD--TTFQEITADTGVE  483 (569)
Q Consensus       406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~--~~l~d~i~D~~~~  483 (569)
                      +|.++.....+++++...+.+..++.|+.++++..+|++.+.+...+.......|++.++.++++  .++.+.+      
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~------  178 (243)
T 1l0o_C          105 VSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQI------  178 (243)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC----------------------------
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCcccchhhcc------
Confidence            99999999999999999999999999999999999999999998887766667788776543322  2223322      


Q ss_pred             ChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          484 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       484 ~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                       |++.+...+....|..+|..||+++|+||.++|+    +++|++|||+.||||.++|++++.+|+++||
T Consensus       179 -~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr  243 (243)
T 1l0o_C          179 -ADADEASWFDKIALKKAIEELDERERLIVYLRYY----KDQTQSEVASRLGISQVQMSRLEKKILQHIK  243 (243)
T ss_dssp             ----------------------------------------------------------------------
T ss_pred             -CcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence             2223344456678899999999999999999998    8999999999999999999999999999997

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=99.89  E-value=9.4e-23  Score=192.94  Aligned_cols=180  Identities=16%  Similarity=0.180  Sum_probs=136.5

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHH
Q 008352          316 CRDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIR  394 (569)
Q Consensus       316 ~~~L~~~l~~G-~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~  394 (569)
                      +.+|+..+..| ..|++.|+..|.+.|+++|+++.+ ..+.+|++||+++++|+++++|++..  .|.+|++.++++.+.
T Consensus        10 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~   86 (194)
T 1or7_A           10 DQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAK   86 (194)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHH
Confidence            45566666555 599999999999999999999999 89999999999999999999999874  599999999999999


Q ss_pred             HHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh
Q 008352          395 KAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ  474 (569)
Q Consensus       395 ~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~  474 (569)
                      +++++..+..+.                            .++..           ...     ..++..      ..  
T Consensus        87 d~~R~~~~~~~~----------------------------~~~~~-----------~~~-----~~~~~~------~~--  114 (194)
T 1or7_A           87 NYLVAQGRRPPS----------------------------SDVDA-----------IEA-----ENFESG------GA--  114 (194)
T ss_dssp             HHHHHHTTCCTH----------------------------HHHHH-----------HHH-----HSCCSS------CC--
T ss_pred             HHHHHHhccCcc----------------------------ccccc-----------ccc-----cccccc------cc--
Confidence            999886532210                            00000           000     000000      00  


Q ss_pred             hcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          475 EITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       475 d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                        +.+.  .+|++.+...+....|..+|..||+++|+||.++|+    +++|++|||+.||||..+|++++.||+++||+
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  123333333455667889999999999999999998    89999999999999999999999999999999


Q ss_pred             Hhhc
Q 008352          555 SLGG  558 (569)
Q Consensus       555 ~l~~  558 (569)
                      .+..
T Consensus       187 ~l~~  190 (194)
T 1or7_A          187 KVQP  190 (194)
T ss_dssp             HHCC
T ss_pred             HHHH
Confidence            8753

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=99.86  E-value=2.9e-21  Score=176.71  Aligned_cols=155  Identities=15%  Similarity=0.189  Sum_probs=108.0

Q ss_pred             CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCC
Q 008352          352 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHS  431 (569)
Q Consensus       352 g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~  431 (569)
                      |.+++|++|||++++|+++.+||+.+ .+|.||+++++++.+.++++++.+..+.+..                      
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 7899999999999999999986533222110                      


Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchh----hcccCCCCCChhHHHHHHHHHHHHHHHHh-cCC
Q 008352          432 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQ----EITADTGVEIPDISVQKQLMRQHVRNLLT-LLN  506 (569)
Q Consensus       432 Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~----d~i~D~~~~~pee~l~~~el~e~L~~aL~-~L~  506 (569)
                                               ..++.+.+..++....+.    +.+.+ ...+|++.+...+....|..+|. .||
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 008352          507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      +++|.||. +|.    +|+|++|||+.||||..+|++++.||+++||+.+...+
T Consensus       112 ~~~r~v~~-~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~~  160 (164)
T 3mzy_A          112 KFEKEVLT-YLI----RGYSYREIATILSKNLKSIDNTIQRIRKKSEEWIKEEE  160 (164)
T ss_dssp             HHHHHHHH-HHT----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence            99999999 676    89999999999999999999999999999999987543

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

Probab=99.71  E-value=1.8e-19  Score=167.34  Aligned_cols=143  Identities=11%  Similarity=0.094  Sum_probs=119.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcccceecchh
Q 008352          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPEN  409 (569)
Q Consensus       330 re~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IRlP~~  409 (569)
                      ++.|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++..  .|.+|++..++|.+.+++++..        
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~--------   72 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGE--------   72 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTS--------
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccC--------
Confidence            567899999999999999999989999999999999999999999763  6999999999999999886531        


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHH
Q 008352          410 IYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISV  489 (569)
Q Consensus       410 ~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l  489 (569)
                                           .+                             +.+.  +           .         
T Consensus        73 ---------------------~~-----------------------------~~~~--e-----------~---------   80 (157)
T 2lfw_A           73 ---------------------AQ-----------------------------TSQS--D-----------A---------   80 (157)
T ss_dssp             ---------------------CC-----------------------------CCCC--S-----------C---------
T ss_pred             ---------------------cc-----------------------------cCCc--c-----------h---------
Confidence                                 00                             0000  0           0         


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          490 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       490 ~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                        .+....|..+|..||+++|+||.|+|.    +|+|++|||+.||||..+|++.+.||+++||+.+....
T Consensus        81 --~~~~~~l~~~l~~Lp~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~  145 (157)
T 2lfw_A           81 --EGTEAVARARLARMTPLSRQALLLTAM----EGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRALE  145 (157)
T ss_dssp             --SSSSSTTTTTTTTSCTTHHHHHTTTSS----SCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSCCC
T ss_pred             --HHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence              001124667889999999999999998    89999999999999999999999999999999886543

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.64  E-value=2.7e-16  Score=163.85  Aligned_cols=85  Identities=41%  Similarity=0.902  Sum_probs=77.2

Q ss_pred             HHHHHHHhcc-H---HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          317 RDLKSELHSG-N---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       317 ~~L~~~l~~G-~---~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      ..|...+..| .   .|++.||..|+++|+++|++|.+++.+++||+||||+|||+++++|++.+|++|+||++|||+|.
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   79999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcc
Q 008352          393 IRKAIFQHS  401 (569)
Q Consensus       393 I~~~Ir~~~  401 (569)
                      |.++++++.
T Consensus       330 ~~~~lr~~~  338 (339)
T 1sig_A          330 ITRSIADQA  338 (339)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHhc
Confidence            999999865

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

Probab=99.56  E-value=2.2e-15  Score=153.39  Aligned_cols=142  Identities=13%  Similarity=0.040  Sum_probs=118.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhccccee
Q 008352          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIR  405 (569)
Q Consensus       326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~r~IR  405 (569)
                      +..+|+.|+..|.+.++.+|++|.++..+.+|++||.|+.+|+..++|++.  ..|.+|++.+++|.+.+++++..    
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            347999999999999999999999999999999999999999999999975  46999999999998877664210    


Q ss_pred             cchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCCh
Q 008352          406 LPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIP  485 (569)
Q Consensus       406 lP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~p  485 (569)
                                               .                                .  ...         +.   . 
T Consensus        93 -------------------------~--------------------------------~--~~~---------~~---~-  100 (286)
T 3n0r_A           93 -------------------------V--------------------------------G--HDQ---------GL---H-  100 (286)
T ss_dssp             ----------------------------------------------------------C--CCC---------CC---C-
T ss_pred             -------------------------c--------------------------------C--CCc---------cc---c-
Confidence                                     0                                0  000         00   0 


Q ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          486 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       486 ee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                              ....|..+|+.||+++|+||.|+|.    +++|++|||+.+|+|..+|+....+|+++|+..+.
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    99999999999999999999999999999997654

>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=99.53  E-value=2.8e-14  Score=124.11  Aligned_cols=80  Identities=29%  Similarity=0.490  Sum_probs=74.6

Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhh
Q 008352          488 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADL  567 (569)
Q Consensus       488 ~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yldl  567 (569)
                      .+...++...|..+|+.||++||+||.+|||++|++++|++|||+.||||++||++++.+|+++||..+....++.|+..
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            45667788899999999999999999999999988999999999999999999999999999999999999999999753

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

Probab=99.33  E-value=1.8e-12  Score=109.37  Aligned_cols=72  Identities=38%  Similarity=0.713  Sum_probs=66.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhh
Q 008352          496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADL  567 (569)
Q Consensus       496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yldl  567 (569)
                      ..|..+|+.||+++|+||.++|+|++++++|++|||+.||||+++|++++.+|+++||..+....+..|+..
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            367889999999999999999999988999999999999999999999999999999999988888888754

>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=9.6e-13  Score=107.11  Aligned_cols=68  Identities=32%  Similarity=0.627  Sum_probs=55.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH-HHhhcCchhhhh
Q 008352          498 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK-QSLGGKASYGYA  565 (569)
Q Consensus       498 L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR-~~l~~~~L~~yl  565 (569)
                      |..+|+.||++||+||.++|+|+|++++|++|||+.||+|.++|++++.+|+++|| ..+....++.|+
T Consensus         4 l~~~l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   72 (73)
T 1ku3_A            4 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL   72 (73)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTC---------
T ss_pred             HHHHHHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHhhHHHHHHhh
Confidence            45678899999999999999998889999999999999999999999999999999 888888888775

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

Probab=99.29  E-value=1.3e-11  Score=104.80  Aligned_cols=75  Identities=16%  Similarity=0.211  Sum_probs=69.8

Q ss_pred             CCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCc
Q 008352          482 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  560 (569)
Q Consensus       482 ~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  560 (569)
                      ..+|++.+...+....|..+|..||+++|+||.|+|.    +++|++|||+.||||..+|++++.||+++||+.+...+
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=99.26  E-value=2.1e-12  Score=103.71  Aligned_cols=66  Identities=33%  Similarity=0.614  Sum_probs=61.0

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352          501 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  566 (569)
Q Consensus       501 aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld  566 (569)
                      +|+.||++||+||.++|||++.+++|++|||+.||+|.++|++++.+|++|||..+....+..|++
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            467899999999999999887799999999999999999999999999999999998888887764

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

Probab=99.00  E-value=6.4e-10  Score=88.52  Aligned_cols=64  Identities=16%  Similarity=0.067  Sum_probs=53.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       494 l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      ....|..+|+.||++++.||.++|.    +++|++|||+.+|+|+.+|+++.++|+++||..+....+
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            4557888999999999999999998    899999999999999999999999999999998876543

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

Probab=98.96  E-value=1.5e-09  Score=94.37  Aligned_cols=82  Identities=16%  Similarity=0.132  Sum_probs=69.4

Q ss_pred             HHHHHHhc-cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHH
Q 008352          318 DLKSELHS-GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKA  396 (569)
Q Consensus       318 ~L~~~l~~-G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~  396 (569)
                      .|+..+.. +..|++.|+..|.+.|+.+|.++ ++..+.+|++||+|+.+|+.+.+|++.  ..|.+|++..++|.+.++
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            34444444 45999999999999999999999 888899999999999999999999974  369999999999999999


Q ss_pred             HHhccc
Q 008352          397 IFQHSR  402 (569)
Q Consensus       397 Ir~~~r  402 (569)
                      ++++.+
T Consensus        90 ~R~~~~   95 (112)
T 2o7g_A           90 IRHVRS   95 (112)
T ss_dssp             TC----
T ss_pred             HHHhhc
Confidence            987654

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

Probab=98.86  E-value=2.7e-09  Score=88.53  Aligned_cols=75  Identities=15%  Similarity=0.135  Sum_probs=67.3

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (569)
Q Consensus       325 ~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~  401 (569)
                      ++..+++.|+..|.+.++.+|.++.++..+.+|++||+++.+|+.+++|++.  ..|.+|++.++++.+.++++++.
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            4458999999999999999999999999999999999999999999999975  47999999999999999988654

>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=98.84  E-value=1.2e-08  Score=90.30  Aligned_cols=69  Identities=22%  Similarity=0.202  Sum_probs=61.6

Q ss_pred             HHHHHHHHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          489 VQKQLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       489 l~~~el~e~L~~aL-~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      ++..+....+..++ ..||+++|+||.++|.    +++|++|||+.||+|..+|+.+..||+++||..+...++
T Consensus         9 ~e~~~~~~~l~~~l~~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   78 (113)
T 1xsv_A            9 LVKTLRMNYLFDFYQSLLTNKQRNYLELFYL----EDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   78 (113)
T ss_dssp             HHHHHHHHHHHHHHGGGSCHHHHHHHHHHHT----SCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            44455566788999 9999999999999998    899999999999999999999999999999999876554

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

Probab=98.73  E-value=1e-11  Score=124.23  Aligned_cols=153  Identities=10%  Similarity=0.044  Sum_probs=109.5

Q ss_pred             HHHHHHhccH-HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHH----HHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHH
Q 008352          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLL----QEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQT  392 (569)
Q Consensus       318 ~L~~~l~~G~-~Are~LI~~nlrLV~sIArry~~~g~~~EDLI----QEG~IGLirAiekFDp~kG~rFSTYA~~wIRqa  392 (569)
                      .|..+++.++ .+++.+...|.+++..+............|+.    ||.++.+|+.+..|++..  .|.+|++..+++.
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            4556666555 78999999999999999988777777788886    999999999999998754  5888877655543


Q ss_pred             HHHHHHhcccceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcc
Q 008352          393 IRKAIFQHSRTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTT  472 (569)
Q Consensus       393 I~~~Ir~~~r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~  472 (569)
                      +.++.+...                                                           +...+.....  
T Consensus       164 ~~d~~r~~~-----------------------------------------------------------~~~~~~~~~~--  182 (258)
T 3clo_A          164 SADQRPEQG-----------------------------------------------------------IYATITQMER--  182 (258)
T ss_dssp             CSCCCCCSS-----------------------------------------------------------CCCEEEETTT--
T ss_pred             HcchhhhhH-----------------------------------------------------------HHHHHHhhcc--
Confidence            322211000                                                           0000000000  


Q ss_pred             hhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 008352          473 FQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  552 (569)
Q Consensus       473 l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKL  552 (569)
                       .+...     ..           .+..++..||+++|+||.|++     +|+|.+|||+.||||..||+.+..||++||
T Consensus       183 -~~~~~-----~~-----------~~~~~~~~L~~~erevl~L~~-----~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL  240 (258)
T 3clo_A          183 -GEVET-----LS-----------LSEEHRNILSEREKEILRCIR-----KGLSSKEIAATLYISVNTVNRHRQNILEKL  240 (258)
T ss_dssp             -TEEEE-----CC-----------CHHHHTTSSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             -ccccc-----ch-----------hhHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence             00000     00           145567899999999999984     799999999999999999999999999999


Q ss_pred             HHH
Q 008352          553 KQS  555 (569)
Q Consensus       553 R~~  555 (569)
                      |..
T Consensus       241 ~~~  243 (258)
T 3clo_A          241 SVG  243 (258)
T ss_dssp             TCS
T ss_pred             cCC
Confidence            864

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=98.69  E-value=2.5e-08  Score=88.35  Aligned_cols=63  Identities=21%  Similarity=0.212  Sum_probs=57.4

Q ss_pred             HHHHHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          495 RQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       495 ~e~L~~aL-~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      ...+..++ ..||+++++||.++|.    +|+|++|||+.+|||+.+|+....+|+++||..+...++
T Consensus        12 ~~~l~~~l~~~L~~~~r~vl~l~y~----~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   75 (113)
T 1s7o_A           12 MNALFEFYAALLTDKQMNYIELYYA----DDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   75 (113)
T ss_dssp             HHHHHHHHGGGSCHHHHHHHHHHHH----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            44677888 8999999999999998    899999999999999999999999999999998876554

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

Probab=98.52  E-value=3.6e-08  Score=83.31  Aligned_cols=59  Identities=20%  Similarity=0.173  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          492 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       492 ~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      ......+..++..|+++|++||.++ .    +|+|.+|||+.||||..+|+.+..++++||+..
T Consensus        17 ~~~~~~l~~~l~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   75 (91)
T 2rnj_A           17 GSHMKKRAELYEMLTEREMEILLLI-A----KGYSNQEIASASHITIKTVKTHVSNILSKLEVQ   75 (91)
T ss_dssp             --------CTGGGCCSHHHHHHHHH-H----TTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            3445578889999999999999995 4    799999999999999999999999999999753

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

Probab=98.49  E-value=1.8e-07  Score=76.20  Aligned_cols=54  Identities=15%  Similarity=0.190  Sum_probs=49.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          496 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       496 e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ..+..++..|+++|++||.++ .    +++|.+|||+.||+|..+|++...++++||+.
T Consensus         8 ~~l~~~l~~L~~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~   61 (79)
T 1x3u_A            8 NDIRARLQTLSERERQVLSAV-V----AGLPNKSIAYDLDISPRTVEVHRANVMAKMKA   61 (79)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHH-T----TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            357788999999999999995 4    79999999999999999999999999999985

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=98.47  E-value=1.9e-07  Score=79.79  Aligned_cols=58  Identities=21%  Similarity=0.268  Sum_probs=45.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       494 l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      ....|..++..|+++|++||.++ .    +|+|.+|||+.||||..+|+..+.++++||+..-
T Consensus        17 ~~~~l~~~l~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~   74 (95)
T 3c57_A           17 RGSHMQDPLSGLTDQERTLLGLL-S----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMER   74 (95)
T ss_dssp             ----------CCCHHHHHHHHHH-H----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCC
Confidence            34567889999999999999997 4    7999999999999999999999999999998643

>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=98.46  E-value=1.2e-07  Score=82.53  Aligned_cols=64  Identities=23%  Similarity=0.206  Sum_probs=54.7

Q ss_pred             HHHHHHHHHH-hcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          493 LMRQHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       493 el~e~L~~aL-~~L~~rER~VL~LRygL~d---~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      ...+.+..++ ..|+++|+.+|.+|||+.+   +.++|++|||+.+|+|+.+|.++ +|+|++|...+.
T Consensus        23 ~~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k   90 (101)
T 1jhg_A           23 YQNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELR   90 (101)
T ss_dssp             HHTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHH
T ss_pred             CCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHH
Confidence            3344566777 6799999999999999975   45699999999999999999999 999999987653

>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=3e-07  Score=76.44  Aligned_cols=55  Identities=16%  Similarity=0.231  Sum_probs=47.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          497 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       497 ~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      .+..++..|+++|++||.++ .    +|+|.+|||+.||||..+|+....++++||+...
T Consensus        14 ~~~~~~~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~   68 (82)
T 1je8_A           14 TTERDVNQLTPRERDILKLI-A----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKS   68 (82)
T ss_dssp             ---CCGGGSCHHHHHHHHHH-T----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSS
T ss_pred             HHHHHHccCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCC
Confidence            35677899999999999995 4    7899999999999999999999999999998643

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

Probab=98.19  E-value=1.4e-06  Score=69.68  Aligned_cols=53  Identities=25%  Similarity=0.238  Sum_probs=45.9

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          498 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       498 L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      +...+..|+++|++||.+. .    +++|.+|||+.||+|..+|++...++++||+..
T Consensus         5 ~~~~~~~L~~~e~~il~~~-~----~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~   57 (74)
T 1fse_A            5 EFQSKPLLTKREREVFELL-V----QDKTTKEIASELFISEKTVRNHISNAMQKLGVK   57 (74)
T ss_dssp             ---CCCCCCHHHHHHHHHH-T----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             cCCCCCCCCHHHHHHHHHH-H----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            4456788999999999994 4    789999999999999999999999999999753

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=97.97  E-value=1e-05  Score=68.62  Aligned_cols=49  Identities=20%  Similarity=0.225  Sum_probs=43.1

Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          500 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       500 ~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .....|+++|++||.+.+     +|+|.+|||+.||||..||+....++++||.
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     6999999999999999999999999999985

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

Probab=97.91  E-value=7.9e-06  Score=63.12  Aligned_cols=43  Identities=14%  Similarity=0.227  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ++|++|+.+ +.    +|+|.+|||+.||+|..+|+....++++||+.
T Consensus         1 ~re~~vl~l-~~----~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   43 (61)
T 2jpc_A            1 LRERQVLKL-ID----EGYTNHGISEKLHISIKTVETHRMNMMRKLQV   43 (61)
T ss_dssp             CHHHHHHHH-HH----TSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHH-HH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCC
Confidence            479999999 55    89999999999999999999999999999975

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

Probab=97.86  E-value=1.9e-05  Score=68.27  Aligned_cols=47  Identities=21%  Similarity=0.275  Sum_probs=43.5

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ..|+++|++||.+.+     +|+|.+|||+.||||..+|+....++++||.-
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     69999999999999999999999999999953

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=97.46  E-value=0.00016  Score=70.69  Aligned_cols=46  Identities=24%  Similarity=0.327  Sum_probs=42.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .|+++|++||.+.+     +|+|.+|||++||||..||+....++++||.-
T Consensus       175 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (236)
T 2q0o_A          175 MLSPREMLCLVWAS-----KGKTASVTANLTGINARTVQHYLDKARAKLDA  220 (236)
T ss_dssp             SCCHHHHHHHHHHH-----TTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            59999999999964     79999999999999999999999999999953

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=97.45  E-value=0.00017  Score=70.54  Aligned_cols=46  Identities=26%  Similarity=0.364  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .|+++|++||.+.+     +|+|.+|||++||||..||+..+.++++||.-
T Consensus       173 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  218 (234)
T 1l3l_A          173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDV  218 (234)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            59999999999964     79999999999999999999999999999953

>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=97.28  E-value=0.00028  Score=69.32  Aligned_cols=46  Identities=20%  Similarity=0.307  Sum_probs=43.0

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|++|+.+..     +|+|.+|||+.||||..||+....++++||.
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     7999999999999999999999999999985

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=97.17  E-value=0.00041  Score=69.52  Aligned_cols=46  Identities=20%  Similarity=0.239  Sum_probs=43.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .|+++|++||.+..     +|+|.+|||++||||..||+..+.++++||.-
T Consensus       197 ~Lt~re~~vl~~~~-----~G~s~~eIA~~l~is~~TV~~~~~~~~~kl~~  242 (265)
T 3qp6_A          197 PLSQREYDIFHWMS-----RGKTNWEIATILNISERTVKFHVANVIRKLNA  242 (265)
T ss_dssp             CCCHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            69999999999985     79999999999999999999999999999953

>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=96.90  E-value=0.0013  Score=47.33  Aligned_cols=40  Identities=20%  Similarity=0.124  Sum_probs=32.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.++..|...|.    +++|..|||+.||||+.+|+.++.+
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            478888866666665    7899999999999999999987654

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.53  E-value=0.005  Score=53.39  Aligned_cols=46  Identities=17%  Similarity=0.147  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .+++.-..|-.++|.    +|+|..|||+.||||+.+|.+++.+|...+.
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    9999999999999999999999999998864

>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=96.47  E-value=0.0059  Score=56.93  Aligned_cols=51  Identities=14%  Similarity=0.316  Sum_probs=45.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          498 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       498 L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      +...+..|+++|++|+.+..     +++|.+|||+.+|+|..||+....++++||.
T Consensus       136 ~~~~~~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~  186 (208)
T 1yio_A          136 LEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLN  186 (208)
T ss_dssp             HHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhcCHHHHHHHHHHH-----cCCcHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence            34456689999999998864     6899999999999999999999999999995

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

Probab=96.30  E-value=0.0024  Score=48.02  Aligned_cols=39  Identities=15%  Similarity=0.204  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      +++..+.|+.+ +.    +++|..|||+.||||+.+|+.++.+|
T Consensus        17 ~~~~~~~i~~l-~~----~g~s~~eIA~~lgis~~TV~~~l~~a   55 (55)
T 2x48_A           17 EDDLVSVAHEL-AK----MGYTVQQIANALGVSERKVRRYLESC   55 (55)
T ss_dssp             HHHHHHHHHHH-HH----TTCCHHHHHHHHTSCHHHHHHHHTC-
T ss_pred             CHHHHHHHHHH-HH----cCCCHHHHHHHHCcCHHHHHHHHHhC
Confidence            34455666666 44    68999999999999999999987654

>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=96.16  E-value=0.0084  Score=56.27  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=42.5

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|++|+.+..     +++|.+|||+.+++|..||+....+.++||.
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            469999999998876     6899999999999999999999999999995

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=95.87  E-value=0.011  Score=56.37  Aligned_cols=46  Identities=22%  Similarity=0.260  Sum_probs=42.2

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..|+++|++|+.+-.     +++|.+|||+.+++|..||+....+.++||.
T Consensus       148 ~~LT~rE~~vL~~l~-----~g~s~~eIa~~l~is~~TV~~hi~~l~~KL~  193 (225)
T 3c3w_A          148 SGLTDQERTLLGLLS-----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLG  193 (225)
T ss_dssp             TTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            469999999998865     6799999999999999999999999999984

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=95.15  E-value=0.018  Score=54.67  Aligned_cols=47  Identities=17%  Similarity=0.197  Sum_probs=42.3

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ...|+++|++|+.+..     +++|.+|||+.+++|..||+....+.++||.
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     6899999999999999999999999999984

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=94.92  E-value=0.066  Score=51.35  Aligned_cols=55  Identities=22%  Similarity=0.306  Sum_probs=49.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       494 l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ........+..|++++++|+.+..     .+++.++||..||+|..+|+....++++||.
T Consensus       188 ~~~~~~~~l~~L~~r~~~i~~~~~-----~g~~~~eia~~l~~s~~tv~~~l~~i~~kl~  242 (258)
T 3p7n_A          188 RRERAAEMLKTLSPRQLEVTTLVA-----SGLRNKEVAARLGLSEKTVKMHRGLVMEKLN  242 (258)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhhcCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            345667889999999999999876     5899999999999999999999999999985

>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=94.30  E-value=0.011  Score=66.14  Aligned_cols=34  Identities=32%  Similarity=0.570  Sum_probs=13.4

Q ss_pred             CCcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHH
Q 008352          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI  286 (569)
Q Consensus       253 ~~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~  286 (569)
                      .+||+++||++||+.||||+|+|++||++|..+.
T Consensus        94 ~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~  127 (613)
T 3iyd_F           94 TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI  127 (613)
T ss_dssp             -----------C--------CSSSTTTHHHHHHH
T ss_pred             CCCcHHHHHHHhcccccCCchhHHHHHHHHHHhH
Confidence            6799999999999999999999999999998743

>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=93.43  E-value=0.087  Score=43.00  Aligned_cols=40  Identities=15%  Similarity=0.335  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      +.++.||.+-.-...|++.|..|||+.+|||+.+|++++.
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~   53 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLY   53 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            4456777665554445689999999999999999886544

>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=93.22  E-value=0.043  Score=39.63  Aligned_cols=33  Identities=21%  Similarity=0.296  Sum_probs=25.6

Q ss_pred             HHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          510 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       510 R~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      +.|+.+ +.    ++.|..+||+.+|||+.+|..++.+
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    5699999999999999999987643

>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=93.03  E-value=0.1  Score=49.21  Aligned_cols=50  Identities=10%  Similarity=0.034  Sum_probs=43.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  554 (569)
                      .|+++|.+||.+-.- +.|+.+|.+|||+.+     ++|..||+....+.++||..
T Consensus       156 ~Lt~rE~~vL~~l~~-~~~~~~s~~~Ia~~lw~~~~~~s~~tv~~hi~~i~~Kl~~  210 (230)
T 2oqr_A          156 TLPLKEFDLLEYLMR-NSGRVLTRGQLIDRVWGADYVGDTKTLDVHVKRLRSKIEA  210 (230)
T ss_dssp             CCCHHHHHHHHHHHH-TTTSCEEHHHHHHHHTSSCCTTHHHHHHHHHHHHHHHHCS
T ss_pred             ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCcCHHHHHHHHHHHHhh
Confidence            599999999987653 334569999999999     99999999999999999963

>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=93.03  E-value=0.081  Score=49.63  Aligned_cols=50  Identities=20%  Similarity=0.121  Sum_probs=42.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG---LSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG---ISrerVRqie~RALkKLR~  554 (569)
                      .|+++|++|+.+-.- +.|+.+|.+|||+.++   +|..||+....+.++||..
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            599999999987553 2345699999999999   9999999999999999963

>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=92.85  E-value=0.15  Score=42.11  Aligned_cols=44  Identities=20%  Similarity=0.453  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +.++.||.+......|+..|..|||+.||||+.+|++    +|.+|.+
T Consensus        10 ~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~----~L~~Le~   53 (81)
T 1qbj_A           10 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINR----VLYSLAK   53 (81)
T ss_dssp             HHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHH----HHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            3456666655544445789999999999999988875    5566654

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=92.70  E-value=0.11  Score=49.53  Aligned_cols=50  Identities=10%  Similarity=-0.049  Sum_probs=42.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  554 (569)
                      .|+++|.+||.+-.- +.|..+|.+|||+.+     ++|..||+....+.++||..
T Consensus       153 ~LT~rE~~vL~~l~~-~~~~~~s~~eIa~~lw~~~~~~s~~tV~~hi~~lr~KL~~  207 (238)
T 2gwr_A          153 SLTPLEFDLLVALAR-KPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKVEK  207 (238)
T ss_dssp             CCCHHHHHHHHHHHH-STTCCBCHHHHHHHHTCCC--CCTHHHHHHHHHHHHHHCS
T ss_pred             ccCHHHHHHHHHHHH-CCCceecHHHHHHHHcCCCCCCCcccHHHHHHHHHHHhcc
Confidence            599999999987653 334569999999999     99999999999999999963

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=91.96  E-value=0.12  Score=48.47  Aligned_cols=50  Identities=12%  Similarity=0.056  Sum_probs=42.8

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  554 (569)
                      .|+++|++|+.+-.- +.|..+|.+|||+.++     +|..||+....+.++||..
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 2235599999999998     9999999999999999964

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*

Probab=91.72  E-value=0.032  Score=55.35  Aligned_cols=51  Identities=18%  Similarity=0.266  Sum_probs=0.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHHHH
Q 008352          498 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG--LSKERVRQLESRALYRLK  553 (569)
Q Consensus       498 L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG--ISrerVRqie~RALkKLR  553 (569)
                      +...+..|++.++. |...||    .+.|.+|||+.||  ||.++|+.++.+|++.|.
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            45566778777777 445666    7899999999999  999999999999988763

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=91.55  E-value=0.11  Score=48.85  Aligned_cols=50  Identities=10%  Similarity=-0.023  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  554 (569)
                      .|+++|.+|+.+-.- +.|..+|.+|||+.++     +|..+|+....+.++||..
T Consensus       159 ~Lt~rE~~vL~~l~~-g~~~~~s~~~Ia~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  213 (233)
T 1ys7_A          159 DLTKREFDLLAVLAE-HKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLEA  213 (233)
T ss_dssp             CCCHHHHHHHHHHHH-TTTCCBCHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHC
T ss_pred             ccCHHHHHHHHHHHh-CCCCeEcHHHHHHHhcCcccCCCccCHHHHHHHHHHHhcc
Confidence            599999999987653 2334599999999998     9999999999999999974

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=91.21  E-value=0.19  Score=44.66  Aligned_cols=35  Identities=9%  Similarity=0.130  Sum_probs=28.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQ  543 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRq  543 (569)
                      ..|..| .+|+.+..     +|+|+.|||+.+|+|..||..
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            456666 67777755     579999999999999999976

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=90.97  E-value=0.26  Score=43.05  Aligned_cols=40  Identities=20%  Similarity=0.124  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.++..|...+.    .|+|..+||+.||||+.+|+....+
T Consensus         6 ~~s~~~r~~i~~~~~----~G~s~~~ia~~lgis~~Tv~r~~~~   45 (141)
T 1u78_A            6 ALSDTERAQLDVMKL----LNVSLHEMSRKISRSRHCIRVYLKD   45 (141)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHc
Confidence            467777766665555    6899999999999999999988765

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=90.78  E-value=0.35  Score=46.46  Aligned_cols=50  Identities=18%  Similarity=0.130  Sum_probs=43.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  554 (569)
                      .|+++|.+||.+... +.|+..|.+||++.+     +++..+|+....+.++||..
T Consensus       176 ~LT~rE~~iL~~l~~-~~~~~~s~~~i~~~lw~~~~~~~~~tv~~~i~~lr~KL~~  230 (250)
T 3r0j_A          176 SLSPTEFTLLRYFVI-NAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDT  230 (250)
T ss_dssp             CCCHHHHHHHHHHHH-TTTCCBCHHHHHHHHTTTSCCSCTHHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHHH-CCCceEcHHHHHHHHcCCCCCCCccCHHHHHHHHHHhhcC
Confidence            599999999988653 446889999999999     78999999999999999964

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=90.74  E-value=0.22  Score=47.82  Aligned_cols=36  Identities=19%  Similarity=0.183  Sum_probs=29.9

Q ss_pred             HHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          509 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       509 ER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      -.++..+ |.    .|+|..|||+.||||+.+|.+++..|.
T Consensus        14 G~ria~~-y~----~g~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           14 GLRLMRM-KN----DGMSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HHHHHHH-HH----TTCCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HHHHHHH-HH----cCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            3445555 65    789999999999999999999988775

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=90.74  E-value=0.2  Score=48.56  Aligned_cols=50  Identities=24%  Similarity=0.246  Sum_probs=42.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe-----~LGISrerVRqie~RALkKLR~  554 (569)
                      .|+++|++||.+..- +.|+.+|.+|||+     .++++..+|+....+.++||..
T Consensus       182 ~LT~rE~evL~ll~~-g~~~~~s~~eIa~~l~~~~l~~s~~TV~~hi~~lr~KL~~  236 (249)
T 3q9s_A          182 RLSPKEFDILALLIR-QPGRVYSRQEIGQEIWQGRLPEGSNVVDVHMANLRAKLRD  236 (249)
T ss_dssp             CCCHHHHHHHHHHHH-STTCCCCHHHHHHHHHTTCSCTTCSHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHHH-CCCceEcHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhhc
Confidence            599999999998763 3356799999999     5888999999999999999864

>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=90.42  E-value=0.42  Score=40.62  Aligned_cols=42  Identities=12%  Similarity=-0.018  Sum_probs=31.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      .+++.+|.-|...+.    .++|..+||+.||||+.+|+.+..+..
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            355555554444444    679999999999999999999887643

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=89.93  E-value=0.099  Score=49.12  Aligned_cols=50  Identities=4%  Similarity=-0.050  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  554 (569)
                      .|+++|++||.+-.- +.|+.+|.+|||+.++     +|..+|+....+.++||..
T Consensus       143 ~Lt~rE~~vL~~l~~-~~~~~~s~~~Ia~~l~~~~~~~s~~tv~~~i~~lr~KL~~  197 (223)
T 2hqr_A          143 EVKGKPFEVLTHLAR-HRDQIVSKEQLLDAIWEEPEMVTPNVIEVAINQIRQKMDK  197 (223)
T ss_dssp             CCCSTTTHHHHHHHH-TCSEEEEHHHHHHHHCCSSCSCGGGTHHHHHHHHHHHHHT
T ss_pred             ecCHHHHHHHHHHHh-CCCCcCCHHHHHHHhcCCccCCCCcCHHHHHHHHHHHHhc
Confidence            599999999987652 1223499999999999     9999999999999999974

>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=88.57  E-value=0.65  Score=41.39  Aligned_cols=42  Identities=12%  Similarity=-0.002  Sum_probs=32.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      .++..+|.-|...+.    .++|..+||+.||||+.+|+.++.+..
T Consensus        32 ~~s~e~r~~iv~~~~----~G~s~~~iA~~lgis~~TV~rw~~~~~   73 (149)
T 1k78_A           32 PLPDVVRQRIVELAH----QGVRPCDISRQLRVSHGCVSKILGRYY   73 (149)
T ss_dssp             CCCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            355555554444444    679999999999999999999987754

>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=88.55  E-value=0.9  Score=37.43  Aligned_cols=43  Identities=21%  Similarity=0.212  Sum_probs=33.0

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      ...|++.+..+|...+.  .+.+.|..|||+.+|+|+.+|++++.
T Consensus        16 ~~~l~~~~~~~l~~l~~--~~~~~t~~ela~~l~is~~tv~~~l~   58 (109)
T 2d1h_A           16 CYKITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVENSLK   58 (109)
T ss_dssp             HHTCCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45789888887755441  12679999999999999999986543

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=88.51  E-value=0.48  Score=37.28  Aligned_cols=44  Identities=27%  Similarity=0.396  Sum_probs=29.3

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +++..+.||.+---  ++.+.|..|||+.+|+|+.+|.+    .++.|++
T Consensus         8 m~~~~~~IL~~L~~--~~~~~s~~eLA~~lglsr~tv~~----~l~~L~~   51 (67)
T 2heo_A            8 GDNLEQKILQVLSD--DGGPVAIFQLVKKCQVPKKTLNQ----VLYRLKK   51 (67)
T ss_dssp             -CHHHHHHHHHHHH--HCSCEEHHHHHHHHCSCHHHHHH----HHHHHHH
T ss_pred             ccHHHHHHHHHHHH--cCCCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            34445556654321  23679999999999999888875    4555654

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=88.40  E-value=0.35  Score=40.20  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=21.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          524 PKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       524 ~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      +.|..|||+.||||+.+|++++.+
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            499999999999999999987654

>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=88.15  E-value=0.5  Score=44.60  Aligned_cols=42  Identities=17%  Similarity=0.235  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHHHHhcc--cCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGI--EDGKPKSLSEVGNIFGLSKERVRQLE  545 (569)
Q Consensus       504 ~L~~rER~VL~LRygL--~d~e~~Tl~EIAe~LGISrerVRqie  545 (569)
                      .|+++|++|+.+-..+  ..|.+.|.+|||+.||+|..+|+.++
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            5899999999875432  23468999999999999988876543

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=87.36  E-value=0.56  Score=47.61  Aligned_cols=36  Identities=14%  Similarity=0.284  Sum_probs=30.6

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      .|..++|.    +++|.+|||+.||||+.|||+.+..+.+
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            46777776    7899999999999999999988776644

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=87.35  E-value=1.1  Score=39.09  Aligned_cols=49  Identities=8%  Similarity=0.137  Sum_probs=36.9

Q ss_pred             HHHhcCCHHHHHHHHHHhcccCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          500 NLLTLLNPKERCIVRLRFGIEDGKP-KSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       500 ~aL~~L~~rER~VL~LRygL~d~e~-~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ...-.|++.+..|+..-..  .+.+ .|..|||+.+|+++.+|..    ++++|.+
T Consensus        19 ~~~~gLt~~e~~il~~L~~--~~~~~~t~~eLa~~l~~s~sTV~r----~L~~L~~   68 (123)
T 3r0a_A           19 KCALNLTKADLNVMKSFLN--EPDRWIDTDALSKSLKLDVSTVQR----SVKKLHE   68 (123)
T ss_dssp             HHHHTCCHHHHHHHHHHHH--STTCCEEHHHHHHHHTSCHHHHHH----HHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHH--CCCCCcCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            3456799999999876553  2234 8999999999999999984    5555543

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=86.92  E-value=1  Score=36.91  Aligned_cols=27  Identities=15%  Similarity=0.139  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESRAL  549 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~RAL  549 (569)
                      .+.|..+||+.||||+.+|+++..+..
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            468999999999999999999876543

>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=86.78  E-value=1.6  Score=37.70  Aligned_cols=50  Identities=16%  Similarity=0.241  Sum_probs=39.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          496 QHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       496 e~L~~aL~~L~~rER~VL~LRygL~d~---e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      ..|...+..|++.|+.|..+...  ..   ..+|..|||+..|+|..+|-+..++
T Consensus        10 ~~i~~~~~~ls~~e~~ia~yil~--~~~~~~~~si~elA~~~~vS~aTv~Rf~kk   62 (111)
T 2o3f_A           10 AIIQSMXHXLPPSERKLADYILA--HPHXAIESTVNEISALANSSDAAVIRLCXS   62 (111)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHH--CHHHHHTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHhccCCHHHHHHHHHHHH--ChHHHHhcCHHHHHHHHCCCHHHHHHHHHH
Confidence            45777788999999999876542  11   3699999999999999999876643

>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=86.77  E-value=3  Score=34.34  Aligned_cols=36  Identities=31%  Similarity=0.373  Sum_probs=27.9

Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          506 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       506 ~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      ++....||.+- .    .++|..|||+.+|+|+.+|++.+.
T Consensus        30 ~~~r~~Il~~L-~----~~~~~~eLa~~l~is~~tv~~~L~   65 (96)
T 1y0u_A           30 NPVRRKILRML-D----KGRSEEEIMQTLSLSKKQLDYHLK   65 (96)
T ss_dssp             CHHHHHHHHHH-H----TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHH-c----CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45566676655 3    579999999999999999986543

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=86.24  E-value=1.3  Score=39.56  Aligned_cols=42  Identities=12%  Similarity=0.245  Sum_probs=32.5

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      ..|++.++.||.+-..   +...|..|||+.+|+|+.+|+.++++
T Consensus         5 ~~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   46 (151)
T 2dbb_A            5 RKLDRVDMQLVKILSE---NSRLTYRELADILNTTRQRIARRIDK   46 (151)
T ss_dssp             -CCCHHHHHHHHHHHH---CTTCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3488999988875432   25799999999999999999865443

>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=86.21  E-value=1.7  Score=40.40  Aligned_cols=53  Identities=11%  Similarity=0.256  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       494 l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      +...+...+..|++.|..||..-+... +.+.|..+||+.+|+++.+|..++.+
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            344556667779999999998766321 25899999999999999999865544

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=85.81  E-value=1.3  Score=39.48  Aligned_cols=41  Identities=20%  Similarity=0.146  Sum_probs=32.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.++.||.+-..   +...|..|||+.+|+|+.+|+.++++
T Consensus         2 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   42 (144)
T 2cfx_A            2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVRQ   42 (144)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            378888888876432   25799999999999999999865543

>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=85.02  E-value=1.3  Score=36.14  Aligned_cols=33  Identities=15%  Similarity=0.427  Sum_probs=23.7

Q ss_pred             cccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          518 GIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       518 gL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +|..|+..|..+||+.||+++..|.    |+|.+|.+
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            3444466899999999999987765    45555543

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=84.96  E-value=1.7  Score=38.87  Aligned_cols=41  Identities=20%  Similarity=0.363  Sum_probs=32.2

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.++.||.+-..  + ...|..|||+.+|+|+.+|++++++
T Consensus         4 ~ld~~~~~il~~L~~--~-~~~s~~ela~~lg~s~~tv~~~l~~   44 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN--D-GKAPLREISKITGLAESTIHERIRK   44 (151)
T ss_dssp             CCCHHHHHHHHHHHH--C-TTCCHHHHHHHHCSCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888875432  2 4799999999999999999866544

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=84.73  E-value=1.6  Score=37.97  Aligned_cols=40  Identities=18%  Similarity=0.149  Sum_probs=31.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.+..||..-+.    .+.|..|||+.+|+|+.+|++++.+
T Consensus        35 ~lt~~~~~iL~~l~~----~~~t~~eLa~~l~~s~~tvs~~l~~   74 (146)
T 3tgn_A           35 ALTNTQEHILMLLSE----ESLTNSELARRLNVSQAAVTKAIKS   74 (146)
T ss_dssp             CCCHHHHHHHHHHTT----CCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            467888888776553    2399999999999999999865544

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=84.61  E-value=1.8  Score=38.76  Aligned_cols=41  Identities=22%  Similarity=0.408  Sum_probs=32.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.++.||.+-..   +...|..|||+.+|+|+.+|++++++
T Consensus         5 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   45 (152)
T 2cg4_A            5 LIDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVEK   45 (152)
T ss_dssp             CCCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888875432   25789999999999999999876544

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=84.49  E-value=2.9  Score=35.14  Aligned_cols=46  Identities=17%  Similarity=0.187  Sum_probs=32.4

Q ss_pred             HHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          497 HVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       497 ~L~~aL~~L~-~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .+..++..|. +....||.+-..    .++|..|||+.+|+|+.+|++.++
T Consensus        15 ~~~~~~~~l~~~~r~~IL~~L~~----~~~~~~ela~~l~is~stvs~~L~   61 (106)
T 1r1u_A           15 RVTEIFKALGDYNRIRIMELLSV----SEASVGHISHQLNLSQSNVSHQLK   61 (106)
T ss_dssp             HHHHHHHHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445555555 445566665432    578999999999999999986544

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=84.40  E-value=1.5  Score=38.43  Aligned_cols=40  Identities=15%  Similarity=0.344  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      |++.++.||..-..   +...|..|||+.+|+|+.+|++.+++
T Consensus         2 ld~~~~~il~~L~~---~~~~~~~ela~~lg~s~~tv~~~l~~   41 (141)
T 1i1g_A            2 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRKRVKA   41 (141)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            67777888875321   25689999999999999999865443

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=84.34  E-value=1.4  Score=38.43  Aligned_cols=46  Identities=11%  Similarity=0.094  Sum_probs=33.9

Q ss_pred             hcCCHHHHHHHHHHhcc-cCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL-~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      ..|++.+..+|..-+.+ ..+.+.|..+||+.+|+++.+|++++++-
T Consensus         9 ~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~L   55 (139)
T 2x4h_A            9 SNLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHL   55 (139)
T ss_dssp             --CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             hhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHH
Confidence            46888888877765543 23468999999999999999998655543

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=84.04  E-value=1.8  Score=32.70  Aligned_cols=32  Identities=6%  Similarity=0.182  Sum_probs=25.8

Q ss_pred             CCC----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Q 008352          524 PKS----LSEVGNIFGLSKERVRQLESRALYRLKQSL  556 (569)
Q Consensus       524 ~~T----l~EIAe~LGISrerVRqie~RALkKLR~~l  556 (569)
                      +.|    ..+||..+||++.+|++...+ ...++..+
T Consensus        21 g~s~~~~~~~vA~~~gIs~~tl~~W~~~-~~~~~~~~   56 (59)
T 2glo_A           21 DNDCKGNQRATARKYNIHRRQIQKWLQC-ESNLRSSV   56 (59)
T ss_dssp             CTTTTTCHHHHHHHTTSCHHHHHHHHTT-HHHHHHHH
T ss_pred             CCCcchHHHHHHHHHCcCHHHHHHHHHH-HHHHHHHH
Confidence            567    999999999999999999764 45555544

>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=84.00  E-value=4  Score=35.01  Aligned_cols=52  Identities=12%  Similarity=0.051  Sum_probs=38.3

Q ss_pred             HHHHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          495 RQHVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       495 ~e~L~~aL--~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      ...+...+  ..|++.+..||..-+.- ++.+.|..|||+.+|+++.+|..++.+
T Consensus        20 ~~~~~~~~~~~~lt~~~~~iL~~l~~~-~~~~~~~~ela~~l~~~~~tvs~~l~~   73 (141)
T 3bro_A           20 STRFDIFAKKYDLTGTQMTIIDYLSRN-KNKEVLQRDLESEFSIKSSTATVLLQR   73 (141)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHHT-TTSCCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCCCcchHHHHHHH
Confidence            34455555  35899999988776642 223799999999999999999865544

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=83.91  E-value=1.7  Score=39.46  Aligned_cols=41  Identities=12%  Similarity=0.057  Sum_probs=32.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.++.||.+-..  + ...|..|||+.+|+|+.+|++++.+
T Consensus         7 ~ld~~~~~il~~L~~--~-~~~s~~ela~~lg~s~~tv~~~l~~   47 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE--N-GRLTNVELSERVALSPSPCLRRLKQ   47 (162)
T ss_dssp             CCCHHHHHHHHHHHH--C-TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888876432  2 4689999999999999999876544

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=83.54  E-value=1.7  Score=39.64  Aligned_cols=40  Identities=15%  Similarity=0.253  Sum_probs=31.0

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      |++.++.||.+--.   +...|..|||+.+|+|+.+|+.++++
T Consensus         1 lD~~d~~il~~L~~---~~~~s~~~la~~lg~s~~tv~~rl~~   40 (162)
T 3i4p_A            1 MDRLDRKILRILQE---DSTLAVADLAKKVGLSTTPCWRRIQK   40 (162)
T ss_dssp             CCHHHHHHHHHHTT---CSCSCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            56777888876432   25789999999999999999976544

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=83.50  E-value=1.9  Score=38.59  Aligned_cols=41  Identities=32%  Similarity=0.331  Sum_probs=32.4

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.++.||.+-..  + ...|..|||+.+|+|+.+|++++++
T Consensus         4 ~ld~~~~~iL~~L~~--~-~~~s~~ela~~lg~s~~tv~~~l~~   44 (150)
T 2w25_A            4 ALDDIDRILVRELAA--D-GRATLSELATRAGLSVSAVQSRVRR   44 (150)
T ss_dssp             CCCHHHHHHHHHHHH--C-TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            488888888876432  2 4799999999999999999866543

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=83.37  E-value=3.3  Score=35.78  Aligned_cols=48  Identities=13%  Similarity=0.173  Sum_probs=36.7

Q ss_pred             HHHHHH--hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          497 HVRNLL--TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       497 ~L~~aL--~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      .+...+  ..|++.+..||..-+    +.+.|..|||+.+|+|+.+|..++.+-
T Consensus        25 ~~~~~~~~~~l~~~~~~iL~~l~----~~~~~~~ela~~l~~s~~tvs~~l~~L   74 (146)
T 2gxg_A           25 ELNRRLGELNLSYLDFLVLRATS----DGPKTMAYLANRYFVTQSAITASVDKL   74 (146)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHT----TSCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHh----cCCcCHHHHHHHhCCCchhHHHHHHHH
Confidence            344444  358999999887765    268999999999999999998655443

>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=83.21  E-value=1.8  Score=38.50  Aligned_cols=40  Identities=13%  Similarity=0.145  Sum_probs=30.3

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      |++.++.||.+--   .+...|..|||+.+|+|+.+|++++++
T Consensus         1 ld~~~~~il~~L~---~~~~~~~~ela~~lg~s~~tv~~~l~~   40 (150)
T 2pn6_A            1 MDEIDLRILKILQ---YNAKYSLDEIAREIRIPKATLSYRIKK   40 (150)
T ss_dssp             CCHHHHHHHHHHT---TCTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CChHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4677777876543   225799999999999999999865443

>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=82.93  E-value=3.9  Score=35.18  Aligned_cols=54  Identities=9%  Similarity=0.137  Sum_probs=40.2

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          494 MRQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       494 l~e~L~~aL~--~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      +...+...+.  .|++.+..||..-+. .++++.|..|||+.+|+++.+|.+++.+-
T Consensus        16 ~~~~~~~~~~~~~lt~~~~~vL~~l~~-~~~~~~t~~ela~~l~~~~~tvs~~l~~L   71 (139)
T 3eco_A           16 MKQKADQKLEQFDITNEQGHTLGYLYA-HQQDGLTQNDIAKALQRTGPTVSNLLRNL   71 (139)
T ss_dssp             HHHHHHHHHGGGTCCHHHHHHHHHHHH-STTTCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHh-cCCCCcCHHHHHHHhCCCcccHHHHHHHH
Confidence            3445555554  589999999887664 22258999999999999999998665543

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=82.87  E-value=2.7  Score=36.57  Aligned_cols=52  Identities=15%  Similarity=0.239  Sum_probs=36.9

Q ss_pred             HHHHHHHHHhc----CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          494 MRQHVRNLLTL----LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       494 l~e~L~~aL~~----L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      +...+...+..    |++.+..||..-+.   ..+.|..|||+.+|+++.+|.+++.+-
T Consensus        20 ~~~~~~~~l~~~~~~lt~~~~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   75 (142)
T 3ech_A           20 VRTRIQSELDCQRLDLTPPDVHVLKLIDE---QRGLNLQDLGRQMCRDKALITRKIREL   75 (142)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHH---TTTCCHHHHHHHHC---CHHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCCHHHHHHHHHHHh---CCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence            34456666654    99999998887654   247999999999999999998766543

>3sqn_A Conserved domain protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MGA family; 2.31A {Enterococcus faecalis}

Probab=82.49  E-value=1.5  Score=47.37  Aligned_cols=107  Identities=16%  Similarity=0.115  Sum_probs=61.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHH
Q 008352          431 SPDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKER  510 (569)
Q Consensus       431 ~Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER  510 (569)
                      ..|..+||+.+|+|...|+.-+..-+..+.-...+.....+-   .+.........             .....+.+.+|
T Consensus        32 ~it~~eLA~~L~VS~RTIr~dI~~In~~L~~~~~I~~~~~Gy---~L~~~~~~~~~-------------~~~~~~~~~eR   95 (485)
T 3sqn_A           32 QLTAKRLAAQIQTTERTVFSDLQYIRSQLPADWSIETDSSGI---RLRNQGNAQTN-------------ELWSLFLPQSI   95 (485)
T ss_dssp             SCBCGGGHHHHTSCHHHHHHHHHHHHTTCCTTEEEEEETTEE---EEEEC---CTH-------------HHHHHHGGGSH
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHhcccCcEEEEcCCEE---EEecCcHHHHH-------------HHHHhcCHHHH
Confidence            578999999999999999987764433321000111000010   11111000110             01122345555


Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ....+.+.|.. ++.|+.++|+.++||+.||.+-+++..+.|++
T Consensus        96 ~~~Il~~LL~~-~~isi~~Lae~l~VS~sTi~~DLk~i~~~L~~  138 (485)
T 3sqn_A           96 SIQLLKELLFT-KELVTTSFLSTSGVSYETLKRHIKKMNQALRD  138 (485)
T ss_dssp             HHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHHHGG
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            54444444443 58999999999999999999877777666654

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=82.48  E-value=1.2  Score=37.75  Aligned_cols=45  Identities=22%  Similarity=0.349  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .+.+....||...+-  .|+..|..|||+.+|||+.+|+    +++++|.+
T Consensus        15 ~~~~~~l~Il~~l~~--~g~~~s~~eLa~~lgvs~~tV~----~~L~~L~~   59 (110)
T 1q1h_A           15 LLGDDVIDVLRILLD--KGTEMTDEEIANQLNIKVNDVR----KKLNLLEE   59 (110)
T ss_dssp             TSCSTTHHHHHHHHH--HCSCBCHHHHHHTTTSCHHHHH----HHHHHHHH
T ss_pred             HcChHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            345666677765532  3467999999999999999998    56666665

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=82.48  E-value=2.2  Score=35.31  Aligned_cols=41  Identities=15%  Similarity=0.189  Sum_probs=29.1

Q ss_pred             CCHHHHH-HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          505 LNPKERC-IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       505 L~~rER~-VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      .++..+. |+.+...  + .+.|..+||..+|||+.+|+++..+.
T Consensus         6 ys~e~k~~~v~~~~~--~-~g~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            6 YSEEFKRDAVALYEN--S-DGASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCHHHHHHHHHHHTT--G-GGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH--c-CCChHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555554 4444432  1 26899999999999999999987653

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=82.37  E-value=1.8  Score=35.42  Aligned_cols=41  Identities=22%  Similarity=0.191  Sum_probs=32.1

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.+..||..-..   +.+.|..|||+.+|+++.+|++++.+
T Consensus        17 ~l~~~~~~il~~l~~---~~~~s~~ela~~l~is~~tv~~~l~~   57 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLKV   57 (109)
T ss_dssp             CCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            578888888876532   25799999999999999999865544

>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=82.30  E-value=0.73  Score=41.67  Aligned_cols=40  Identities=13%  Similarity=0.007  Sum_probs=29.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .++..+|.-|...+-    .++|..+||+.||||+.+|+.++++
T Consensus        25 ~~s~e~r~~ii~l~~----~G~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           25 PLPEVVRQRIVDLAH----QGVRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             SSCHHHHHHHHHHHH----HTCCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            355555544444443    5799999999999999999998765

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=82.11  E-value=2  Score=37.36  Aligned_cols=40  Identities=13%  Similarity=0.228  Sum_probs=28.9

Q ss_pred             cCCHHHHHHHHHHhcccC--CCCCCHHHHHHHhCCCHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIED--GKPKSLSEVGNIFGLSKERVRQ  543 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d--~e~~Tl~EIAe~LGISrerVRq  543 (569)
                      -+++.|+.-|..|+-+..  .+|+|+.||++.+|+|..||.+
T Consensus        36 L~T~~E~~alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsR   77 (107)
T 3frw_A           36 VCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISR   77 (107)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHH
Confidence            366776665555443321  1579999999999999999975

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=82.07  E-value=4  Score=33.49  Aligned_cols=50  Identities=20%  Similarity=0.229  Sum_probs=32.9

Q ss_pred             HHHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          497 HVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       497 ~L~~aL~~L~-~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      .+..++..|. +....||.+-   .+ .+.|..|||+.+|+|+.+|++.    +++|++
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L---~~-~~~~~~ela~~l~is~~tvs~~----L~~L~~   62 (98)
T 3jth_A           12 KAVVLLKAMANERRLQILCML---HN-QELSVGELCAKLQLSQSALSQH----LAWLRR   62 (98)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHT---TT-SCEEHHHHHHHHTCCHHHHHHH----HHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHH---hc-CCCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            3445555554 4444555433   23 5899999999999999999754    455544

>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=82.01  E-value=3.7  Score=34.02  Aligned_cols=45  Identities=22%  Similarity=0.231  Sum_probs=30.4

Q ss_pred             HHHHHHhcCCH-HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHH
Q 008352          497 HVRNLLTLLNP-KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  545 (569)
Q Consensus       497 ~L~~aL~~L~~-rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie  545 (569)
                      .+..++..|.. .-..||.+-.   + .++|..|||+.+|+|+.+|++.+
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L~---~-~~~~~~ela~~l~is~~tvs~~L   57 (102)
T 3pqk_A           12 EVANLLKTLSHPVRLMLVCTLV---E-GEFSVGELEQQIGIGQPTLSQQL   57 (102)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHHH---T-CCBCHHHHHHHHTCCTTHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH---h-CCCCHHHHHHHHCcCHHHHHHHH
Confidence            34455555554 4444544432   2 46999999999999999998644

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=81.90  E-value=2  Score=35.02  Aligned_cols=46  Identities=26%  Similarity=0.261  Sum_probs=31.7

Q ss_pred             HHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          498 VRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       498 L~~aL~~L~-~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      +..++..|. +.+..||.+-.   .+.+.|..|||+.+|+|+.+|++.+.
T Consensus        14 ~~~~~~~l~~~~~~~il~~l~---~~~~~s~~ela~~l~is~~tvs~~l~   60 (99)
T 3cuo_A           14 AAALLKAMSHPKRLLILCMLS---GSPGTSAGELTRITGLSASATSQHLA   60 (99)
T ss_dssp             HHHHHHHHCSHHHHHHHHHHT---TCCSEEHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHHH---hCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            334444443 56666665432   34589999999999999999986554

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=81.41  E-value=4.1  Score=35.07  Aligned_cols=61  Identities=16%  Similarity=0.222  Sum_probs=45.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHhcccCC---CCCCHHHHHHHhCCCHHHHHHHHHH----HHHHHHHHhh
Q 008352          495 RQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR----ALYRLKQSLG  557 (569)
Q Consensus       495 ~e~L~~aL~~L~~rER~VL~LRygL~d~---e~~Tl~EIAe~LGISrerVRqie~R----ALkKLR~~l~  557 (569)
                      ...|...+..|++.|+.|..+..  ...   ..+|..|||+..|+|..+|-+..++    ...-||..+.
T Consensus         5 ~~~I~~~~~~lt~~e~~ia~yil--~~~~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~gf~efk~~l~   72 (107)
T 3iwf_A            5 LYKIDNQYPYFTKNEKKIAQFIL--NYPHKVVNMTSQEIANQLETSSTSIIRLSKKVTPGGFNELKTRLS   72 (107)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHH--HCHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHH--hCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            34677888999999999987543  221   4799999999999999999876654    3444554443

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=81.36  E-value=1.4  Score=37.26  Aligned_cols=38  Identities=18%  Similarity=0.209  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      +|...|+.+...    .+.|..+||+.+|||..||+..++.-
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            345556555443    34899999999999999999988753

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=81.26  E-value=4.4  Score=34.60  Aligned_cols=50  Identities=14%  Similarity=0.101  Sum_probs=37.6

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          495 RQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       495 ~e~L~~aL~--~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      ...+...+.  .|++.+..||..-+.   +.+.|..|||+.+|+|+.+|..++.+
T Consensus        15 ~~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~~~~ela~~l~~s~~tvs~~l~~   66 (138)
T 3bpv_A           15 RVFIGRELGHLNLTDAQVACLLRIHR---EPGIKQDELATFFHVDKGTIARTLRR   66 (138)
T ss_dssp             HHHHHHHSGGGTCCHHHHHHHHHHHH---STTCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            334455553  589999888876553   26799999999999999999865544

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=80.71  E-value=2.5  Score=35.28  Aligned_cols=38  Identities=24%  Similarity=0.259  Sum_probs=28.5

Q ss_pred             CHHHHHHHH-HHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          506 NPKERCIVR-LRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       506 ~~rER~VL~-LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      +|....||. +.-.    .+++..|||+.+|+|+.+|++.++.
T Consensus        26 ~~~Rl~IL~~l~~~----~~~~~~ela~~l~is~stvs~hL~~   64 (99)
T 2zkz_A           26 HPMRLKIVNELYKH----KALNVTQIIQILKLPQSTVSQHLCK   64 (99)
T ss_dssp             SHHHHHHHHHHHHH----SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHC----CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            466666773 3222    4799999999999999999977654

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=80.61  E-value=3.3  Score=34.71  Aligned_cols=46  Identities=11%  Similarity=0.094  Sum_probs=31.8

Q ss_pred             HHHHHhcCC-HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          498 VRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       498 L~~aL~~L~-~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      +..++..|. +....||.+-.   + .+.|..|||+.+|+|+.+|++.+.+
T Consensus        11 ~~~~~~~l~~~~r~~IL~~L~---~-~~~~~~ela~~l~is~~tv~~~l~~   57 (114)
T 2oqg_A           11 LASVFAALSDETRWEILTELG---R-ADQSASSLATRLPVSRQAIAKHLNA   57 (114)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHH---H-SCBCHHHHHHHSSSCHHHHHHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHHH---c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            344455554 55556666432   2 4699999999999999999865543

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=80.44  E-value=3.9  Score=34.77  Aligned_cols=46  Identities=15%  Similarity=0.228  Sum_probs=33.0

Q ss_pred             HHHHHhc-CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          498 VRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       498 L~~aL~~-L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      +..++.. .++.+..||.+-..    .+.|..|||+.+|+|+.+|.+.+++
T Consensus        22 ~~~~~~~l~~~~~~~il~~L~~----~~~s~~ela~~l~is~stvsr~l~~   68 (119)
T 2lkp_A           22 VASTLQALATPSRLMILTQLRN----GPLPVTDLAEAIGMEQSAVSHQLRV   68 (119)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHHH----CCCCHHHHHHHHSSCHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3344433 34667777766543    4799999999999999999866544

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=80.38  E-value=2.5  Score=39.06  Aligned_cols=42  Identities=19%  Similarity=0.211  Sum_probs=32.3

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      ..|++.++.||.+-..  + ...|..|||+.+|+|+.+|+.++++
T Consensus        13 ~~ld~~d~~IL~~L~~--~-~~~s~~eLA~~lglS~~tv~~~l~~   54 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKK--D-ARLTISELSEQLKKPESTIHFRIKK   54 (171)
T ss_dssp             -CCCHHHHHHHHHHHH--C-TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4578888888876432  2 4689999999999999999866544

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=80.34  E-value=1.7  Score=35.82  Aligned_cols=45  Identities=11%  Similarity=0.060  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHHHHhccc-CCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~-d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      .|+.++..||...+.-. +|.+.|..|||+.+|+++.+|.+++.+-
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~L   54 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKF   54 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            47888888887655322 2344899999999999999998765543

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=80.29  E-value=6.2  Score=34.81  Aligned_cols=52  Identities=17%  Similarity=0.080  Sum_probs=39.0

Q ss_pred             HHHHHHH---hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          496 QHVRNLL---TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       496 e~L~~aL---~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      ..+...+   -.|++.|..||..-+.   +.+.|..|||+.+|+++.+|.+++.+-.+
T Consensus        35 ~~~~~~l~~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~Le~   89 (162)
T 2fa5_A           35 GNIAKVYGDRYGMAIPEWRVITILAL---YPGSSASEVSDRTAMDKVAVSRAVARLLE   89 (162)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHHHHH---STTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3444444   3699999998877654   25899999999999999999876655433

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=80.27  E-value=4.8  Score=34.49  Aligned_cols=42  Identities=7%  Similarity=0.036  Sum_probs=33.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      .|++.+..||..-+.   +.+.|..|||+.+|+|+.+|.+.+.+-
T Consensus        28 ~l~~~~~~iL~~l~~---~~~~~~~ela~~l~is~~~vs~~l~~L   69 (142)
T 3bdd_A           28 GISLTRYSILQTLLK---DAPLHQLALQERLQIDRAAVTRHLKLL   69 (142)
T ss_dssp             SSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            799999988877543   247999999999999999998655443

>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=80.03  E-value=4.8  Score=34.71  Aligned_cols=42  Identities=21%  Similarity=0.316  Sum_probs=33.5

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.+..|+.+.+ +.+ .+.|..|||+.+|+++.+|..++.+
T Consensus        23 gl~~~~~~il~~L~-~~~-~~~t~~ela~~l~~~~stvs~~l~~   64 (152)
T 1ku9_A           23 GLNKSVGAVYAILY-LSD-KPLTISDIMEELKISKGNVSMSLKK   64 (152)
T ss_dssp             TCCHHHHHHHHHHH-HCS-SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCChhHHHHHHHHH-HcC-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            58999998887764 223 5799999999999999999865543

>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=80.01  E-value=9.2  Score=32.89  Aligned_cols=78  Identities=10%  Similarity=0.101  Sum_probs=48.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCCcchhhcccCCCCCChhHHHHHHHHHHHHHHHHhcCCHHHH-
Q 008352          432 PDKEDLARRVGITVEKLERLIFITRMPLSMQQPVWADQDTTFQEITADTGVEIPDISVQKQLMRQHVRNLLTLLNPKER-  510 (569)
Q Consensus       432 Pt~eEIA~~lgis~e~v~~ll~~~~~~~SLD~~v~~d~~~~l~d~i~D~~~~~pee~l~~~el~e~L~~aL~~L~~rER-  510 (569)
                      -+..+||+.+|++...|...+......-       ..   .      ....  |                 ..|++.+. 
T Consensus        23 ~s~~~ia~~lgis~~Tv~r~~~~~~~~g-------~~---~------~~gr--~-----------------~~l~~~~~~   67 (141)
T 1u78_A           23 VSLHEMSRKISRSRHCIRVYLKDPVSYG-------TS---K------RAPR--R-----------------KALSVRDER   67 (141)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHSGGGTT-------CC---C------CCCC--C-----------------CSSCHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcccccC-------Cc---C------CCCC--C-----------------CcCCHHHHH
Confidence            4789999999999999999886432110       00   0      0000  0                 01222222 


Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhC--CCHHHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFG--LSKERVRQLESRA  548 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LG--ISrerVRqie~RA  548 (569)
                      .|+.+.-.    ..+|..+|+..||  +|.++|++++.+.
T Consensus        68 ~i~~~~~~----~~~s~~~i~~~lg~~~s~~tV~r~l~~~  103 (141)
T 1u78_A           68 NVIRAASN----SCKTARDIRNELQLSASKRTILNVIKRS  103 (141)
T ss_dssp             HHHHHHHH----CCCCHHHHHHHTTCCSCHHHHHHHHHHT
T ss_pred             HHHHHHhC----CCCCHHHHHHHHCCCccHHHHHHHHHHC
Confidence            23333111    4589999999999  8999999998763

---

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	569
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	1e-28
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	2e-27
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	4e-20
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	7e-20
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	4e-16
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	1e-15
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	4e-09
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	6e-07
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	7e-07
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	2e-06
d1or7a1	68	a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escheri	2e-04

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 180

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score =  110 bits (275), Expect = 1e-28
 Identities = 57/179 (31%), Positives = 92/179 (51%), Gaps = 30/179 (16%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIR------------------LEKEKSKLQ 296
           DP+R +L       LLT +EE +L  ++++ +                   + + K    
Sbjct: 2   DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGT 61

Query: 297 SQFGREPTLIEWAKAIGLSCRDLKSE------------LHSGNSSREKLINANLRLVVHV 344
           ++  + P L E      +   D K +               G ++R+ LI ANLRLVV +
Sbjct: 62  ARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSI 121

Query: 345 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRT 403
           AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F++YA WW+RQ I +AI   +RT
Sbjct: 122 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 180

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

 Score =  111 bits (277), Expect = 2e-27
 Identities = 46/190 (24%), Positives = 84/190 (44%)

Query: 208 KQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETR 267
           + F Q R + ++      S   + +      R             + + + LF     + 
Sbjct: 142 EVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSD 201

Query: 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 327
               A          +     E+    LQ     E       + +    R +        
Sbjct: 202 TWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKAR 261

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYW 387
            ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F++YA W
Sbjct: 262 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 321

Query: 388 WVRQTIRKAI 397
           W+RQ I ++I
Sbjct: 322 WIRQAITRSI 331

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 87

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 82.6 bits (204), Expect = 4e-20
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 324 HSGNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 6   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 65

Query: 381 FASYAYWWVRQTIRKAI 397
             +Y    ++  I   +
Sbjct: 66  AEAYIKLRIKGAIYDYL 82

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]} Length = 87

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

 Score = 82.1 bits (203), Expect = 7e-20
 Identities = 30/80 (37%), Positives = 51/80 (63%)

Query: 489 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 548
             + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +A
Sbjct: 3   AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62

Query: 549 LYRLKQSLGGKASYGYADLL 568
           L +L+     K       L+
Sbjct: 63  LRKLRHPSRSKYLKSLLSLM 82

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

 Score = 70.9 bits (174), Expect = 4e-16
 Identities = 22/67 (32%), Positives = 41/67 (61%)

Query: 500 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 559
           ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +L+     +
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 560 ASYGYAD 566
               + D
Sbjct: 61  VLRSFLD 67

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]} Length = 61

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

 Score = 68.9 bits (169), Expect = 1e-15
 Identities = 22/57 (38%), Positives = 41/57 (71%)

Query: 498 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 554
           +   L+ L+ +E  ++++R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 2   LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 58

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 51.0 bits (122), Expect = 4e-09
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 544
            +  V K+ + + V+  ++ L  +E+ +++L F     +     EV  I   S  RV QL
Sbjct: 2   VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQL 57

Query: 545 ESRALYRLKQSL 556
           +++AL RL++ L
Sbjct: 58  KAKALERLREML 69

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 45.1 bits (107), Expect = 6e-07
 Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 9/82 (10%)

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

Query: 459 LSMQQPVWADQDTTFQEITADT 480
           LS+++  + D    + E+   +
Sbjct: 56  LSLEEV-FRDFARDYSELIPSS 76

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 44.3 bits (105), Expect = 7e-07
 Identities = 10/56 (17%), Positives = 27/56 (48%)

Query: 402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFITRM 457
            T+++  ++  + +K+ +AK    +    +P   ++A  +GI+ E +       R+
Sbjct: 2   GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRL 57

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score = 43.1 bits (102), Expect = 2e-06
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLSM 461
           IR+P ++   ++K+    R   QE    P  E++A  +G     +++E  + I + P+S+
Sbjct: 1   IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 60

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 14/63 (22%), Positives = 22/63 (34%), Gaps = 4/63 (6%)

Query: 494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 553
           +RQ V   +  L    R  + LR  ++     S  E+  I       VR    RA   + 
Sbjct: 8   LRQIVFRTIESLPEDLRMAITLRE-LDG---LSYEEIAAIMDCPVGTVRSRIFRAREAID 63

Query: 554 QSL 556
             +
Sbjct: 64  NKV 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	569
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	100.0
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.82
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.77
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.65
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.62
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.54
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.38
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.21
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.18
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.0
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.79
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.79
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.75
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.59
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.34
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.29
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	98.05
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.89
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.83
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.48
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	95.42
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	95.09
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	94.12
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.07
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	91.72
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	91.1
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.05
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	91.03
d1hlva1	66	DNA-binding domain of centromere binding protein B	90.28
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	89.64
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	89.63
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	86.45
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	86.4
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	85.99
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	85.92
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	85.89
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	85.83
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	85.56
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	85.41
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	85.16
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	84.14
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	83.7
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	83.69
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	83.58
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	83.19
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	83.08
d1zyba1	73	Probable transcription regulator BT4300, C-termina	82.8
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	82.79
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	82.67
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	82.57
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	81.9
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	81.75
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	81.49
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	81.35
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	80.97
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	80.9
d1y7ya1	69	Restriction-modification controller protein C.AhdI	80.73
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	80.72
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	80.71
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	80.35

>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=1.4e-33  Score=267.54  Aligned_cols=150  Identities=37%  Similarity=0.640  Sum_probs=122.3

Q ss_pred             CcHHHHHHccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh------------------hhhCCCCcHHHHH------
Q 008352          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ------------------SQFGREPTLIEWA------  309 (569)
Q Consensus       254 ~d~l~~yl~~~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~l~------------------~~~g~~pt~~ewA------  309 (569)
                      +||+++||++|+++||||+|||++|+++|+.+..+.....+..                  ...+..|...+|.      
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            5899999999999999999999999999998765443322221                  1122333333332      


Q ss_pred             ---HHcCC---CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhh
Q 008352          310 ---KAIGL---SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAS  383 (569)
Q Consensus       310 ---~a~g~---~~~~L~~~l~~G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFST  383 (569)
                         .....   ..+.+......|+.|+++||.+|++||++||++|.+.|++++||||||+|||++|+++|||++|++|+|
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               22222   134556677788999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcccc
Q 008352          384 YAYWWVRQTIRKAIFQHSRT  403 (569)
Q Consensus       384 YA~~wIRqaI~~~Ir~~~r~  403 (569)
                      ||+|||+++|.++|++++|+
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=99.82  E-value=4.7e-21  Score=195.73  Aligned_cols=75  Identities=44%  Similarity=0.939  Sum_probs=72.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhc
Q 008352          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQH  400 (569)
Q Consensus       326 G~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~  400 (569)
                      ...|+++||++|++||++||++|.++|++++||+|+|++||++|+++|||.+|++|+|||+||||++|.++|+++
T Consensus       260 ~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         260 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHHHHHHhCC
Confidence            347999999999999999999999999999999999999999999999999999999999999999999999875

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.77  E-value=4.7e-19  Score=148.83  Aligned_cols=74  Identities=24%  Similarity=0.379  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHHhcc
Q 008352          328 SSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHS  401 (569)
Q Consensus       328 ~Are~LI~~nlrLV~sIArry~~~---g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir~~~  401 (569)
                      ..+++||..|++||.++|++|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|.+++|+..
T Consensus        10 ~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~d   86 (87)
T d1rp3a3          10 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD   86 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            468999999999999999998654   78999999999999999999999999999999999999999999999764

>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=99.65  E-value=3.6e-17  Score=137.01  Aligned_cols=75  Identities=39%  Similarity=0.737  Sum_probs=71.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhhhh
Q 008352          494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL  568 (569)
Q Consensus       494 l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yldll  568 (569)
                      +++.|..+|+.|+++|+.||.+||||++++++|+.|||+.||||+++|||++.+|++|||.......++.|+|++
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            455788999999999999999999999999999999999999999999999999999999998889999999975

>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=99.62  E-value=5.9e-17  Score=129.67  Aligned_cols=66  Identities=33%  Similarity=0.614  Sum_probs=63.1

Q ss_pred             HHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Q 008352          501 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  566 (569)
Q Consensus       501 aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yld  566 (569)
                      +|+.|+++|+.||.+||||++++++|++|||+.||||+++|||++.+|++|||+......++.|++
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            468899999999999999999999999999999999999999999999999999999899999986

>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=99.54  E-value=1.5e-15  Score=118.99  Aligned_cols=58  Identities=38%  Similarity=0.726  Sum_probs=54.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          498 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       498 L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      |..+|+.|+++|+.||.+||||++++++|++|||+.||||+++|||++.+|++|||+.
T Consensus         2 l~~~L~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR~~   59 (61)
T d1ku3a_           2 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH   59 (61)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcC
Confidence            3457899999999999999999999999999999999999999999999999999974

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.38  E-value=7.4e-13  Score=105.35  Aligned_cols=69  Identities=29%  Similarity=0.418  Sum_probs=65.7

Q ss_pred             hhHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          485 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       485 pee~l~~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      +++.+...+..+.|..+|+.||+++|+||.++|+    +++|++|||+.||+|.++|+++..||+++||+.+.
T Consensus         2 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~L~   70 (71)
T d1rp3a2           2 VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQLKAKALERLREMLS   70 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHT----SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHh----HhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHcc
Confidence            6778888899999999999999999999999998    99999999999999999999999999999999875

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=99.18  E-value=3.5e-11  Score=95.15  Aligned_cols=63  Identities=22%  Similarity=0.153  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Q 008352          491 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  557 (569)
Q Consensus       491 ~~el~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  557 (569)
                      .++....|..+|+.||+++|+||.++|.    +++|++|||+.||+|.++|++...||+++||..++
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            3566778999999999999999999999    99999999999999999999999999999999874

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=99.00  E-value=2.9e-10  Score=88.11  Aligned_cols=58  Identities=26%  Similarity=0.461  Sum_probs=55.0

Q ss_pred             eecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCCccc
Q 008352          404 IRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVG--ITVEKLERLIFITRMPLSM  461 (569)
Q Consensus       404 IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lg--is~e~v~~ll~~~~~~~SL  461 (569)
                      ||||.|+.+.+++++++.+++.+++||+||.+|||+.+|  +++++|+.++...+.++||
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=98.79  E-value=2.8e-09  Score=81.57  Aligned_cols=54  Identities=17%  Similarity=0.244  Sum_probs=51.1

Q ss_pred             cceecchhHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc
Q 008352          402 RTIRLPENIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT  455 (569)
Q Consensus       402 r~IRlP~~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~  455 (569)
                      ++||+|+|+.+.++|++++.+.+.+++||+||.+|||+.+|+++++|..++...
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            579999999999999999999999999999999999999999999999988653

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=98.79  E-value=9.7e-09  Score=88.14  Aligned_cols=60  Identities=22%  Similarity=0.217  Sum_probs=52.0

Q ss_pred             HHHHH-hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          498 VRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       498 L~~aL-~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      |.... .-||++||.||.+||.    +++|+.|||+.||||+++|+++++||+++||+....-++
T Consensus        11 L~d~y~~LLpe~QR~vl~L~~~----e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~ye~kL~l   71 (106)
T d1xsva_          11 LFDFYQSLLTNKQRNYLELFYL----EDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   71 (106)
T ss_dssp             HHHHHGGGSCHHHHHHHHHHHT----SCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHH----hCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            33333 3499999999999999    999999999999999999999999999999997554443

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.75  E-value=1.1e-08  Score=87.73  Aligned_cols=55  Identities=24%  Similarity=0.244  Sum_probs=49.8

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcCch
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  561 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  561 (569)
                      .-||+++|.||.|+|+    +++|++|||+.||||+++|+.+++||+++||+...+-++
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=98.59  E-value=3e-08  Score=78.98  Aligned_cols=70  Identities=16%  Similarity=0.138  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCCCCCchhhHHHHHHHHHHHHHHH
Q 008352          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIF  398 (569)
Q Consensus       327 ~~Are~LI~~nlrLV~sIArry~~~g~~~EDLIQEG~IGLirAiekFDp~kG~rFSTYA~~wIRqaI~~~Ir  398 (569)
                      ..++++++..|.+.++.+|.++.++..+.+|++||.++.+|+..++|++.  .+|.+|++..++|.+.+++|
T Consensus         6 ~~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   75 (75)
T d1h3la_           6 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYR   75 (75)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHhC
Confidence            36799999999999999999999999999999999999999999999875  46999999999999988753

>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=98.34  E-value=5.6e-08  Score=78.23  Aligned_cols=70  Identities=16%  Similarity=0.242  Sum_probs=57.6

Q ss_pred             hHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCCcccCCCCCCCCCcchhhcccC
Q 008352          409 NIYTLLSKVLEAKRLYIQEGNHSPDKEDLARRVGITVEKLERLIFIT--RMPLSMQQPVWADQDTTFQEITAD  479 (569)
Q Consensus       409 ~~~~~l~ki~ka~~~l~~~~gr~Pt~eEIA~~lgis~e~v~~ll~~~--~~~~SLD~~v~~d~~~~l~d~i~D  479 (569)
                      .+..++++++++...|.+++||.||.+|||+.|||++++|.+++...  ..++|||.++.+ ++..+.+++++
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            34578899999999999999999999999999999999999998643  467899986643 34456676665

>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=98.29  E-value=9.8e-07  Score=69.67  Aligned_cols=55  Identities=13%  Similarity=0.311  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          494 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       494 l~e~L~~aL~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ..+.+...++.|+|+|++|+.+..     .|+|.+|||+.||||..||+....++++||.
T Consensus         2 ~~~~~~~~~~~LT~rE~~vl~~l~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   56 (70)
T d1yioa1           2 TQDQLEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLN   56 (70)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            345678888999999999999976     6999999999999999999999999999984

>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=98.05  E-value=3.8e-06  Score=65.56  Aligned_cols=47  Identities=19%  Similarity=0.301  Sum_probs=44.1

Q ss_pred             HhcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          502 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       502 L~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      +..|+|+|++|+.+..     +|+|.+|||+.||||..||+....++++||.
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     6999999999999999999999999999984

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.89  E-value=1.1e-05  Score=62.33  Aligned_cols=45  Identities=27%  Similarity=0.383  Sum_probs=42.3

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .|+++|++|+.+.-     +|+|.+|||+.||+|..||+....++++||.
T Consensus         4 ~Lt~rE~~vl~l~~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   48 (65)
T d1l3la1           4 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD   48 (65)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             ccCHHHHHHHHHHH-----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            69999999998875     7999999999999999999999999999984

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=97.83  E-value=1.6e-05  Score=61.76  Aligned_cols=45  Identities=29%  Similarity=0.378  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .|+++|++|+.+.-     +|+|.+|||+.||+|..||+....++++||-
T Consensus         4 ~LT~rE~~vl~l~~-----~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~   48 (67)
T d1fsea_           4 LLTKREREVFELLV-----QDKTTKEIASELFISEKTVRNHISNAMQKLG   48 (67)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH-----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            49999999998865     7999999999999999999999999999984

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=97.48  E-value=7.1e-05  Score=61.07  Aligned_cols=45  Identities=22%  Similarity=0.297  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      .|+++|++|+.+..     .|++.+|||+.||+|..+|+....++++||.
T Consensus        22 ~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~   66 (87)
T d1p4wa_          22 RLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG   66 (87)
T ss_dssp             SCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            59999999999987     6999999999999999999999999999984

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.42  E-value=0.015  Score=43.13  Aligned_cols=38  Identities=32%  Similarity=0.482  Sum_probs=33.5

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHHh
Q 008352          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH  324 (569)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l~  324 (569)
                      ++.++..+|...+|++||.+|.|+.+|++.+++...+.
T Consensus        16 ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~   53 (57)
T d1l0oc_          16 KIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQE   53 (57)
T ss_dssp             HHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            56678889999999999999999999999998876654

>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=95.09  E-value=0.012  Score=45.69  Aligned_cols=43  Identities=16%  Similarity=0.285  Sum_probs=36.0

Q ss_pred             cCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhCC-CHHHHHHHHH
Q 008352          504 LLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGL-SKERVRQLES  546 (569)
Q Consensus       504 ~L~~rER~VL~L--RygL~d~e~~Tl~EIAe~LGI-SrerVRqie~  546 (569)
                      .|+++|++||..  .|....|-+-|++|||+.+|+ |..+|+..+.
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            599999999887  444445788999999999999 8999998754

>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=94.12  E-value=0.033  Score=39.86  Aligned_cols=37  Identities=16%  Similarity=0.251  Sum_probs=30.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL  544 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqi  544 (569)
                      .|++.+.+-++-.+-    .|.|..+||+.||||+.||.+.
T Consensus         5 ~lt~~q~~~a~~l~~----~G~s~~~iA~~~gVSr~TiYry   41 (47)
T d1ijwc_           5 AINKHEQEQISRLLE----KGHPRQQLAIIFGIGVSTLYRY   41 (47)
T ss_dssp             SSCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHhh
Confidence            477777777766665    7899999999999999999865

>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=94.07  E-value=0.04  Score=42.88  Aligned_cols=38  Identities=39%  Similarity=0.554  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHhhhhCCCCcHHHHHHHcCCCHHHHHHHH
Q 008352          286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSEL  323 (569)
Q Consensus       286 ~~le~~~~~l~~~~g~~pt~~ewA~a~g~~~~~L~~~l  323 (569)
                      -+++++...|+..+||+||.+|.|..+||+.+++...+
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            35778899999999999999999999999998886554

>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=91.72  E-value=0.21  Score=37.21  Aligned_cols=40  Identities=20%  Similarity=0.385  Sum_probs=32.9

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      |++.+++||..--.   +...|+.|||+.+|+|..+|+.++.+
T Consensus         3 lD~~D~~IL~~L~~---~~r~s~~eiA~~l~ls~~~v~~Ri~r   42 (63)
T d2cg4a1           3 IDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVEK   42 (63)
T ss_dssp             CCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            67888888887553   25789999999999999999977654

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=91.10  E-value=0.22  Score=37.07  Aligned_cols=37  Identities=32%  Similarity=0.608  Sum_probs=29.7

Q ss_pred             HHHHHHHHHhhhhCCCCcHHHHHHHcCC--CHHHHHHHH
Q 008352          287 RLEKEKSKLQSQFGREPTLIEWAKAIGL--SCRDLKSEL  323 (569)
Q Consensus       287 ~le~~~~~l~~~~g~~pt~~ewA~a~g~--~~~~L~~~l  323 (569)
                      ++.++..+|...+||+||.+|.|+++|+  +.+.+...+
T Consensus        13 rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l   51 (60)
T d1ku2a1          13 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETL   51 (60)
T ss_dssp             HHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHG
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHH
Confidence            5667888999999999999999999974  455555443

>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=91.05  E-value=0.21  Score=36.88  Aligned_cols=40  Identities=18%  Similarity=0.382  Sum_probs=31.2

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      |++.+++||.+--.  + ...|+.|||+.+|+|+++|.+++.+
T Consensus         1 lD~~D~kIl~~L~~--n-~r~s~~~lA~~~gls~~~v~~Ri~~   40 (60)
T d1i1ga1           1 IDERDKIILEILEK--D-ARTPFTEIAKKLGISETAVRKRVKA   40 (60)
T ss_dssp             CCSHHHHHHHHHHH--C-TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45677888876543  2 5679999999999999999976654

>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=91.03  E-value=0.21  Score=37.21  Aligned_cols=41  Identities=22%  Similarity=0.183  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++.++.||..--.  + ...|+.|||+.+|+|+.+|.+++.+
T Consensus         2 klD~~D~~IL~~L~~--n-~r~s~~~iA~~lgis~~tv~~Ri~~   42 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK--D-SRLSMRELGRKIKLSPPSVTERVRQ   42 (63)
T ss_dssp             CCCHHHHHHHHHHHH--C-SCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            477888888876543  2 5789999999999999999976654

>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=90.28  E-value=0.18  Score=38.35  Aligned_cols=45  Identities=9%  Similarity=0.111  Sum_probs=32.9

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  550 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALk  550 (569)
                      .|+-.|+.=|..+|-  +|+.++..|||..|||+++||+.++++-=+
T Consensus         7 ~LT~~eK~~ii~~~e--~g~k~sq~eIA~~fGv~~STvs~IlKnK~k   51 (66)
T d1hlva1           7 QLTFREKSRIIQEVE--ENPDLRKGEIARRFNIPPSTLSTILKNKRA   51 (66)
T ss_dssp             CCCHHHHHHHHHHHH--HCTTSCHHHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             cCCHHHHHHHHHHHH--cCCcchHHHHHHHhCCChhHHHHHHHHHHH
Confidence            466666654444442  345679999999999999999999887433

>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=89.64  E-value=0.44  Score=34.92  Aligned_cols=40  Identities=18%  Similarity=0.353  Sum_probs=30.6

Q ss_pred             CCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          505 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       505 L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      |++.++.||..--.   +...|+.|||+.+|+|+.+|..++++
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            45667777776433   25679999999999999999876654

>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=89.63  E-value=0.16  Score=35.50  Aligned_cols=32  Identities=6%  Similarity=0.207  Sum_probs=27.0

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      +|..|+-     +++.-.+||+.|||++.+|-.+++.
T Consensus        10 ~V~~L~~-----~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1          10 AVLNMWQ-----QGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            4666664     8999999999999999999887653

>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=86.45  E-value=0.33  Score=38.74  Aligned_cols=43  Identities=28%  Similarity=0.277  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHHH--HhcccCCCCCCHHHHHHHhC--CCHHHHHHHHH
Q 008352          504 LLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFG--LSKERVRQLES  546 (569)
Q Consensus       504 ~L~~rER~VL~L--RygL~d~e~~Tl~EIAe~LG--ISrerVRqie~  546 (569)
                      .|++|+++||..  .+.+..|.+-+.++|++.+|  +|..+||..+.
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~   47 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMK   47 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHH
Confidence            489999999875  23355679999999999966  58999997653

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=86.40  E-value=0.35  Score=35.75  Aligned_cols=25  Identities=12%  Similarity=0.135  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .++|.+|+|+.+|||+.+|+++++.
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            5699999999999999999999974

>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=85.99  E-value=0.007  Score=51.84  Aligned_cols=32  Identities=13%  Similarity=0.280  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +|+|++|||++||.|+..|..++++|++++++
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            68999999999999999999999999999875

>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=85.92  E-value=0.48  Score=37.24  Aligned_cols=50  Identities=16%  Similarity=0.217  Sum_probs=39.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHhcccC---CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          496 QHVRNLLTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       496 e~L~~aL~~L~~rER~VL~LRygL~d---~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      ..|...+..|++.|+.|..+  .+++   -..+|.+|||+..|||..+|-+..++
T Consensus         7 ~~i~~~~~~Ls~~e~~ia~y--il~~~~~~~~~si~~lA~~~~vS~sTi~Rf~kk   59 (83)
T d2o3fa1           7 AIIQSMKHKLPPSERKLADY--ILAHPHKAIESTVNEISALANSSDAAVIRLCKS   59 (83)
T ss_dssp             HHHHHHGGGSCHHHHHHHHH--HHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHHHH--HHcCHHHHHHccHHHHHHHHCCCHHHHHHHHHH
Confidence            46778889999999998754  3332   25799999999999999999876554

>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=85.89  E-value=0.56  Score=39.46  Aligned_cols=39  Identities=18%  Similarity=0.151  Sum_probs=29.4

Q ss_pred             CCHHHHH-HHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          505 LNPKERC-IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       505 L~~rER~-VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      |+...|. ||.+ |.    ++++..+||+.||||+.+|..+..+=
T Consensus        17 Ls~dlR~rIv~~-~~----~G~s~r~iA~~~~VS~~tV~k~l~r~   56 (123)
T d1pdnc_          17 LPNNIRLKIVEM-AA----DGIRPCVISRQLRVSHGCVSKILNRY   56 (123)
T ss_dssp             CCHHHHHHHHHH-HH----TTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH-HH----hcCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4444444 5555 44    68999999999999999999887663

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.83  E-value=0.39  Score=35.70  Aligned_cols=42  Identities=19%  Similarity=0.324  Sum_probs=30.5

Q ss_pred             CHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          506 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       506 ~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +....+||.+-   .++...|.+|+|+.||||+.+|+..+    ++|++
T Consensus         4 ~~~~~~iL~~L---~~~~~~s~~eLa~~l~vS~~ti~r~i----~~L~~   45 (63)
T d1biaa1           4 NTVPLKLIALL---ANGEFHSGEQLGETLGMSRAAINKHI----QTLRD   45 (63)
T ss_dssp             CHHHHHHHHHH---TTSSCBCHHHHHHHHTSCHHHHHHHH----HHHHH
T ss_pred             cHHHHHHHHHH---HHCCcCCHHHHHHHHCcCHHHHHHHH----HHHHH
Confidence            34455555543   45577899999999999999999665    45554

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=85.56  E-value=0.43  Score=37.64  Aligned_cols=35  Identities=17%  Similarity=0.207  Sum_probs=28.1

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  548 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RA  548 (569)
                      ++|.+..-   ++|+|..+||+.|||+..+|+++..+.
T Consensus        13 ~aV~l~~~---~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          13 DAVALYEN---SDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHTT---GGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHH---cCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            46666541   147999999999999999999998765

>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=85.41  E-value=0.4  Score=36.91  Aligned_cols=28  Identities=25%  Similarity=0.396  Sum_probs=24.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      ++|.+|||..+|+|+++|.    |++++|++.
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            6899999999999999997    677777763

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=85.16  E-value=1.1  Score=37.74  Aligned_cols=42  Identities=19%  Similarity=0.223  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          504 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       504 ~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .|++-+-.|+.+-+. . ++++|..|||+.+|+|+.+|...+.+
T Consensus        23 Gl~~~~~~i~~~L~~-~-~~plt~~ela~~l~vsk~~vs~~l~~   64 (151)
T d1ku9a_          23 GLNKSVGAVYAILYL-S-DKPLTISDIMEELKISKGNVSMSLKK   64 (151)
T ss_dssp             TCCHHHHHHHHHHHH-C-SSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh-C-CCCcCHHHHHHHhCCCcchHHHHHHH
Confidence            579999999988774 3 36799999999999999999865543

>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=84.14  E-value=1.9  Score=35.54  Aligned_cols=54  Identities=11%  Similarity=0.107  Sum_probs=39.8

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Q 008352          495 RQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  553 (569)
Q Consensus       495 ~e~L~~aL~--~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~RALkKLR  553 (569)
                      ...+...+.  .|++.|-.||..-+. .+|.+.|..||++.+|+++.+|..    ++++|-
T Consensus        15 ~~~~~~~l~~~glt~~q~~vL~~l~~-~~~~~it~~ela~~~~~~~~~vs~----~l~~L~   70 (135)
T d3broa1          15 STRFDIFAKKYDLTGTQMTIIDYLSR-NKNKEVLQRDLESEFSIKSSTATV----LLQRME   70 (135)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHH-TTTSCCBHHHHHHHHTCCHHHHHH----HHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH-cCCCCCCHHHHHHHHCcCHhHHHH----HHHHHH
Confidence            334444443  489999999877664 344679999999999999999974    555553

>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=83.70  E-value=0.66  Score=35.39  Aligned_cols=43  Identities=12%  Similarity=0.108  Sum_probs=37.6

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHh-CCCHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-GLSKERVRQLE  545 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~L-GISrerVRqie  545 (569)
                      +.|++.+++|+.+.-.-.+.+|.+..||+..| |++...|++..
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            46999999999998877777999999999999 89999988654

>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=83.69  E-value=0.54  Score=36.09  Aligned_cols=29  Identities=34%  Similarity=0.491  Sum_probs=24.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  555 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  555 (569)
                      -++|.+|||..+|+|+++|.    |++++|++.
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            46899999999999999987    667777763

>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=83.58  E-value=0.58  Score=35.48  Aligned_cols=24  Identities=21%  Similarity=0.342  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .++|.+|+|+.||||+.+|.+.+.
T Consensus        13 ~gltQ~elA~~LGvs~~ti~~yE~   36 (67)
T d2auwa1          13 NNLSLTTAAEALGISRRMVSYYRT   36 (67)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Confidence            679999999999999999999876

>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=83.19  E-value=1.3  Score=33.59  Aligned_cols=39  Identities=21%  Similarity=0.364  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHhCC-CHHHHHHHHHh
Q 008352          416 KVLEAKRLYIQEGNHSPDKEDLARRVGI-TVEKLERLIFI  454 (569)
Q Consensus       416 ki~ka~~~l~~~~gr~Pt~eEIA~~lgi-s~e~v~~ll~~  454 (569)
                      ++-.....+..+.|..|+..|||+.+|+ +...|...+..
T Consensus         9 ~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~   48 (71)
T d1jhfa1           9 EVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   48 (71)
T ss_dssp             HHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            3444455667778999999999999999 78888877653

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=83.08  E-value=0.58  Score=36.95  Aligned_cols=43  Identities=16%  Similarity=0.179  Sum_probs=32.5

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH-----HHHHHHHHhh
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR-----ALYRLKQSLG  557 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R-----ALkKLR~~l~  557 (569)
                      .|-.+|--    .|+|.+|+|+.+|||+.+|.++++-     .+.+|.+.+.
T Consensus        15 ~i~~~r~~----~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~   62 (89)
T d2o38a1          15 ALNAVIDR----ARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLN   62 (89)
T ss_dssp             HHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHH
T ss_pred             HHHHHHHH----cCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHH
Confidence            34455555    7899999999999999999999972     2555555443

>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=82.80  E-value=0.51  Score=36.04  Aligned_cols=27  Identities=7%  Similarity=0.257  Sum_probs=23.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      ++|.+|||..+|+|+++|.    |++++|++
T Consensus        27 ~lt~~elA~~lg~sr~tvs----r~l~~l~~   53 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNIS----KTLNELQD   53 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             ecCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4799999999999999886    67777776

>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=82.79  E-value=0.67  Score=34.69  Aligned_cols=32  Identities=13%  Similarity=0.182  Sum_probs=27.3

Q ss_pred             HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          511 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       511 ~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .|-.+|.-    .++|.+|+|+.+||++.+|..+++
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            34455555    899999999999999999999996

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=82.67  E-value=0.65  Score=37.56  Aligned_cols=43  Identities=21%  Similarity=0.244  Sum_probs=34.0

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      -.|++.+..||..-+.  .+.++|..|||+.+|+++.+|+.++.+
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            3699999999865432  124799999999999999999866554

>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=82.57  E-value=0.59  Score=35.81  Aligned_cols=28  Identities=14%  Similarity=0.100  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      -++|.+|||..+|+|+++|.    |++++|++
T Consensus        28 ~~lt~~eLA~~~G~sretvs----r~L~~l~~   55 (81)
T d2gaua1          28 IYLSREELATLSNMTVSNAI----RTLSTFVS   55 (81)
T ss_dssp             CCCCHHHHHHHTTSCHHHHH----HHHHHHHH
T ss_pred             ecCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            36899999999999999987    66777766

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=81.90  E-value=1.7  Score=34.82  Aligned_cols=46  Identities=11%  Similarity=0.209  Sum_probs=31.7

Q ss_pred             HHHHHHhcCCH-HHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          497 HVRNLLTLLNP-KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       497 ~L~~aL~~L~~-rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .+..++..|.. .-..||.+-.   + .+++..||++.+|+|+.+|++.++
T Consensus        12 ~la~~~kaL~~p~Rl~Il~~L~---~-~~~~v~ela~~l~is~stvS~HL~   58 (98)
T d1r1ta_          12 SLAEFFAVLADPNRLRLLSLLA---R-SELCVGDLAQAIGVSESAVSHQLR   58 (98)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHT---T-CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH---c-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence            34455555554 4444554432   3 579999999999999999997654

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=81.75  E-value=0.92  Score=33.80  Aligned_cols=29  Identities=17%  Similarity=0.224  Sum_probs=22.9

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          522 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       522 ~e~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +..-+..+||+.||||+.+|.+.    +++|.+
T Consensus        21 ~~~v~~~~iA~~L~vs~~SVt~m----vkrL~~   49 (63)
T d2isya1          21 GVTPLRARIAERLDQSGPTVSQT----VSRMER   49 (63)
T ss_dssp             TCCCCHHHHHHHHTCCHHHHHHH----HHHHHH
T ss_pred             CCCCcHHHHHHHhCCCchhHHHH----HHHHHH
Confidence            35689999999999999999854    555543

>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=81.49  E-value=0.52  Score=35.28  Aligned_cols=27  Identities=37%  Similarity=0.506  Sum_probs=22.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Q 008352          524 PKSLSEVGNIFGLSKERVRQLESRALYRLKQ  554 (569)
Q Consensus       524 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  554 (569)
                      +.|.+|||..+|+|+++|.    |.|++|++
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            4899999999999999997    55666654

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=81.35  E-value=0.69  Score=34.19  Aligned_cols=25  Identities=24%  Similarity=0.405  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .++|.+|+|+.+|||+.+|.++++.
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            6899999999999999999999863

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=80.97  E-value=1.7  Score=34.57  Aligned_cols=47  Identities=19%  Similarity=0.245  Sum_probs=34.0

Q ss_pred             HHHHHHHhcCCHHHH-HHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          496 QHVRNLLTLLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       496 e~L~~aL~~L~~rER-~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      +.+.+++..|...-| .||.+-..    .+++..||++.+|+|+.+|++.++
T Consensus         6 e~~a~~fkaL~d~~Rl~Il~~L~~----~~~~v~el~~~l~~s~~~vS~HL~   53 (94)
T d1r1ua_           6 ERVTEIFKALGDYNRIRIMELLSV----SEASVGHISHQLNLSQSNVSHQLK   53 (94)
T ss_dssp             HHHHHHHHHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHc----CCccHHHHHHHHCCCHHHHHHHHH
Confidence            356667777776555 45444332    579999999999999999997643

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=80.90  E-value=0.82  Score=37.53  Aligned_cols=41  Identities=22%  Similarity=0.123  Sum_probs=32.5

Q ss_pred             hcCCHHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          503 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       503 ~~L~~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      ..|+|-|.-.-.-++. +  .++|.++||+.+|+|+.+|++++.
T Consensus        12 ~~L~p~e~A~a~~~l~-~--~g~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_          12 NELTPREIADFIGREL-A--KGKKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             TCCCHHHHHHHHHHHH-H--TTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             cCCCHHHHHHHHHHHH-H--hCCCHHHHHHHHCCcHHHHHHHHH
Confidence            3588887776555543 2  578999999999999999999875

>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=80.73  E-value=0.86  Score=33.89  Aligned_cols=25  Identities=24%  Similarity=0.231  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .++|.+++|+.+|||+.+|.++++.
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

>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=80.72  E-value=0.86  Score=33.48  Aligned_cols=24  Identities=13%  Similarity=0.297  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLES  546 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~  546 (569)
                      .++|.+|+|+.+|||+.+|.++++
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

>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=80.71  E-value=1.1  Score=33.21  Aligned_cols=39  Identities=18%  Similarity=0.209  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHhcccCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          507 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       507 ~rER~VL~LRygL~d~e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      +|...||.+-.  ......|..|+|+.||||+.||++-+..
T Consensus         7 eR~~~Il~~L~--~~~~~vs~~~La~~l~VS~~TI~rdi~~   45 (65)
T d1j5ya1           7 ERLKSIVRILE--RSKEPVSGAQLAEELSVSRQVIVQDIAY   45 (65)
T ss_dssp             HHHHHHHHHHH--HCSSCBCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHH--HcCCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence            44455665432  1224579999999999999999977653

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=80.35  E-value=0.91  Score=33.01  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 008352          523 KPKSLSEVGNIFGLSKERVRQLESR  547 (569)
Q Consensus       523 e~~Tl~EIAe~LGISrerVRqie~R  547 (569)
                      .++|.+|+|+.+|||+.+|.++++.
T Consensus        13 ~g~sq~elA~~~gvs~~~is~~E~g   37 (63)
T d1r69a_          13 LGLNQAELAQKVGTTQQSIEQLENG   37 (63)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cCCcHHHHHHHhCcCHHHHHHHHCC
Confidence            7899999999999999999999874