Citrus Sinensis ID: 011992

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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---
Protein Sequence
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccHHcHHcccccHHHHHHHHcccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcHHHHHHHHccccccccccccccccccccccHHHHHHHcccHHHHHHHHHcccccccccccccccccHHHHHHHHccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHcHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHcccccccccccccccccccccccccccccccccccccccccccccccHHHccccccHcccccccccccHHHHHccccHHHHcHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHcccccHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHcHcccccccEEEEHEccccccccccccccHHHHHHHHHHHHHHHHcccHcccccHHHHHHHHHHHcccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHccccccccHHHcHEcc
Coil and Loop (DISEMBL)
meagrnllssppsfpsrtrvkhslsssasssssssVLMHneqsapavasvptssvarhfptsvllqeqrdeyrpllhmfkedktsqatsdsrnIETEAFFveeknsgdlDQLVQDLEHqflhwpdlwnlsppmkrgedpsvsltmqslsndteesvdaepfDAVALARKALSASKEAAslaenpklngaeftdisltsslgypleevkqfsqprflerrskkrkvskpqvtnhetynSRKASVKKKLsegfdrndplrlflwgpetrklltaDEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRdlkselhsgnssREKLINANLRLVVHVAKQYqgrgislhdLLQEGSMGLMKSVEkfkpqagcrfantgveipdisVQKQLMRQHVRNLLtllnpkerCIVRLRFgiedgkpkslsevgnIFGLSKERVRQLESRALYRLKQSLggkasygyadlli
Flexible Loop (DISEMBL)
meagrnllssppsfpsrtrVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMfkedktsqatsdsrNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAslaenpklngaeFTDISLTSslgypleevkqfsqprflerrskkrkvskpqvtnhetynsrkasvkkklsegfdrndplrlfLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLqsqfgreptLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNlltllnpkerCIVRLRfgiedgkpkslsevgnifglskeRVRQLESRALYrlkqslggkasygyadlli
Low Complexity Region (SEG)
MEAGRNLLSSPPSFPSRTRVKHslsssasssssssVLMHNEQsapavasvptssvaRHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDavalarkalsaskeaaslaeNPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered region (IsUnstruct)
**************************************************************************************************FFV******DLDQLVQDLEHQFLHWPDLWNL******************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE*********FGREPTLIEWAKAIGLSCRDL************KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGY*****
Disordered Region (DISOPRED)
****************************************************************************************************************VQDLEHQFL***************************************FDAVALARKALSASKEAASLAENPKLNGAEF**************************************************************NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS*********PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKE*****************LSEVGNIFGLSKERVRQLESRALYRLKQSL**KASYGYADLLI
Disordered Region (DISEMBL)
******************************************************VARHFPTSVLLQEQRDEYRPLLHMFKED*********RNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQS**********AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLE*************TNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK********SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Disordered Region (DISPRO)
************************************************************************RPLLHMFKEDKTSQATSDSRNIETEAFFVE***SGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFExxxxxxxxxxxxxxxxxxxxxFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLLI
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	473	2.2.26 [Sep-21-2011]
Q9LD95	547	RNA polymerase sigma fact	yes	no	0.744	0.643	0.494	7e-85
O22056	572	RNA polymerase sigma fact	no	no	0.427	0.353	0.360	5e-29
P26683	390	RNA polymerase sigma fact	yes	no	0.348	0.423	0.365	1e-24
Q31ME3	320	RNA polymerase sigma fact	yes	no	0.397	0.587	0.323	3e-22
Q31QG5	320	RNA polymerase sigma fact	no	no	0.243	0.359	0.456	8e-22
P38023	399	RNA polymerase sigma fact	no	no	0.272	0.323	0.418	1e-21
Q03065	332	RNA polymerase sigma-B fa	no	no	0.310	0.442	0.360	3e-18
Q59996	404	Probable RNA polymerase s	N/A	no	0.399	0.467	0.296	3e-18
Q03066	416	RNA polymerase sigma-C fa	no	no	0.274	0.312	0.329	6e-16
P74565	425	RNA polymerase sigma fact	N/A	no	0.298	0.331	0.306	1e-15

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

 Score =  315 bits (806), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 193/390 (49%), Positives = 248/390 (63%), Gaps = 38/390 (9%)

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 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
           ++  DLLQEGSMGLMKSVEKFKPQ+GCRFA
Sbjct: 331 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFA 360

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

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

 Score =  129 bits (324), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 74/205 (36%), Positives = 115/205 (56%), Gaps = 3/205 (1%)

Query: 244 KKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 303
           K+ +++  D NDPLR       + KLLT  EE EL A IQDL++LE+ +++L  + GR+P
Sbjct: 247 KRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSAGIQDLLKLERLQTELTERSGRQP 306

Query: 304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGS 363
           T  +WA A G+  + L+  +H G   ++K+I +N+RLV+ +AK YQG G++L DL+QEG 
Sbjct: 307 TFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGC 366

Query: 364 MGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQH--VRNLLTLLNPKERCI-VRLR 420
            GL++  EKF    G +F+         +V+K L  Q   +R    ++    R    R +
Sbjct: 367 RGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATYRVKEARKQ 426

Query: 421 FGIEDGKPKSLSEVGNIFGLSKERV 445
              E GK     E+    GLS +R+
Sbjct: 427 LYSETGKHPKNEEIAEATGLSMKRL 451

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  114 bits (286), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 65/178 (36%), Positives = 104/178 (58%), Gaps = 13/178 (7%)

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 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
           G  +++K++ +NLRLVV +AK+Y  RG+S  DL+QEGS+GL+++ EKF  + G +F+ 
Sbjct: 151 GRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFST 208

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

 Score =  107 bits (266), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 65/201 (32%), Positives = 109/201 (54%), Gaps = 13/201 (6%)

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 PQAGCRFANTGVEIPDISVQKQLMRQ--------HVRNLLTLLNPKERCIVRLRFGIEDG 426
           P  G +F+         ++ + + +Q        H+   L  L   +R + +     + G
Sbjct: 131 PSKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQ-----QLG 185

Query: 427 KPKSLSEVGNIFGLSKERVRQ 447
           +  + SE+  +  L  E+VR+
Sbjct: 186 RSATASELAEVLELPLEQVRE 206

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity). This sigma factor is a component of the biological clock pathway that affects the circadian expression of a subset of genes in this bacterium.

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

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

 Score =  105 bits (262), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 53/116 (45%), Positives = 79/116 (68%), Gaps = 1/116 (0%)

Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFG-REPTLIEWAKAIGLSCRDLKSELHSGN 327
           LLT +EE  L  ++Q  ++L++ +  LQS+ G R+P+ +EWA A GLS  +L+ + H G 
Sbjct: 24  LLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAAGLSIEELRQQQHLGE 83

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
            ++ K+I ANLRLVV VAK+Y  R + L DL+QEG++G+ + VEKF P  G RF+ 
Sbjct: 84  QAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFST 139

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

 Score =  104 bits (260), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 54/129 (41%), Positives = 82/129 (63%)

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 PQAGCRFAN 383
            + G +F+ 
Sbjct: 209 HEKGYKFST 217

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|Q03065|RPSB_NOSS1 RNA polymerase sigma-B factor OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=sigB PE=3 SV=1

 Score = 93.6 bits (231), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 53/147 (36%), Positives = 83/147 (56%)

Query: 237 NSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ 296
            S+   +K K +E     D + ++L       LL+ ++E     Q+Q ++ +   K +L 
Sbjct: 5   TSQVTKLKSKNNEFSYTADAVSIYLHKIGRVPLLSHEQEIFFAQQVQQMMVMFTAKEELA 64

Query: 297 SQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLH 356
            +  REPTL EWA  + L    L  +L  G  +++K+I ANLRLVV +AK+YQ R +   
Sbjct: 65  EKLQREPTLQEWADKMQLKEDVLLQQLSQGQIAKQKMIQANLRLVVSIAKKYQKRNLEFL 124

Query: 357 DLLQEGSMGLMKSVEKFKPQAGCRFAN 383
           DL+QEG++GL + VEKF P  G +F+ 
Sbjct: 125 DLIQEGALGLERGVEKFDPTLGYKFST 151

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

 Score = 93.6 bits (231), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 112/246 (45%), Gaps = 57/246 (23%)

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 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------T 384
            +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF+         
Sbjct: 168 HMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYSYWWIRQ 227

Query: 385 GVEIPDISVQKQLMR--QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK 442
           G+    I+ Q +++R   H+   L  +   +R I +     E G    + EV    G++ 
Sbjct: 228 GI-TRAIATQSRMIRLPVHITEKLNKIKRAQRKISQ-----EKGHTPKIDEVAEELGMTP 281

Query: 443 ERVRQL 448
           E+VR++
Sbjct: 282 EQVREV 287

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

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

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

 Score = 85.9 bits (211), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 57/173 (32%), Positives = 81/173 (46%), Gaps = 43/173 (24%)

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 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
           E +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF+ 
Sbjct: 179 EHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFST 231

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

 Score = 85.1 bits (209), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/189 (30%), Positives = 92/189 (48%), Gaps = 48/189 (25%)

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 FGREPTLIEWAKAIG----------------LSCRDLKSELHSGNS-------------- 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 PQAGCRFAN 383
            + G +F+ 
Sbjct: 235 HEKGYKFST 243

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)

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	473
224068757	535	predicted protein [Populus trichocarpa]	0.782	0.691	0.550	1e-116
297741628	561	unnamed protein product [Vitis vinifera]	0.909	0.766	0.520	1e-115
359481391	572	PREDICTED: RNA polymerase sigma factor r	0.928	0.767	0.516	1e-113
255556952	548	RNA polymerase sigma factor rpoD, putati	0.807	0.697	0.551	1e-113
356536959	571	PREDICTED: RNA polymerase sigma factor r	0.841	0.697	0.525	3e-98
356548319	574	PREDICTED: RNA polymerase sigma factor r	0.843	0.695	0.501	2e-96
449451030	562	PREDICTED: RNA polymerase sigma factor s	0.824	0.693	0.495	3e-90
312282671	547	unnamed protein product [Thellungiella h	0.746	0.645	0.506	6e-87
297827203	546	RNA polymerase sigma-70 factor [Arabidop	0.742	0.642	0.502	8e-86
18404292	547	RNApolymerase sigma-subunit F [Arabidops	0.744	0.643	0.494	4e-83

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

 Score =  423 bits (1088), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 223/405 (55%), Positives = 285/405 (70%), Gaps = 35/405 (8%)

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 EGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNL 405
           EG++GLMKS+EKFKPQAGCRFA         ++ K +  QH R +
Sbjct: 327 EGTVGLMKSIEKFKPQAGCRFATYAYWWIRQTITKAIF-QHSRTI 370

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  420 bits (1080), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 240/461 (52%), Positives = 311/461 (67%), Gaps = 31/461 (6%)

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 LHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVR------NLLTL 408
           L DLLQEGSMGLM SVEKFKP AGCRFA+        +V+K +  QH R      N+ +L
Sbjct: 347 LQDLLQEGSMGLMNSVEKFKPNAGCRFASYAYWWIRQAVRKAIF-QHSRTIRLPENMYSL 405

Query: 409 LNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQL 448
           L   +      R  I++G    +  E+    G++ E++++L
Sbjct: 406 LGKVKEA---KRLFIQEGHHDPTKEEIAERVGITIEKLQRL 443

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  416 bits (1069), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 239/463 (51%), Positives = 311/463 (67%), Gaps = 24/463 (5%)

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 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVR------NLL 406
           ++L DLLQEGSMGLM SVEKFKP AGCRFA+        +V+K +  QH R      N+ 
Sbjct: 356 LNLQDLLQEGSMGLMNSVEKFKPNAGCRFASYAYWWIRQAVRKAIF-QHSRTIRLPENMY 414

Query: 407 TLLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQL 448
           +LL   +      R  I++G    +  E+    G++ E++++L
Sbjct: 415 SLLGKVKEA---KRLFIQEGHHDPTKEEIAERVGITIEKLQRL 454

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 =  414 bits (1064), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 224/406 (55%), Positives = 280/406 (68%), Gaps = 24/406 (5%)

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 QEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNL 405
           QEGSMGLMKS+EKFKPQ GCRFA         +V+K +  QH R +
Sbjct: 339 QEGSMGLMKSIEKFKPQVGCRFATYAYWWIRQTVRKAIF-QHSRTI 383

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 =  365 bits (937), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 217/413 (52%), Positives = 279/413 (67%), Gaps = 15/413 (3%)

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 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNL 405
           +SL DLLQEGSMGLMKSVEKF P AG RF N        +++K + R H R +
Sbjct: 355 LSLQDLLQEGSMGLMKSVEKFNPLAGSRFGNYAFWWIRQAIRKAVFR-HSRTI 406

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 =  359 bits (921), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 208/415 (50%), Positives = 272/415 (65%), Gaps = 16/415 (3%)

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

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

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

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

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

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

Query: 351 RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNL 405
           RG+SL DLLQEGSMGLMKSVEKF P  G RF N        +++K + R H R +
Sbjct: 356 RGLSLQDLLQEGSMGLMKSVEKFNPLVGSRFGNYAFWWIRQAIRKAVFR-HSRTI 409

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 =  338 bits (867), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 204/412 (49%), Positives = 263/412 (63%), Gaps = 22/412 (5%)

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 SLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNL 405
           SLHDLLQ GS+GLMKSVEKFKPQAGCRF +        S+ K +  QH R +
Sbjct: 347 SLHDLLQVGSLGLMKSVEKFKPQAGCRFGSYAYWWIRHSITKAIF-QHSRTI 397

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 =  327 bits (839), Expect = 6e-87,   Method: Compositional matrix adjust.
 Identities = 198/391 (50%), Positives = 247/391 (63%), Gaps = 38/391 (9%)

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 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
           ++  DLLQEGSMGLMKSVEKFKPQ+GCRFA 
Sbjct: 331 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 361

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 =  324 bits (830), Expect = 8e-86,   Method: Compositional matrix adjust.
 Identities = 196/390 (50%), Positives = 251/390 (64%), Gaps = 39/390 (10%)

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 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
           ++  DLLQEGSMGLMKSVEKFKPQ+GCRFA
Sbjct: 330 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFA 359

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 =  315 bits (806), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 193/390 (49%), Positives = 248/390 (63%), Gaps = 38/390 (9%)

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 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
           ++  DLLQEGSMGLMKSVEKFKPQ+GCRFA
Sbjct: 331 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFA 360

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	473
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.733	0.634	0.412	1.2e-56
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.503	0.416	0.359	1.1e-36
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.522	0.431	0.337	3.8e-30
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.164	0.241	0.455	2.7e-23
TIGR_CMR|DET_0551	520	DET_0551 "RNA polymerase sigma	0.143	0.130	0.420	2.2e-21
TIGR_CMR|VC_0534	335	VC_0534 "RNA polymerase sigma	0.312	0.441	0.314	1.6e-20
TIGR_CMR|CPS_1079	296	CPS_1079 "RNA polymerase sigma	0.164	0.263	0.397	8.8e-18
TIGR_CMR|CBU_1669	352	CBU_1669 "RNA polymerase sigma	0.342	0.460	0.301	1.2e-17
TIGR_CMR|SPO_1750	660	SPO_1750 "RNA polymerase sigma	0.131	0.093	0.444	2.2e-17
UNIPROTKB|Q9KUK1	625	VC_0517 "RNA polymerase sigma	0.230	0.174	0.350	3.5e-17

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

 Score = 583 (210.3 bits), Expect = 1.2e-56, P = 1.2e-56
 Identities = 155/376 (41%), Positives = 211/376 (56%)

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 CRFANTGVEIPDISVQKQLMRQH--VR---NLLTLLNPKERCIVRLRFGIEDGKPK-SLS 432
             CRFA         S++K + +    +R   N+  LL        R +  +++G  + S  
Sbjct:   357 CRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEA--R-KTCVQEGNYRPSKE 413

Query:   433 EVGNIFGLSKERVRQL 448
             E+    G+S E++ +L
Sbjct:   414 ELAGHVGVSTEKLDKL 429

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 = 395 (144.1 bits), Expect = 1.1e-36, P = 1.1e-36
 Identities = 87/242 (35%), Positives = 142/242 (58%)

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 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDI 391
             K+  +N RLV+HVA++Y+G G+ + DL+Q+G  GLMK+ EKF P  GCRF          
Sbjct:   336 KMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQ 395

Query:   392 SVQKQLMRQ-HVRNLLTLLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLE 449
             S++K + +   +  L   +    R + + R   I +G+  + + V    G++ E++ +L 
Sbjct:   396 SIKKSIFKNSRLIRLPESVYALLRKVGKARMECIMEGEQPTNANVARRAGITIEKLAKLR 455

Query:   450 SR 451
             ++
Sbjct:   456 AK 457

GO:0009536 "plastid" evidence=RCA

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

 Score = 338 (124.0 bits), Expect = 3.8e-30, P = 3.8e-30
 Identities = 86/255 (33%), Positives = 138/255 (54%)

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 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDIS 392
             +I +N+RLV+ +AK YQG G++L DL+QEG  GL++  EKF    G +F+         +
Sbjct:   336 MIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQA 395

Query:   393 VQKQLMRQH--VRNLLTLLNPKERCI-VRLRFGIEDGK-PKSLSEVGNIFGLSKERVRQ- 447
             V+K L  Q   +R    ++    R    R +   E GK PK+  E+    GLS +R+   
Sbjct:   396 VRKSLSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKN-EEIAEATGLSMKRLMAV 454

Query:   448 -LESRALYRLKQSLG 461
              L  +    L Q +G
Sbjct:   455 LLSPKPPRSLDQKIG 469

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

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

 Score = 172 (65.6 bits), Expect = 2.7e-23, Sum P(2) = 2.7e-23
 Identities = 36/79 (45%), Positives = 56/79 (70%)

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 MGLMKSVEKFKPQAGCRFA 382
             +GL++++EKF    G +F+
Sbjct:   121 LGLIRAMEKFDYTKGFKFS 139

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

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

 Score = 166 (63.5 bits), Expect = 2.2e-21, Sum P(3) = 2.2e-21
 Identities = 29/69 (42%), Positives = 53/69 (76%)

Query:   389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
             PD +  +QL+++ +  +L  L P+ER +++LRFG+EDG+ ++L EVG  F +++ER+RQ+
Sbjct:   440 PD-AASRQLLKEQIDTVLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQI 498

Query:   449 ESRALYRLK 457
             E++AL +L+
Sbjct:   499 EAKALRKLR 507

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|VC_0534 VC_0534 "RNA polymerase sigma factor RpoS" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 175 (66.7 bits), Expect = 1.6e-20, Sum P(2) = 1.6e-20
 Identities = 49/156 (31%), Positives = 85/156 (54%)

Query:   249 EGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEW 308
             E FD  D     L   ET   LT+DEE   +    + +R E + S  +S    +  L E 
Sbjct:    11 EEFDFEDEALEVL---ETDAELTSDEELVAVEGASEDVREEFDASA-KSLDATQMYLSEI 66

Query:   309 AKAIGLSCRD----LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSM 364
               +  L+  +     +  L    ++R+++I +NLRLVV ++++Y  RG++L DL++EG++
Sbjct:    67 GFSPLLTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNL 126

Query:   365 GLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQ 400
             GL+++VEKF P+ G RF+         ++++ LM Q
Sbjct:   127 GLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQ 162

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

GO:0006950 "response to stress" evidence=ISS

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|CPS_1079 CPS_1079 "RNA polymerase sigma factor RpoS" [Colwellia psychrerythraea 34H (taxid:167879)]

 Score = 164 (62.8 bits), Expect = 8.8e-18, Sum P(2) = 8.8e-18
 Identities = 31/78 (39%), Positives = 53/78 (67%)

Query:   323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
             L     SR+++I +NLRLVV +A++Y  RG+ L DL++EG++GL+++VEKF P+ G RF+
Sbjct:    50 LKGDEPSRKRMIESNLRLVVKIARRYNNRGLPLLDLIEEGNLGLIRAVEKFDPERGFRFS 109

Query:   383 NTGVEIPDISVQKQLMRQ 400
                      ++++ +M Q
Sbjct:   110 TYATWWIRQTIERAIMNQ 127

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

GO:0006950 "response to stress" evidence=ISS

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|CBU_1669 CBU_1669 "RNA polymerase sigma factor RpoS" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 168 (64.2 bits), Expect = 1.2e-17, Sum P(2) = 1.2e-17
 Identities = 56/186 (30%), Positives = 97/186 (52%)

Query:   223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQI 282
             +K+ KP  +  +   + K S  KK  +  D      +F    +T+K  T  E+ EL A  
Sbjct:    15 KKIKKP--SKRKIKKTAKKSRPKKPIKASDHG---LIFA---KTKKETTEKEDAEL-ANA 65

Query:   283 QDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLS-CRDLKSEL------HSGN-SSREKLI 334
             +      K K + +++   +PT I + + +G     + K EL      H G+  +R+++I
Sbjct:    66 K-----AKTKKRRETR-SSDPTQI-YLRELGFQPLLNAKEELKIARRVHKGDPKARKQMI 118

Query:   335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQ 394
              ANLRLVV +A+ Y  RG+   DL++EG++GL+ +VEKF P+ G RF+         +++
Sbjct:   119 EANLRLVVKIARHYVNRGLPFLDLIEEGNLGLLTAVEKFDPERGFRFSTYATWWIRQTIE 178

Query:   395 KQLMRQ 400
             + +M Q
Sbjct:   179 RAIMNQ 184

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

GO:0006950 "response to stress" evidence=ISS

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|SPO_1750 SPO_1750 "RNA polymerase sigma-70 factor RpoD" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 148 (57.2 bits), Expect = 2.2e-17, Sum P(3) = 2.2e-17
 Identities = 28/63 (44%), Positives = 46/63 (73%)

Query:   320 KSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGC 379
             K E  +  + +E ++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G 
Sbjct:   414 KGEKEARQAKKE-MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 472

Query:   380 RFA 382
             +F+
Sbjct:   473 KFS 475

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

GO:0016987 "sigma factor activity" evidence=ISS

UNIPROTKB|Q9KUK1 VC_0517 "RNA polymerase sigma factor" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 155 (59.6 bits), Expect = 3.5e-17, Sum P(2) = 3.5e-17
 Identities = 41/117 (35%), Positives = 73/117 (62%)

Query:   268 KLLTADEEFELIAQIQDLIR-LEKEKSKLQSQFGREPTL-IEWAKAIGLSCRDLKSELHS 325
             K+L +D+ +  +A++++    + +   KLQ    +E +L +E  K I  S R    E  +
Sbjct:   330 KVLASDKPY--VAKVREQEEEIRRSIQKLQ-MIEQETSLSVERIKDI--SRRMSIGEAKA 384

Query:   326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
               + +E ++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F+
Sbjct:   385 RRAKKE-MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 440

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

GO:0016987 "sigma factor activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	473
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	3e-36
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	5e-31
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	4e-30
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	4e-27
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	1e-22
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	6e-22
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	2e-20
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	3e-19
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	2e-18
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-17
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	2e-16
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	4e-16
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	5e-16
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	6e-16
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	1e-15
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	3e-15
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	5e-15
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	7e-15
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	8e-15
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	1e-14
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	1e-14
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	3e-14
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	8e-14
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	9e-14
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	1e-12
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	4e-12
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	6e-12
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	7e-12
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	2e-11
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	2e-11
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	3e-11
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	8e-11
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	1e-10
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	2e-10
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	3e-10
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	1e-09
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	2e-09
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	2e-09
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	2e-09
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	5e-09
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	6e-09
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	5e-08
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	5e-08
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	9e-08
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	1e-07
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	2e-07
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	3e-07
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	4e-07
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	7e-07
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	6e-06
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	8e-06
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	3e-05
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	3e-05
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	6e-05
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	5e-04
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	0.002
COG1595	182	COG1595, RpoE, DNA-directed RNA polymerase special	0.002
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	0.002

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

 Score =  135 bits (342), Expect = 3e-36
 Identities = 60/113 (53%), Positives = 81/113 (71%)

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 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
           ++EK+I ANLRLVV VAK+YQ RG+ L DL+QEGS+GL ++VEKF P  G +F
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKF 127

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 =  122 bits (309), Expect = 5e-31
 Identities = 56/145 (38%), Positives = 89/145 (61%), Gaps = 5/145 (3%)

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 LLQEGSMGLMKSVEKFKPQAGCRFA 382
           L+QEGS+GL+++ EKF  + G +F+
Sbjct: 166 LIQEGSLGLIRAAEKFDHEKGYKFS 190

Length = 373

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

 Score =  119 bits (299), Expect = 4e-30
 Identities = 56/128 (43%), Positives = 82/128 (64%)

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 PQAGCRFA 382
           P  G RF+
Sbjct: 128 PTKGYRFS 135

Length = 317

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

 Score =  110 bits (277), Expect = 4e-27
 Identities = 52/114 (45%), Positives = 76/114 (66%)

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 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
           +++K+I ANLRLVV +AK+YQ R +   DL+QEG++GL + VEKF P  G +F+
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFS 145

Length = 327

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

 Score = 98.1 bits (245), Expect = 1e-22
 Identities = 63/212 (29%), Positives = 98/212 (46%), Gaps = 33/212 (15%)

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 SVEKFKPQAGCRFANTGVEIPDISVQKQLMRQ--------HVRNLLTLLNPKERCIVRLR 420
           +VEKF P+ G +F+         ++ + +  Q        H   L+  L   +R      
Sbjct: 143 AVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKR-----E 197

Query: 421 FGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452
              E G+  +  E+    G+S ++VR++  RA
Sbjct: 198 LLQELGREPTPEEIAEELGVSPDKVREMLKRA 229

Length = 342

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

 Score = 97.2 bits (242), Expect = 6e-22
 Identities = 70/248 (28%), Positives = 111/248 (44%), Gaps = 57/248 (22%)

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 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------TG 385
           +I ANLRLVV VAK+YQ RG+ L DL+QEG++GL ++VEKF P  G RF+         G
Sbjct: 180 MIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQG 239

Query: 386 VEIPDISVQKQLMRQ--HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 443
           +    I+ Q + +R   H+   L  +   +R I +     E G+  ++ ++     ++  
Sbjct: 240 I-TRAIATQSRTIRLPVHITEKLNKIKKAQRKISQ-----EKGRTPTIEDIAQELEMTPT 293

Query: 444 RVRQLESR 451
           +VR++  R
Sbjct: 294 QVREVLLR 301

Length = 415

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

 Score = 90.8 bits (226), Expect = 2e-20
 Identities = 49/173 (28%), Positives = 86/173 (49%), Gaps = 34/173 (19%)

Query: 285 LIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV 344
           L +++K + +L  + GR P+  E A+A+ L    ++  L        +     + L   V
Sbjct: 160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELL--------QRARQPVSLDAPV 211

Query: 345 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRN 404
                     L DLL++                         E P+  V+++ +RQ + +
Sbjct: 212 G---DEEDTELGDLLEDDG-----------------------ESPEEQVERESLRQDLES 245

Query: 405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           LL  L P+ER ++RLRFG++ G+P +L+E+G    LS+ERVRQ+E++AL +L+
Sbjct: 246 LLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 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|223642 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]

 Score = 88.5 bits (220), Expect = 3e-19
 Identities = 49/182 (26%), Positives = 94/182 (51%), Gaps = 38/182 (20%)

Query: 279 IAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKS--ELHSGNSSREKLINA 336
           + Q++ + +L + K +L  + GREPT  E A+ +G+S   ++   +  S   S +  I  
Sbjct: 182 VHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGD 241

Query: 337 NLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQ 396
           +                 L D L++                  +  +     P+ +V+++
Sbjct: 242 D-------------EDSELGDFLEDD-----------------KSVS-----PEDAVERE 266

Query: 397 LMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 455
            +++ +  +L   L  +ER ++RLRFG++DG+PK+L E+G  FG+S+ERVRQ+E++AL +
Sbjct: 267 SLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRK 326

Query: 456 LK 457
           L+
Sbjct: 327 LR 328

Length = 342

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

 Score = 84.3 bits (209), Expect = 2e-18
 Identities = 54/180 (30%), Positives = 93/180 (51%), Gaps = 36/180 (20%)

Query: 278 LIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINAN 337
           ++  I  LI+ E+   +L  + GREPT  E A+ +G+                EK+    
Sbjct: 82  MVETINKLIKAER---QLTQELGREPTDEELAERMGMPA--------------EKV---- 120

Query: 338 LRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQL 397
            R +  +A++     ISL     E  +G     E+     G    +T +E PD    K+L
Sbjct: 121 -REIKKIAQE----PISL-----ETPIG-----EEEDSFLGDFIEDTSIESPDDYAAKEL 165

Query: 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           +R+ +  +L  L  +E  ++R+R+G+ DG+P +L EVG  F +++ER+RQ+ES+AL +L+
Sbjct: 166 LREQLDEVLETLTEREEKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLR 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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 83.1 bits (206), Expect = 5e-17
 Identities = 44/106 (41%), Positives = 59/106 (55%), Gaps = 13/106 (12%)

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 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
            ++  L+ ANLRLVV +AK+Y  RG+S  DL+QEG++GL+K+VEKF
Sbjct: 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKF 316

Length = 509

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

 Score = 78.2 bits (193), Expect = 2e-16
 Identities = 48/174 (27%), Positives = 80/174 (45%), Gaps = 46/174 (26%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----- 383
           +R  LI  NLRLV H+ K++   G  + DL+  G++GL+K+++ F P  G R A      
Sbjct: 49  ARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARC 108

Query: 384 -----------------------------TGVEIP--DI----------SVQKQLMRQHV 402
                                         G EI   DI           V+  L  + +
Sbjct: 109 IENEILMHLRALKKTKGEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKL 168

Query: 403 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 456
              L++L+ +ER ++ +R+G+ DG+ K+  E+  I G+S+  V ++E RAL +L
Sbjct: 169 YKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKL 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|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated

 Score = 79.4 bits (196), Expect = 4e-16
 Identities = 31/71 (43%), Positives = 55/71 (77%)

Query: 387 EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR 446
           E P+  V K L+R+ +  +L  L+P+ER ++RLR+G++DG+ K+L E+G IF +++ER+R
Sbjct: 290 ETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 349

Query: 447 QLESRALYRLK 457
           Q+E++AL +L+
Sbjct: 350 QIEAKALRKLR 360

Length = 373

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

 Score = 76.9 bits (190), Expect = 5e-16
 Identities = 39/179 (21%), Positives = 80/179 (44%), Gaps = 48/179 (26%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA------ 382
           +R  LI  NLRLV H+ K+++  G  + DL+  G++GL+K++E F    G + A      
Sbjct: 50  ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARC 109

Query: 383 -----------------------------------------NTGVEIPDISVQKQLMRQH 401
                                                    +   ++ +  V+ ++  + 
Sbjct: 110 IENEILMHLRNLKKTKKEVSLQDPIGVDKEGNEISLIDILGSEEDDVIEQ-VELKMEVEK 168

Query: 402 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460
           +   + +L+ +E+ ++ +R+G+ +GK K+  E+    G+S+  V ++E RAL +L + L
Sbjct: 169 LYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227

Length = 233

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

 Score = 77.0 bits (190), Expect = 6e-16
 Identities = 28/52 (53%), Positives = 42/52 (80%)

Query: 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
           +++L+ +NLRLVV +AK+Y  RG+S  DL+QEG++GLMK+VEKF  + G +F
Sbjct: 2   KKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKF 53

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

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

 Score = 77.1 bits (190), Expect = 1e-15
 Identities = 48/129 (37%), Positives = 77/129 (59%), Gaps = 15/129 (11%)

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 KPQAGCRFA 382
               G +F+
Sbjct: 132 DYTKGFKFS 140

Length = 324

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

 Score = 74.9 bits (184), Expect = 3e-15
 Identities = 48/180 (26%), Positives = 84/180 (46%), Gaps = 46/180 (25%)

Query: 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--- 383
            S++  LI  NLRLVV++A++++  GI + DL+  G++GL+K+V  F P    + A    
Sbjct: 51  ESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYAS 110

Query: 384 -------------------------------------------TGVEIPDISVQKQLMRQ 400
                                                      T  +I    +++++ R+
Sbjct: 111 RCIENEILMYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRE 170

Query: 401 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460
            +R  L  LN +E+ I+ LRFG+  G  K+  EV ++ G+S+  + +LE R L RLK+ +
Sbjct: 171 LLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEI 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|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated

 Score = 76.2 bits (188), Expect = 5e-15
 Identities = 48/135 (35%), Positives = 65/135 (48%), Gaps = 42/135 (31%)

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 MKSVEKFKPQAGCRF 381
           MK+VEKF  + G +F
Sbjct: 168 MKAVEKFDYRKGFKF 182

Length = 367

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

 Score = 76.1 bits (187), Expect = 7e-15
 Identities = 35/77 (45%), Positives = 53/77 (68%), Gaps = 4/77 (5%)

Query: 386 VEIPDISVQKQLMRQHVRN----LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS 441
           +E  DIS ++ LMR+ ++     LL  L  +ER ++R+RFG+ DG   SL+E+G    LS
Sbjct: 324 LETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLS 383

Query: 442 KERVRQLESRALYRLKQ 458
           +ERVRQ+ES+AL +L+Q
Sbjct: 384 RERVRQIESKALQKLRQ 400

Length = 415

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

 Score = 76.2 bits (188), Expect = 8e-15
 Identities = 51/177 (28%), Positives = 89/177 (50%), Gaps = 38/177 (21%)

Query: 282 IQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV 341
           I  L R+E+E   L  + GREPT  E AK +G +               EK        V
Sbjct: 357 INKLGRIERE---LLQELGREPTPEELAKEMGFTP--------------EK--------V 391

Query: 342 VHVAKQYQGRGISLHDLL-QEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQ 400
             + ++Y    ISL   + +EG       +E           ++    P  +V   L++ 
Sbjct: 392 REI-QKYNREPISLDKTIGKEGDSQFGDFIE-----------DSEAVSPVDAVSFTLLQD 439

Query: 401 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
            ++ +L  L+ +E  ++R+RFG+ DG+PK+L E+G ++G+++ER+RQ+ES+ L +L+
Sbjct: 440 QLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496

Length = 509

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

 Score = 74.0 bits (182), Expect = 1e-14
 Identities = 29/54 (53%), Positives = 42/54 (77%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
           +R+ +I +NLRLVV +AK Y  RG+ L DL++EG++GLM +VEKF P+ G RF+
Sbjct: 47  ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFS 100

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

 Score = 70.8 bits (174), Expect = 1e-14
 Identities = 34/162 (20%), Positives = 68/162 (41%), Gaps = 33/162 (20%)

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR-FANT-- 384
            + E+L    L LV   A++Y G      DL+QE  + L++++++F P+   + +     
Sbjct: 1   EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIA 60

Query: 385 --------------------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVR 418
                                         P+  ++++  R+ +R  L  L  +ER ++ 
Sbjct: 61  RNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLV 120

Query: 419 LRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460
           LR+     +  S  E+  I G+S   V++   RA  +L++ L
Sbjct: 121 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|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 73.1 bits (180), Expect = 3e-14
 Identities = 28/54 (51%), Positives = 46/54 (85%)

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
           ++R+++I +NLRLVV +AK+Y  RG++L DL++EG++GL+++VEKF P+ G RF
Sbjct: 86  AARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRF 139

Length = 325

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

 Score = 72.2 bits (177), Expect = 8e-14
 Identities = 36/78 (46%), Positives = 52/78 (66%)

Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
           PD  + ++L+RQ + NLL  L P++R ++ LRFG+EDGK  SL++VG    LS+ERVRQL
Sbjct: 247 PDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQL 306

Query: 449 ESRALYRLKQSLGGKASY 466
           E +AL  L++       Y
Sbjct: 307 EHQALAHLRRRRANVKEY 324

Length = 327

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

 Score = 71.7 bits (176), Expect = 9e-14
 Identities = 27/67 (40%), Positives = 50/67 (74%)

Query: 392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451
           +V   L+   +R++L  L+ +E+ ++RLRFG++DG+P++L ++G +FGLS+ERVRQ+E  
Sbjct: 246 AVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 305

Query: 452 ALYRLKQ 458
            + +L+ 
Sbjct: 306 VMSKLRN 312

Length = 324

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

 Score = 67.7 bits (166), Expect = 1e-12
 Identities = 24/51 (47%), Positives = 38/51 (74%)

Query: 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
           KL+ ++LR VV +A+ Y+G G+   DL+QEG++GLMK+V++F P+ G R  
Sbjct: 39  KLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLV 89

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

 Score = 60.1 bits (147), Expect = 4e-12
 Identities = 24/54 (44%), Positives = 36/54 (66%), Gaps = 4/54 (7%)

Query: 405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458
            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|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated

 Score = 66.5 bits (163), Expect = 6e-12
 Identities = 25/62 (40%), Positives = 49/62 (79%)

Query: 397 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL 456
           L+++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L
Sbjct: 294 LLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 353

Query: 457 KQ 458
           + 
Sbjct: 354 RH 355

Length = 367

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

 Score = 65.6 bits (161), Expect = 7e-12
 Identities = 24/51 (47%), Positives = 39/51 (76%)

Query: 332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
           +L+ ++LR VVH+A+ Y+G G+   DL+QEG++GLMK+V++F P+ G R  
Sbjct: 52  QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLV 102

Length = 284

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

 Score = 64.0 bits (156), Expect = 2e-11
 Identities = 26/72 (36%), Positives = 44/72 (61%)

Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
           P+  VQ   ++Q +   L  LN ++R ++  RFG+   +P +L EV    GL++ERVRQ+
Sbjct: 203 PESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQI 262

Query: 449 ESRALYRLKQSL 460
           +  AL +L++ L
Sbjct: 263 QVEALKKLRRIL 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|218138 pfam04542, Sigma70_r2, Sigma-70 region 2

 Score = 59.1 bits (144), Expect = 2e-11
 Identities = 21/49 (42%), Positives = 32/49 (65%)

Query: 333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
           L+   L LV  +A++Y G G    DL+QEG +GL+++VE+F P+ G  F
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSF 49

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|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 65.2 bits (160), Expect = 3e-11
 Identities = 32/94 (34%), Positives = 55/94 (58%), Gaps = 8/94 (8%)

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

Query: 340 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
           LV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF
Sbjct: 392 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 425

Length = 619

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

 Score = 61.5 bits (150), Expect = 8e-11
 Identities = 22/52 (42%), Positives = 37/52 (71%)

Query: 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
           REKL+  NL LV  +A++++ RG    DL+Q G++GL+K++++F P  G +F
Sbjct: 5   REKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKF 56

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

 Score = 62.1 bits (151), Expect = 1e-10
 Identities = 52/184 (28%), Positives = 87/184 (47%), Gaps = 38/184 (20%)

Query: 285 LIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINAN--LRLVV 342
           L +++K + +L  Q GR  T+ E A+ + L+ + +          RE L  A   L L +
Sbjct: 167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQV----------REYLERARQPLSLDL 216

Query: 343 HVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHV 402
            V          L +LL++       S E F  Q+              S+Q  L R   
Sbjct: 217 RVGDNQD---TELGELLEDTG----ASPEDFATQS--------------SLQLDLER--- 252

Query: 403 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462
             L+  L P+++ ++ LRFG+EDG+P +L+++G    +S+ERVRQ+E  AL +L++    
Sbjct: 253 --LMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRKAN 310

Query: 463 KASY 466
              Y
Sbjct: 311 IQEY 314

Length = 317

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

 Score = 60.7 bits (148), Expect = 2e-10
 Identities = 28/71 (39%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

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

Query: 376 QAGCRFANTGV 386
               +F+   V
Sbjct: 85  SQNVKFSTYAV 95

Length = 258

>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 = 55.2 bits (134), Expect = 3e-10
 Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           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|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 59.2 bits (144), Expect = 1e-09
 Identities = 26/72 (36%), Positives = 43/72 (59%)

Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
           P+ + Q   M+Q +   L  LN K+R ++  RFG+   +  +L +V    GL++ERVRQ+
Sbjct: 243 PEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQI 302

Query: 449 ESRALYRLKQSL 460
           +  AL RL++ L
Sbjct: 303 QVEALRRLREIL 314

Length = 325

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

 Score = 57.9 bits (140), Expect = 2e-09
 Identities = 30/71 (42%), Positives = 45/71 (63%), Gaps = 1/71 (1%)

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

Query: 376 QAGCRFANTGV 386
               +F+   V
Sbjct: 82  SQNVKFSTYAV 92

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

 Score = 57.7 bits (140), Expect = 2e-09
 Identities = 33/179 (18%), Positives = 73/179 (40%), Gaps = 40/179 (22%)

Query: 283 QDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342
           +   R+E+   +L+ + GREPT  E A+ +G+   +    L + N S+   ++ ++    
Sbjct: 107 ELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDV---- 162

Query: 343 HVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHV 402
                                                      +E PD  V+K+ + + +
Sbjct: 163 ----LKDDDDDVDDQ----------------------------IENPDDGVEKEELLEIL 190

Query: 403 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461
           +  +  L  +E+ ++ LR+  E     +  E+  + G+S+ RV +L  +A+ +L++ L 
Sbjct: 191 KEAIEPLPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVSRLHKKAIKKLRKELN 245

Length = 247

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

 Score = 57.7 bits (140), Expect = 2e-09
 Identities = 26/63 (41%), Positives = 39/63 (61%), Gaps = 2/63 (3%)

Query: 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
            R+ +   L  LN +E  I+R R   ED    +L  +G   G+SKERVRQ+E+RAL +L+
Sbjct: 217 RRRWLTQALQTLNERELRIIRERRLRED--GATLEALGEELGISKERVRQIEARALEKLR 274

Query: 458 QSL 460
           ++L
Sbjct: 275 RAL 277

Length = 289

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

 Score = 56.6 bits (137), Expect = 5e-09
 Identities = 37/137 (27%), Positives = 62/137 (45%), Gaps = 7/137 (5%)

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

Query: 376 QAGCRFANTGVEIPDISVQKQLMRQ---HV-RNLLTLLNPKERCIVRLRFGIEDGKPKSL 431
             G +F+   V      +   L +     V R+L  L    E  I  L    E G+  + 
Sbjct: 72  SKGTKFSTYAVRRIRGEILDYLRKNDSVKVPRSLRELGRRIEEAIDELE--QELGREPTD 129

Query: 432 SEVGNIFGLSKERVRQL 448
            E+    G+ KE   + 
Sbjct: 130 EEIAEELGIDKEEYIEA 146

Length = 247

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

 Score = 57.9 bits (141), Expect = 6e-09
 Identities = 23/63 (36%), Positives = 44/63 (69%)

Query: 395 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454
           ++ +R+   ++L  L P+E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL 
Sbjct: 543 QESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602

Query: 455 RLK 457
           +L+
Sbjct: 603 KLR 605

Length = 619

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

 Score = 53.9 bits (130), Expect = 5e-08
 Identities = 21/71 (29%), Positives = 46/71 (64%)

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

Query: 389 PDISVQKQLMR 399
              S+Q  ++R
Sbjct: 101 IRASIQDYILR 111

Length = 289

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

 Score = 53.4 bits (129), Expect = 5e-08
 Identities = 21/51 (41%), Positives = 32/51 (62%), Gaps = 1/51 (1%)

Query: 324 HSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
             G+  +R+ L+  NLRLV  V +++  RG    DL Q G +GL+K+V+KF
Sbjct: 27  QDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKF 77

Length = 252

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

 Score = 52.6 bits (127), Expect = 9e-08
 Identities = 24/60 (40%), Positives = 41/60 (68%), Gaps = 1/60 (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

Length = 234

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

 Score = 52.4 bits (126), Expect = 1e-07
 Identities = 24/66 (36%), Positives = 39/66 (59%), Gaps = 1/66 (1%)

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

Query: 383 NTGVEI 388
              V +
Sbjct: 66  TYAVPM 71

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

 Score = 51.5 bits (124), Expect = 2e-07
 Identities = 44/180 (24%), Positives = 79/180 (43%), Gaps = 39/180 (21%)

Query: 282 IQDL-IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRL 340
           +++L +++ K   +L  + GR PT+ E A+ +G+S  ++   L +GN+ +   ++     
Sbjct: 85  LKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVVEALEAGNAYQALSLD----- 139

Query: 341 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQ 400
                +   G  I+L D L +    L    +                           R 
Sbjct: 140 --ASIEDDDGDPIALLDTLGDEDDALETVED---------------------------RL 170

Query: 401 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460
            ++ LL  L  +ER I+ LRF  ED   K+ SE+    G+S+  V +L  RAL +L++ L
Sbjct: 171 ALKPLLAALPERERRILLLRF-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|233885 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA/WhiG family

 Score = 50.7 bits (122), Expect = 3e-07
 Identities = 44/177 (24%), Positives = 85/177 (48%), Gaps = 38/177 (21%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
           +LE+   +L+++ GREPT  E A+ +G+  ++ +  L+  N          L LV     
Sbjct: 84  KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEIN---------ALSLV----- 129

Query: 347 QYQGRGISLHDLLQEG--SMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRN 404
                  SL +LL+ G     L+  +E  K            E P+  ++++ +R+ +  
Sbjct: 130 -------SLDELLESGDDGGSLIDRIEDDKS-----------EDPEEELEREELREALAE 171

Query: 405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461
            +  L+ +E+ ++ L +  E     +L E+G + GL++ RV Q+ S+AL +L+  L 
Sbjct: 172 AIESLSEREQLVLSLYYYEE----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|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH

 Score = 51.1 bits (123), Expect = 4e-07
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 2/65 (3%)

Query: 396 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR 455
           +L RQ + N L  L+ + R I+  R+  +D    +L E+   +G+S ER+RQ+E  A+ +
Sbjct: 206 ELQRQALANALGSLDARSRRIIEARWLDDD--KLTLQELAAEYGVSAERIRQIEKNAMKK 263

Query: 456 LKQSL 460
           LK +L
Sbjct: 264 LKAAL 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|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed

 Score = 49.9 bits (120), Expect = 7e-07
 Identities = 22/60 (36%), Positives = 37/60 (61%), Gaps = 4/60 (6%)

Query: 403 RNLLTL----LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458
           R LL      L+ +E+ I+ LRFG+  G+ K+  EV ++ G+S+  + +LE R + RLK+
Sbjct: 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228

Length = 234

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

 Score = 47.3 bits (113), Expect = 6e-06
 Identities = 32/175 (18%), Positives = 74/175 (42%), Gaps = 34/175 (19%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
           ++E    KL+ ++ R  T  E A  +G++  ++++                      + +
Sbjct: 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEAT---------------------MNE 148

Query: 347 QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLL 406
            +    +S+ +   +   G   SV     +            P+  + K+ + + +   +
Sbjct: 149 GFFANLLSIDEKTHDQDDGENVSVTIRDDKT---------PTPEEKLLKEELIEELAEKI 199

Query: 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG 461
             L+ KE+ ++ L +  E     +L+E+G +  LS  R+ Q+ S+AL++LK+ L 
Sbjct: 200 KQLSEKEQLVISLFYKEE----LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE 250

Length = 251

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

 Score = 46.6 bits (111), Expect = 8e-06
 Identities = 38/174 (21%), Positives = 77/174 (44%), Gaps = 40/174 (22%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
           ++   K +L  + GREPT+ E A+A+G+S  ++   L S  S +                
Sbjct: 98  KIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQ---------------- 141

Query: 347 QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLL 406
                  SL+D + +     +  +++   +                    L +  ++  +
Sbjct: 142 -------SLYDTVHQDDGDPIYLLDQIADKGS-------------EDSDWLEKIALKEAI 181

Query: 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460
           + L+ +ER I+ LR+     K K+ +EV N+ G+S+ +V +LE + L ++K+ L
Sbjct: 182 SKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 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|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed

 Score = 45.2 bits (108), Expect = 3e-05
 Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 2/56 (3%)

Query: 409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA 464
           L+ + R I+  R+  +D    +L E+   +G+S ERVRQ+E  A+ +LK ++   A
Sbjct: 231 LDERSRDIIEARWLDDD--KSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEAAA 284

Length = 284

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

 Score = 45.2 bits (107), Expect = 3e-05
 Identities = 18/57 (31%), Positives = 33/57 (57%)

Query: 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGV 386
           R++++   L L  H+A+++ GRG    DL+Q   +GL+ +V +F  + G  F +  V
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAV 98

Length = 264

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

 Score = 44.1 bits (105), Expect = 6e-05
 Identities = 37/176 (21%), Positives = 73/176 (41%), Gaps = 37/176 (21%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
            + +   +L+ + GREPT  E A+ +GLS  + +  L   N S+                
Sbjct: 96  EVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQL--------------- 140

Query: 347 QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLL 406
                  S+ +L  E         +        +  +   ++ D  +++ L+       +
Sbjct: 141 ------FSIDELRGE-------HGDSILVTEDHQDEDPLQQLEDEELREALVE-----AI 182

Query: 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462
             L  +E+ ++ L +  E     +L E+G + G+S+ RV Q+ S+A+ RL+  LG 
Sbjct: 183 ESLPEREQLVLSLYYQEE----LNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE 234

Length = 236

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

 Score = 41.2 bits (97), Expect = 5e-04
 Identities = 40/183 (21%), Positives = 83/183 (45%), Gaps = 40/183 (21%)

Query: 283 QDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV 342
           Q   ++E+  + L+++ GR P+  E A  +G+S  +        NS   KL   ++    
Sbjct: 115 QKARQIERAIAMLEARLGRTPSDEEIADELGISLEEY-------NSLLSKLSGTSV---- 163

Query: 343 HVAKQYQGRGISLHDLLQEGSMG----LMKSVEKFKPQAGCRFANTGVEIPDISVQKQLM 398
                     +SL+DL   G  G    LM ++E           +     PD   +++ +
Sbjct: 164 ----------VSLNDLWFGGDEGDEVSLMDTLE-----------SPAALNPDEIAEREEI 202

Query: 399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458
           ++ +   +  L  +E+ ++ L +  ED    +L E+G + G+++ R+ QL ++A+ +L+ 
Sbjct: 203 KRVIVEAIKTLPEREKKVLILYY-YED---LTLKEIGKVLGVTESRISQLHTKAVLQLRA 258

Query: 459 SLG 461
            L 
Sbjct: 259 KLA 261

Length = 268

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

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 42/176 (23%), Positives = 79/176 (44%), Gaps = 42/176 (23%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
           ++ K+K +L  + GREPT+ E A+ +G++  ++   + +  +SR      ++   VH   
Sbjct: 119 KIRKDKDELSKELGREPTIEELAEYLGVTPEEV---VLAQEASRSP---QSIHETVH--- 169

Query: 347 QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLL 406
           +  G  I+L D                             +I D S +    +  ++  +
Sbjct: 170 ENDGDPITLLD-----------------------------QIADQSEEDWFDKIALKEAI 200

Query: 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG 462
             L+ +ER IV LR+     K K+ SEV    G+S+ +V +LE + L ++K+ L  
Sbjct: 201 RELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLDE 252

Length = 252

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

 Score = 38.9 bits (91), Expect = 0.002
 Identities = 30/169 (17%), Positives = 59/169 (34%), Gaps = 36/169 (21%)

Query: 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQA------------- 377
           E+L+      +  +A++  G      DL+QE  +   ++++ F+ ++             
Sbjct: 18  EELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSFRGRSSFKAWLYRIARNL 77

Query: 378 -------GCRFANTGVEI------------PDISVQKQLMRQHVRNLLTLLNPKERCIVR 418
                    R      E                 +  +   + +R  L  L P++R    
Sbjct: 78  AIDRLRKRKRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFL 137

Query: 419 LRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYG 467
           LR+ +E     S  E+  I G+S   V+    RA  +L++ L      G
Sbjct: 138 LRY-LEG---LSYEEIAEILGISVGTVKSRLHRARKKLREQLEEAGERG 182

Length = 182

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

 Score = 39.6 bits (92), Expect = 0.002
 Identities = 43/177 (24%), Positives = 76/177 (42%), Gaps = 37/177 (20%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
           +L      L+   G+EPT  E  + + +S ++L       +S+R  LI            
Sbjct: 111 KLADAMDSLRQSLGKEPTDGELCEYLNISQQELS---GWFSSARPALI------------ 155

Query: 347 QYQGRGISLHD---LLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVR 403
                 +SL++      +   GL  ++E+         A TG ++    V K+     + 
Sbjct: 156 ------LSLNEEFPCQSDDEAGL--ALEERIAD---ERAETGYDV----VDKKEFSSILA 200

Query: 404 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460
             +  L  KER ++ L +  E      L E+G I G+S+ RV Q+ S+AL +L+ +L
Sbjct: 201 EAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKLRATL 253

Length = 257

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	473
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	99.97
PRK05901	509	RNA polymerase sigma factor; Provisional	99.97
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	99.96
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	99.96
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	99.92
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	99.92
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	99.91
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	99.91
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.91
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.9
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	99.9
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	99.9
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.88
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.87
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	99.87
PRK08215	258	sporulation sigma factor SigG; Reviewed	99.86
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	99.86
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	99.85
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	99.85
PRK08583	257	RNA polymerase sigma factor SigB; Validated	99.85
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	99.84
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.84
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.84
PRK07670	251	RNA polymerase sigma factor SigD; Validated	99.82
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.82
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.81
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.81
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.81
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	99.8
PRK12513	194	RNA polymerase sigma factor; Provisional	99.8
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.8
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	99.8
PRK12514	179	RNA polymerase sigma factor; Provisional	99.8
PRK05572	252	sporulation sigma factor SigF; Validated	99.8
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	99.8
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	99.8
PRK12538	233	RNA polymerase sigma factor; Provisional	99.8
PRK12524	196	RNA polymerase sigma factor; Provisional	99.79
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.79
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.79
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.79
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.79
PRK12537	182	RNA polymerase sigma factor; Provisional	99.79
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.79
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.79
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.79
PRK12542	185	RNA polymerase sigma factor; Provisional	99.78
PRK12534	187	RNA polymerase sigma factor; Provisional	99.78
PRK12515	189	RNA polymerase sigma factor; Provisional	99.78
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	99.77
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.77
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.77
PRK12519	194	RNA polymerase sigma factor; Provisional	99.77
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.77
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.77
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.76
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.76
PRK12543	179	RNA polymerase sigma factor; Provisional	99.76
PRK11924	179	RNA polymerase sigma factor; Provisional	99.76
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.76
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.75
PRK11922	231	RNA polymerase sigma factor; Provisional	99.75
PRK12531	194	RNA polymerase sigma factor; Provisional	99.75
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.75
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.75
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.75
PRK12526	206	RNA polymerase sigma factor; Provisional	99.74
PRK12529	178	RNA polymerase sigma factor; Provisional	99.74
PRK12520	191	RNA polymerase sigma factor; Provisional	99.73
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.73
PRK12539	184	RNA polymerase sigma factor; Provisional	99.73
PRK12522	173	RNA polymerase sigma factor; Provisional	99.73
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.72
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.72
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.72
PRK12512	184	RNA polymerase sigma factor; Provisional	99.72
PRK12518	175	RNA polymerase sigma factor; Provisional	99.72
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.71
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.71
PRK12516	187	RNA polymerase sigma factor; Provisional	99.71
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.71
PRK12533	216	RNA polymerase sigma factor; Provisional	99.71
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.71
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.71
PRK12536	181	RNA polymerase sigma factor; Provisional	99.7
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.7
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.69
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.69
PRK12547	164	RNA polymerase sigma factor; Provisional	99.69
PRK12528	161	RNA polymerase sigma factor; Provisional	99.68
PRK12541	161	RNA polymerase sigma factor; Provisional	99.67
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.67
PRK12517	188	RNA polymerase sigma factor; Provisional	99.67
PRK12535	196	RNA polymerase sigma factor; Provisional	99.67
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.67
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.66
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.66
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.66
PRK12540	182	RNA polymerase sigma factor; Provisional	99.66
PRK12530	189	RNA polymerase sigma factor; Provisional	99.65
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.65
PRK12545	201	RNA polymerase sigma factor; Provisional	99.65
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.65
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.65
PRK12532	195	RNA polymerase sigma factor; Provisional	99.65
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.65
PRK12544	206	RNA polymerase sigma factor; Provisional	99.64
PRK12525	168	RNA polymerase sigma factor; Provisional	99.63
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.62
PRK12546	188	RNA polymerase sigma factor; Provisional	99.61
PRK12511	182	RNA polymerase sigma factor; Provisional	99.61
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.56
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.55
PRK09191	261	two-component response regulator; Provisional	99.5
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.48
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.48
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.47
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.46
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	99.39
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.3
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	99.3
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.24
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	99.21
PF07638	185	Sigma70_ECF: ECF sigma factor	99.1
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	99.1
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	99.0
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	98.94
PRK06930	170	positive control sigma-like factor; Validated	98.88
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	98.74
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	98.74
PRK05901	509	RNA polymerase sigma factor; Provisional	98.68
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	98.6
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	98.56
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	98.56
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	98.55
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	98.54
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	98.52
PRK00118	104	putative DNA-binding protein; Validated	98.51
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.42
PRK07598	415	RNA polymerase sigma factor SigC; Validated	98.4
PRK05949	327	RNA polymerase sigma factor; Validated	98.4
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	98.26
PRK04217	110	hypothetical protein; Provisional	98.19
PRK07405	317	RNA polymerase sigma factor SigD; Validated	98.17
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	98.14
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	98.13
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.11
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.11
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	98.05
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	98.03
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	98.01
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	97.99
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	97.98
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.88
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	97.87
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.87
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	97.78
PRK08215	258	sporulation sigma factor SigG; Reviewed	97.74
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.72
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	97.72
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.7
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	97.69
PRK07670	251	RNA polymerase sigma factor SigD; Validated	97.69
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.68
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	97.59
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.57
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.42
PRK05572	252	sporulation sigma factor SigF; Validated	97.4
PRK10840	216	transcriptional regulator RcsB; Provisional	97.36
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.35
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.34
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	97.34
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.33
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.33
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.31
PRK13870	234	transcriptional regulator TraR; Provisional	97.3
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	97.27
COG2197	211	CitB Response regulator containing a CheY-like rec	97.27
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	97.23
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	97.13
COG4566	202	TtrR Response regulator [Signal transduction mecha	97.1
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.1
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	97.08
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.06
PRK09483	217	response regulator; Provisional	96.99
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	96.94
PRK15369	211	two component system sensor kinase SsrB; Provision	96.93
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.9
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	96.84
COG3413	215	Predicted DNA binding protein [General function pr	96.79
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.75
PRK09390	202	fixJ response regulator FixJ; Provisional	96.71
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	96.69
PRK10651	216	transcriptional regulator NarL; Provisional	96.64
PRK08583	257	RNA polymerase sigma factor SigB; Validated	96.36
COG1342	99	Predicted DNA-binding proteins [General function p	96.21
PRK01381	99	Trp operon repressor; Provisional	96.17
PRK10403	215	transcriptional regulator NarP; Provisional	96.16
PRK15320	251	transcriptional activator SprB; Provisional	96.04
COG1356	143	tfx Transcriptional regulator [DNA replication, re	95.96
PRK04841	903	transcriptional regulator MalT; Provisional	95.84
PRK09935	210	transcriptional regulator FimZ; Provisional	95.73
PRK13558	665	bacterio-opsin activator; Provisional	95.68
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	95.65
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	95.63
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	95.63
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.61
COG4941	415	Predicted RNA polymerase sigma factor containing a	95.53
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	95.47
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	95.26
PRK15418	318	transcriptional regulator LsrR; Provisional	95.24
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	95.17
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	94.56
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	94.51
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	94.32
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	93.48
PF10668	60	Phage_terminase: Phage terminase small subunit; In	93.3
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.98
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	92.97
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	92.96
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	92.8
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	92.77
PHA00675	78	hypothetical protein	92.73
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	92.7
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	92.63
PF13518	52	HTH_28: Helix-turn-helix domain	92.62
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	92.2
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	92.19
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	92.17
smart00351	125	PAX Paired Box domain.	91.91
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	91.86
PRK05932	455	RNA polymerase factor sigma-54; Reviewed	91.25
PF13730	55	HTH_36: Helix-turn-helix domain	91.16
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	90.49
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	90.19
PRK11083	228	DNA-binding response regulator CreB; Provisional	89.84
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	89.45
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	89.17
cd00131	128	PAX Paired Box domain	89.15
COG3415	138	Transposase and inactivated derivatives [DNA repli	89.14
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	88.9
PHA02591	83	hypothetical protein; Provisional	88.68
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	88.5
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	88.21
PRK12469	481	RNA polymerase factor sigma-54; Provisional	87.97
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	87.92
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	87.65
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	87.64
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	87.54
PRK10046	225	dpiA two-component response regulator DpiA; Provis	87.4
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	87.29
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	86.76
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	86.75
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	86.73
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	86.59
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	86.48
PRK15479	221	transcriptional regulatory protein TctD; Provision	86.08
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	85.99
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	85.95
PRK12423	202	LexA repressor; Provisional	85.9
PF12728	51	HTH_17: Helix-turn-helix domain	85.74
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	85.53
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	85.49
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	85.16
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	84.44
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	84.21
CHL00148	240	orf27 Ycf27; Reviewed	83.98
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	83.57
TIGR01764	49	excise DNA binding domain, excisionase family. An	83.12
PRK00215	205	LexA repressor; Validated	82.95
PRK13413	200	mpi multiple promoter invertase; Provisional	82.13
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	82.07
COG2973	103	TrpR Trp operon repressor [Transcription]	82.05
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	81.58
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	81.53
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	81.5
COG1522	154	Lrp Transcriptional regulators [Transcription]	81.38
PRK11169	164	leucine-responsive transcriptional regulator; Prov	81.31
COG3355	126	Predicted transcriptional regulator [Transcription	81.07
PF13551	112	HTH_29: Winged helix-turn helix	80.94
PHA01976	67	helix-turn-helix protein	80.82

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=1.9e-38  Score=331.35  Aligned_cols=219  Identities=39%  Similarity=0.664  Sum_probs=199.1

Q ss_pred             ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHH--------------------HHHHHHHHHHHhCCCCCHHHHHHHcC
Q 011992          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAIG  313 (473)
Q Consensus       254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~k--------------------le~a~~~L~~~lGRePT~eEiA~~lG  313 (473)
                      .|++|.|++.++++|+||++||++|++++|.+.+                    |++++.+|..++|++||..|||+++|
T Consensus        59 ~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~  138 (415)
T PRK07598         59 TDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTAD  138 (415)
T ss_pred             CChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhC
Confidence            4589999999999999999999999999999998                    89999999999999999999995555


Q ss_pred             ----------------------CCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhh
Q 011992          314 ----------------------LSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE  371 (473)
Q Consensus       314 ----------------------ms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAie  371 (473)
                                            |+.++|...+..|..|+++||..|+++|+++|++|.+++.+++||+|||++|||++++
T Consensus       139 ~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~rave  218 (415)
T PRK07598        139 ISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVE  218 (415)
T ss_pred             CcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHH
Confidence                                  5566666667788899999999999999999999999999999999999999999999


Q ss_pred             hhCccCCCccccC-------------------------------------------------------------------
Q 011992          372 KFKPQAGCRFANT-------------------------------------------------------------------  384 (473)
Q Consensus       372 kFDp~kg~~FsT~-------------------------------------------------------------------  384 (473)
                      +|||.+|++|+|+                                                                   
T Consensus       219 kFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~  298 (415)
T PRK07598        219 KFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREV  298 (415)
T ss_pred             HcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            9999999999990                                                                   


Q ss_pred             ----------------------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHH
Q 011992          385 ----------------------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN  436 (473)
Q Consensus       385 ----------------------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe  436 (473)
                                                  ....|++.+....+...|..+|..||+++|.||.|+|+|+||+++|++|||+
T Consensus       299 l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~EIA~  378 (415)
T PRK07598        299 LLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGR  378 (415)
T ss_pred             HHHccCCcccccccCCCccccHHHhccCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHHHHH
Confidence                                        0123455566677788899999999999999999999999999999999999


Q ss_pred             HHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhhhh
Q 011992          437 IFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL  472 (473)
Q Consensus       437 ~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yldll  472 (473)
                      .||||+++|++++++|++|||+.-....+++|++-|
T Consensus       379 ~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~~~  414 (415)
T PRK07598        379 ALDLSRERVRQIESKALQKLRQPKRRNRIRDYLELL  414 (415)
T ss_pred             HHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHHhc
Confidence            999999999999999999999988888899998754

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

Probab=100.00  E-value=6.8e-36  Score=300.93  Aligned_cols=202  Identities=47%  Similarity=0.798  Sum_probs=188.7

Q ss_pred             hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (473)
Q Consensus       256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~  335 (473)
                      +++.|++.+.+.|+||+|||.+|+++++....++..+..|..++|++||..|||+++|++..++...+..|..|++.||.
T Consensus         2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~   81 (298)
T TIGR02997         2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK   81 (298)
T ss_pred             cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence            57789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCC-----------------------------
Q 011992          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGV-----------------------------  386 (473)
Q Consensus       336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~-----------------------------  386 (473)
                      .|+++|+++|++|.+++.+++||+|||++|||+++++|||.+|++|+|+..                             
T Consensus        82 ~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~  161 (298)
T TIGR02997        82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLN  161 (298)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHH
Confidence            999999999999999999999999999999999999999999999988110                             


Q ss_pred             ------------------------------------------------------------------CCchHHHHHHHHHH
Q 011992          387 ------------------------------------------------------------------EIPDISVQKQLMRQ  400 (473)
Q Consensus       387 ------------------------------------------------------------------~~pee~le~~el~e  400 (473)
                                                                                        ..|++.+...+...
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~~pe~~~~~~~~~~  241 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEEQVERESLRQ  241 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCCCCHHHHHHHHHHHH
Confidence                                                                              12345556666777


Q ss_pred             HHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          401 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       401 ~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .|.++|+.||+++|.||.++|||++++++|++|||+.||||+++|+|++++|++|||
T Consensus       242 ~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr  298 (298)
T TIGR02997       242 DLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR  298 (298)
T ss_pred             HHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            899999999999999999999998889999999999999999999999999999986

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

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=1.4e-35  Score=302.86  Aligned_cols=215  Identities=42%  Similarity=0.685  Sum_probs=198.0

Q ss_pred             ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHH
Q 011992          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (473)
Q Consensus       254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~L  333 (473)
                      .|+++.|++.+.+.|+||++||++|+++++.+..++..+..|..++|++|+..|||.+++++..+|...++.|+.|++.|
T Consensus        17 ~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~L   96 (327)
T PRK05949         17 ADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKM   96 (327)
T ss_pred             CCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHH
Confidence            35799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC----------------------------
Q 011992          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG----------------------------  385 (473)
Q Consensus       334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~----------------------------  385 (473)
                      |..|+++|+++|++|.+++.+++||+|||++|||+++++||+.+|++|+|+.                            
T Consensus        97 i~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~  176 (327)
T PRK05949         97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK  176 (327)
T ss_pred             HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHH
Confidence            9999999999999999999999999999999999999999999999999900                            


Q ss_pred             -------------------------------------------------------------------CCCchHHHHHHHH
Q 011992          386 -------------------------------------------------------------------VEIPDISVQKQLM  398 (473)
Q Consensus       386 -------------------------------------------------------------------~~~pee~le~~el  398 (473)
                                                                                         ...|++.+.....
T Consensus       177 ~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~~~pe~~~~~~~~  256 (327)
T PRK05949        177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQYITQELL  256 (327)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCCCCHHHHHHHHHH
Confidence                                                                               1234555666777


Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992          399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  470 (473)
Q Consensus       399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yld  470 (473)
                      ...|..+|+.||+++|.||.++|||++++++|++|||+.||||+++|+|++.+|++|||+..  ..+..|+.
T Consensus       257 ~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~~--~~l~~~~~  326 (327)
T PRK05949        257 RQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRR--ANVKEYLA  326 (327)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH--HHHHHHHh
Confidence            88899999999999999999999999999999999999999999999999999999999943  45566653

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=2.6e-35  Score=299.65  Aligned_cols=215  Identities=38%  Similarity=0.639  Sum_probs=197.1

Q ss_pred             ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHH
Q 011992          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (473)
Q Consensus       254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~L  333 (473)
                      .+++..|+..+++.|+||+|||.+|+++++.+..+++.+..|..++|++|+..|||.+++++..++...+..|..|++.|
T Consensus         7 ~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L   86 (317)
T PRK07405          7 TDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKM   86 (317)
T ss_pred             CcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHH
Confidence            34789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC----------------------------
Q 011992          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG----------------------------  385 (473)
Q Consensus       334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~----------------------------  385 (473)
                      |..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+|+.                            
T Consensus        87 ~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~  166 (317)
T PRK07405         87 VEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK  166 (317)
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHH
Confidence            9999999999999999999999999999999999999999999999998810                            


Q ss_pred             -------------------------------------------------------------------CCCchHHHHHHHH
Q 011992          386 -------------------------------------------------------------------VEIPDISVQKQLM  398 (473)
Q Consensus       386 -------------------------------------------------------------------~~~pee~le~~el  398 (473)
                                                                                         ...|++.+...++
T Consensus       167 ~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~~~pe~~~~~~~~  246 (317)
T PRK07405        167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFATQSSL  246 (317)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCCCCHHHHHHHHHH
Confidence                                                                               1134555666777


Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992          399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  470 (473)
Q Consensus       399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yld  470 (473)
                      ...|.++|+.||+++|.||.++|+|+|++++|++|||+.||||++||+|++.+|++|||+..  ..+..|+.
T Consensus       247 ~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~~--~~l~~~~~  316 (317)
T PRK07405        247 QLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRK--ANIQEYLA  316 (317)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH--HHHHHHHh
Confidence            88899999999999999999999999999999999999999999999999999999999863  45556653

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.8e-35  Score=306.43  Aligned_cols=215  Identities=39%  Similarity=0.743  Sum_probs=202.0

Q ss_pred             hhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHH
Q 011992          255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  334 (473)
Q Consensus       255 ~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li  334 (473)
                      ++++.|+..+++.|+||+|||++|+++++.+..+++.+..|..++|++|+..+||.+.|++..+|.+.+..|..|++.||
T Consensus        63 d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li  142 (373)
T PRK07406         63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV  142 (373)
T ss_pred             CHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999998899999999


Q ss_pred             HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------------------
Q 011992          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------------------  383 (473)
Q Consensus       335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------------------  383 (473)
                      ..|+++|+++|++|.+++.+++||+|||++|||+++++||+.+|++|+|                               
T Consensus       143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~  222 (373)
T PRK07406        143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI  222 (373)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999                               


Q ss_pred             ----------------------------------------------------------------CCCCCchHHHHHHHHH
Q 011992          384 ----------------------------------------------------------------TGVEIPDISVQKQLMR  399 (473)
Q Consensus       384 ----------------------------------------------------------------~~~~~pee~le~~el~  399 (473)
                                                                                      +....|++.+....+.
T Consensus       223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~~~pee~~~~~~~~  302 (373)
T PRK07406        223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDDVAKNLLR  302 (373)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCCCCHHHHHHHHHHH
Confidence                                                                            0123456667777788


Q ss_pred             HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhh
Q 011992          400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA  469 (473)
Q Consensus       400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yl  469 (473)
                      ..|..+|..||++||.||.+||++++++++|++|||+.||||++||+|++.+|++|||.......+..|+
T Consensus       303 ~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~  372 (373)
T PRK07406        303 EDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI  372 (373)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence            8999999999999999999999998889999999999999999999999999999999998888887775

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=99.97  E-value=4.8e-31  Score=269.20  Aligned_cols=203  Identities=37%  Similarity=0.658  Sum_probs=173.9

Q ss_pred             ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHH
Q 011992          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (473)
Q Consensus       254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~L  333 (473)
                      .+.+..|+....+.|+||+|||.+|+++++....++..          .+....++..   ...++...+..|..|++.|
T Consensus        25 ~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~----------~~~~~~~~~~---~~~~l~~~~~~~~~A~~~L   91 (324)
T PRK07921         25 ADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL----------LETRKRLSEA---RKRDLAAVVRDGEAARRHL   91 (324)
T ss_pred             CChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh----------hccccccchh---HHHHHHHHHhcCHHHHHHH
Confidence            35789999999999999999999999999876555443          1111111111   3457888888889999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------------
Q 011992          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------------  383 (473)
Q Consensus       334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------------  383 (473)
                      |..|+++|+++|++|.+++.+++||+|||++|||+++++|||++|++|+|                              
T Consensus        92 v~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~  171 (324)
T PRK07921         92 LEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ  171 (324)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999                              


Q ss_pred             ------------------------------------------------------------------CCCCCchHHHHHHH
Q 011992          384 ------------------------------------------------------------------TGVEIPDISVQKQL  397 (473)
Q Consensus       384 ------------------------------------------------------------------~~~~~pee~le~~e  397 (473)
                                                                                        .....|++.+...+
T Consensus       172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~  251 (324)
T PRK07921        172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGL  251 (324)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHHHH
Confidence                                                                              00123455566677


Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhh
Q 011992          398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA  469 (473)
Q Consensus       398 l~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yl  469 (473)
                      +...|..+|..|+++|+.||.+||||++|+++|++|||+.||||++||+||+.+|++|||.......+..|+
T Consensus       252 ~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~  323 (324)
T PRK07921        252 LHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA  323 (324)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence            888899999999999999999999999999999999999999999999999999999999998777777775

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=99.97  E-value=3.9e-31  Score=282.61  Aligned_cols=209  Identities=36%  Similarity=0.607  Sum_probs=176.2

Q ss_pred             cccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992          246 KLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS  325 (473)
Q Consensus       246 ~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~  325 (473)
                      +.++..|   +++.|+..++++|+||++||++|+++++.....+.   .+..       ..+|+.   ....++...+..
T Consensus       205 ~~~~~~d---~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~---~~~~-------~~~~~~---~~~~~l~~~~~~  268 (509)
T PRK05901        205 KLTATAD---PVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEE---LLAE-------GEKLDP---ELRRDLQWIGRD  268 (509)
T ss_pred             hcccccc---HHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhh---hhhh-------cccchh---hhhhhhhhhccc
Confidence            3456544   79999999999999999999999999987532222   1111       012221   234667778888


Q ss_pred             cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------  383 (473)
Q Consensus       326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------  383 (473)
                      |..|++.||..|+++|+++|++|.+++++++||||||++||++|+++|||.+|++|+|                      
T Consensus       269 g~~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IR  348 (509)
T PRK05901        269 GKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIR  348 (509)
T ss_pred             hHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCcee
Confidence            8899999999999999999999999999999999999999999999999999999999                      


Q ss_pred             --------------------------------------------------------------------------CCCCCc
Q 011992          384 --------------------------------------------------------------------------TGVEIP  389 (473)
Q Consensus       384 --------------------------------------------------------------------------~~~~~p  389 (473)
                                                                                                .....|
T Consensus       349 vP~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p  428 (509)
T PRK05901        349 IPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSP  428 (509)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCH
Confidence                                                                                      001234


Q ss_pred             hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhh
Q 011992          390 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYA  469 (473)
Q Consensus       390 ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yl  469 (473)
                      ++.+....++..|..+|..|+++||.||.+||||++++++|++|||+.||||++|||||+.+||.|||.......+..|+
T Consensus       429 ~~~~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l  508 (509)
T PRK05901        429 VDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFL  508 (509)
T ss_pred             HHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            45566777888899999999999999999999999889999999999999999999999999999999998888888887


Q ss_pred             h
Q 011992          470 D  470 (473)
Q Consensus       470 d  470 (473)
                      +
T Consensus       509 ~  509 (509)
T PRK05901        509 D  509 (509)
T ss_pred             C
Confidence            4

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

Probab=99.96  E-value=2.9e-28  Score=248.40  Aligned_cols=216  Identities=38%  Similarity=0.659  Sum_probs=189.2

Q ss_pred             hhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHH-HhCCCCCHH---------------HHHHHcCCCH-H
Q 011992          255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC-R  317 (473)
Q Consensus       255 ~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~-~lGRePT~e---------------EiA~~lGms~-e  317 (473)
                      +.++.|+......+++++++|.++...++....+......+.. .+|+.|+..               +++..+..++ .
T Consensus         9 d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee~   88 (342)
T COG0568           9 DAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEEK   88 (342)
T ss_pred             hHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHHH
Confidence            3678888888899999999999999999887766667777777 688999987               6666666665 6


Q ss_pred             HHHHHHhhcc---hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992          318 DLKSELHSGN---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------  383 (473)
Q Consensus       318 eL~~~l~~g~---~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------  383 (473)
                      ++...+..|.   .|..+||.+|+++|++||++|.++|+++.||||||++||++|+++|||++|++|+|           
T Consensus        89 ~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI~  168 (342)
T COG0568          89 ALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAIT  168 (342)
T ss_pred             HHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHHH
Confidence            6777787774   59999999999999999999999999999999999999999999999999999999           


Q ss_pred             --------------------------------------------------------------------------------
Q 011992          384 --------------------------------------------------------------------------------  383 (473)
Q Consensus       384 --------------------------------------------------------------------------------  383 (473)
                                                                                                      
T Consensus       169 raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~l~  248 (342)
T COG0568         169 RAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELG  248 (342)
T ss_pred             HHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccHHH
Confidence                                                                                            


Q ss_pred             -----CCCCCchHHHHHHHHHHHHHHHHhh-CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          384 -----TGVEIPDISVQKQLMRQHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       384 -----~~~~~pee~le~~el~e~L~~aL~~-LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                           .....|++.+....+.+.+...|.. |+++|+.||.+||+++|+++.|++|||+.+|||++|||||+.+|++|||
T Consensus       249 d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~KLr  328 (342)
T COG0568         249 DFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLR  328 (342)
T ss_pred             HHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHHHH
Confidence                 1133678888888999999999999 9999999999999999999999999999999999999999999999999


Q ss_pred             HHhcc-Cchhhhhh
Q 011992          458 QSLGG-KASYGYAD  470 (473)
Q Consensus       458 ~~L~~-~~l~~yld  470 (473)
                      ..... ..+.+|++
T Consensus       329 ~~~~~~~~~~~~l~  342 (342)
T COG0568         329 RHPERSALLRSYLD  342 (342)
T ss_pred             HhhhhhhHHHHhhC
Confidence            55444 34566763

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=99.96  E-value=2e-28  Score=253.73  Aligned_cols=177  Identities=40%  Similarity=0.745  Sum_probs=159.7

Q ss_pred             ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHH
Q 011992          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (473)
Q Consensus       254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~L  333 (473)
                      .+.++.|+..+.+.|+||++||.+|+++++.                                        ++..|++.|
T Consensus        95 ~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~~~L  134 (367)
T PRK09210         95 NDPVRMYLKEIGRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAKQRL  134 (367)
T ss_pred             CcHHHHHHHHhhccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHHHHH
Confidence            4579999999999999999999999887654                                        234789999


Q ss_pred             HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------------
Q 011992          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------------  383 (473)
Q Consensus       334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------------  383 (473)
                      |..|+++|+++|++|.+++.+++||+|||++|||+++++||+.+|++|+|                              
T Consensus       135 i~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~~  214 (367)
T PRK09210        135 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET  214 (367)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHHH
Confidence            99999999999999999999999999999999999999999999999999                              


Q ss_pred             ------------------------------------------------------------------CCCCCchHHHHHHH
Q 011992          384 ------------------------------------------------------------------TGVEIPDISVQKQL  397 (473)
Q Consensus       384 ------------------------------------------------------------------~~~~~pee~le~~e  397 (473)
                                                                                        .....|+..+....
T Consensus       215 ~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~~~  294 (367)
T PRK09210        215 INKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYEL  294 (367)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHHHH
Confidence                                                                              00124555566777


Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992          398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  470 (473)
Q Consensus       398 l~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yld  470 (473)
                      ++..|..+|..||++||.||.+||||+||+++|++|||+.||||++|||||+.+||.|||.......+..|++
T Consensus       295 ~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~  367 (367)
T PRK09210        295 LKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE  367 (367)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence            8889999999999999999999999999999999999999999999999999999999999998888888863

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=99.92  E-value=2.7e-24  Score=236.42  Aligned_cols=165  Identities=34%  Similarity=0.663  Sum_probs=144.9

Q ss_pred             HHHHHHcCCCHHHHHHH---Hhhcc----hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCC
Q 011992          306 IEWAKAIGLSCRDLKSE---LHSGN----SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAG  378 (473)
Q Consensus       306 eEiA~~lGms~eeL~~~---l~~g~----~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg  378 (473)
                      .++....+++.+++..+   +..|+    .|+++||..|+++|+++|++|.+++++++||+|||++||++|+++|||.+|
T Consensus       351 ~~ie~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G  430 (619)
T PRK05658        351 EAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG  430 (619)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCC
Confidence            45667777777665444   34443    688999999999999999999999999999999999999999999999999


Q ss_pred             Ccccc---------------------------------------------------------------------------
Q 011992          379 CRFAN---------------------------------------------------------------------------  383 (473)
Q Consensus       379 ~~FsT---------------------------------------------------------------------------  383 (473)
                      ++|+|                                                                           
T Consensus       431 ~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~  510 (619)
T PRK05658        431 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEP  510 (619)
T ss_pred             CchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCC
Confidence            99999                                                                           


Q ss_pred             ---------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992          384 ---------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK  442 (473)
Q Consensus       384 ---------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~  442 (473)
                                           .....|...+....++..|..+|..||++|+.||.+||||++++++|++|||+.||||+
T Consensus       511 ~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~  590 (619)
T PRK05658        511 ISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR  590 (619)
T ss_pred             CcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCH
Confidence                                 00123455566778888999999999999999999999998889999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992          443 ERVRQLESRALYRLKQSLGGKASYGYAD  470 (473)
Q Consensus       443 ~rVrqi~~RAL~KLR~~L~~~~l~~yld  470 (473)
                      +|||||+.+|++|||.......++.|++
T Consensus       591 eRVrQie~~al~kLr~~~~~~~l~~~~~  618 (619)
T PRK05658        591 ERIRQIEAKALRKLRHPSRSRKLRSFLD  618 (619)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence            9999999999999999998889999986

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

Probab=99.92  E-value=1.3e-24  Score=212.09  Aligned_cols=192  Identities=28%  Similarity=0.422  Sum_probs=152.8

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF  299 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l  299 (473)
                      .|..+.+|.+|+|||.|||+     |+|.++   ++...|   .|++.              .+...++.++..+|.+.+
T Consensus        43 ~~fd~~~g~~FstYA~~~Ir-----~~I~~~---l~~~~~~vrip~~~--------------~~~~~~~~~~~~~l~~~~  100 (238)
T TIGR02393        43 EKFDYRKGYKFSTYATWWIR-----QAITRA---IADQARTIRIPVHM--------------VETINKLIKAERQLTQEL  100 (238)
T ss_pred             HHhCCCCCCChHHHhHHHHH-----HHHHHH---HHHcCCcEEeCHHH--------------HHHHHHHHHHHHHHHHHh
Confidence            35678899999999999999     999874   665554   45444              456778889999999999


Q ss_pred             CCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHH-HHHHHhhhhCccCC
Q 011992          300 GREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSM-GLMKSVEKFKPQAG  378 (473)
Q Consensus       300 GRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~l-gL~kAiekFDp~kg  378 (473)
                      |++||.+|+|+.+|++.+++.......                       ....++++.++++.- .+...+.       
T Consensus       101 g~~pt~~eia~~l~~~~~~v~~~~~~~-----------------------~~~~SLd~~~~~~~~~~l~d~l~-------  150 (238)
T TIGR02393       101 GREPTDEELAERMGMPAEKVREIKKIA-----------------------QEPISLETPIGEEEDSFLGDFIE-------  150 (238)
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHh-----------------------ccCCCcCCCCCCCCcccHHHHhc-------
Confidence            999999999999999999987654321                       123556655543211 1111111       


Q ss_pred             CccccCCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          379 CRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       379 ~~FsT~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                          ......|+..+...+....|..+|+.||++||.||.++|+|++++++|++|||+.||||.++|+|++.+|++|||.
T Consensus       151 ----d~~~~~p~~~~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~  226 (238)
T TIGR02393       151 ----DTSIESPDDYAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRH  226 (238)
T ss_pred             ----CCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence                1123567788888889999999999999999999999998888899999999999999999999999999999999


Q ss_pred             HhccCchhhhhh
Q 011992          459 SLGGKASYGYAD  470 (473)
Q Consensus       459 ~L~~~~l~~yld  470 (473)
                      .+....+..|+|
T Consensus       227 ~~~~~~~~~~~~  238 (238)
T TIGR02393       227 PSRSKKLKSFLD  238 (238)
T ss_pred             hHHHhHHHHhhC
Confidence            998888888875

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

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

Probab=99.91  E-value=1.7e-24  Score=213.11  Aligned_cols=178  Identities=24%  Similarity=0.351  Sum_probs=149.6

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhh--cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL--WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG  300 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~--~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG  300 (473)
                      .|+++.+|.+|+|||.++|+     |+|+|   .||+-+  |.||+.              .+..+++..+..+|++++|
T Consensus        67 eryd~~kg~kF~tyA~~~I~-----Gei~d---~LR~~~~v~vpR~~--------------~~~~~~i~~~~~~l~~el~  124 (247)
T COG1191          67 ERYDPSKGTKFSTYAVRRIR-----GEILD---YLRKNDSVKVPRSL--------------RELGRRIEEAIDELEQELG  124 (247)
T ss_pred             HHcCcccCcchHHHHHHHHH-----HHHHH---HHHhCCCccCcHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence            36789999999999999999     99999   499999  999998              5888899999999999999


Q ss_pred             CCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCc
Q 011992          301 REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR  380 (473)
Q Consensus       301 RePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~  380 (473)
                      |+||++|||+.+|++.+++...+..+...                     ...++++.+....-+           .   
T Consensus       125 r~pt~~EIA~~L~i~~ee~~~~~~~~~~~---------------------~~~sld~~~~~~~d~-----------~---  169 (247)
T COG1191         125 REPTDEEIAEELGIDKEEYIEALLAINGS---------------------QLLSLDEDVLKDDDD-----------D---  169 (247)
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHhccc---------------------cccchhhhhcccccc-----------c---
Confidence            99999999999999999999887765421                     123333333211100           0   


Q ss_pred             cccCCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          381 FANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       381 FsT~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                       ..+....|...+++.+....|.+++..|+++||.|+.+||+    +++|++|||++||||+++|+|++++|+.|||..|
T Consensus       170 -~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~----eelt~kEI~~~LgISes~VSql~kkai~kLr~~l  244 (247)
T COG1191         170 -VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYK----EELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL  244 (247)
T ss_pred             -hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHH----hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence             11224567778888899999999999999999999999999    9999999999999999999999999999999987


Q ss_pred             cc
Q 011992          461 GG  462 (473)
Q Consensus       461 ~~  462 (473)
                      ..
T Consensus       245 ~~  246 (247)
T COG1191         245 NK  246 (247)
T ss_pred             cc
Confidence            64

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=99.91  E-value=1.7e-23  Score=213.78  Aligned_cols=171  Identities=36%  Similarity=0.574  Sum_probs=150.6

Q ss_pred             hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (473)
Q Consensus       256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~  335 (473)
                      .++.|+..++..|+||+++|.+|+++++.                                        ++..|++.||.
T Consensus        54 ~~~~y~~~~~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~Li~   93 (325)
T PRK05657         54 ATQLYLNEIGYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQRMIE   93 (325)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence            57889999999999999999999877543                                        44589999999


Q ss_pred             HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC------------------------------
Q 011992          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG------------------------------  385 (473)
Q Consensus       336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~------------------------------  385 (473)
                      .|.++|+++|++|.+++.+++|++||||+|+|+++++|++.+|++|+|+.                              
T Consensus        94 ~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~~l~  173 (325)
T PRK05657         94 SNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELN  173 (325)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHHHHH
Confidence            99999999999999999999999999999999999999999998886400                              


Q ss_pred             ------------------------------------------------------------------CCCchHHHHHHHHH
Q 011992          386 ------------------------------------------------------------------VEIPDISVQKQLMR  399 (473)
Q Consensus       386 ------------------------------------------------------------------~~~pee~le~~el~  399 (473)
                                                                                        ...|+..+...+..
T Consensus       174 ~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~e~~  253 (325)
T PRK05657        174 VYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMK  253 (325)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHHHHH
Confidence                                                                              01234445556667


Q ss_pred             HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchh
Q 011992          400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASY  466 (473)
Q Consensus       400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~  466 (473)
                      ..|..+|..||+++|.||.++|||.+.+++|++|||+.||||+++|++++++|+++||+.+...++.
T Consensus       254 ~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~  320 (325)
T PRK05657        254 QSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS  320 (325)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            7899999999999999999999887779999999999999999999999999999999999887764

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.91  E-value=3.9e-23  Score=205.55  Aligned_cols=165  Identities=33%  Similarity=0.622  Sum_probs=137.6

Q ss_pred             hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (473)
Q Consensus       256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~  335 (473)
                      ++..|+......|+|++++|.+|+.++..                                       .++..|++.||.
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            36678888889999999999998876422                                       134589999999


Q ss_pred             HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC-------------------------------
Q 011992          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT-------------------------------  384 (473)
Q Consensus       336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~-------------------------------  384 (473)
                      .|+++|+++|++|.+++.+++||+|+|++|||+++++||+.+|++|+|+                               
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            9999999999999999999999999999999999999999999999990                               


Q ss_pred             ------------C--C------------------------------------------------------CCchHHHHH-
Q 011992          385 ------------G--V------------------------------------------------------EIPDISVQK-  395 (473)
Q Consensus       385 ------------~--~------------------------------------------------------~~pee~le~-  395 (473)
                                  .  .                                                      ..|+..+.. 
T Consensus       123 ~~~~~~~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~~~pe~~~~~~  202 (270)
T TIGR02392       123 FFNLRKMKKRLQGWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKTSDPEDTLEEE  202 (270)
T ss_pred             HHHHHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCCCChHHHHHHH
Confidence                        0  0                                                      001111111 


Q ss_pred             ---HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          396 ---QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       396 ---~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                         ......|..+|..||++||.||.++|+ . ++++|++|||+.||||.++|+|++.+|++|||..+.
T Consensus       203 ~~~~~~~~~L~~al~~L~~rer~vl~l~y~-~-~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~  269 (270)
T TIGR02392       203 QWEELQRQALANALGSLDARSRRIIEARWL-D-DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA  269 (270)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHhc-C-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence               123467899999999999999999996 1 268999999999999999999999999999999775

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.

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.90  E-value=5.6e-23  Score=206.25  Aligned_cols=169  Identities=31%  Similarity=0.551  Sum_probs=141.8

Q ss_pred             CChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHH
Q 011992          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (473)
Q Consensus       253 ~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~  332 (473)
                      +.+.+..|+....+.|+||.++|.+|+.+++.                                       .++..|++.
T Consensus        12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~~   52 (284)
T PRK06596         12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAKQ   52 (284)
T ss_pred             CccHHHHHHHHHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHHH
Confidence            34578889999999999999999999886432                                       134489999


Q ss_pred             HHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC----------------------------
Q 011992          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT----------------------------  384 (473)
Q Consensus       333 Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~----------------------------  384 (473)
                      ||..|+++|+++|++|.+++.+++||+|+|++||++++++||+.+|++|+|+                            
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            9999999999999999999999999999999999999999999999999980                            


Q ss_pred             -----------------C--------------------------------------C---------------CCchHHHH
Q 011992          385 -----------------G--------------------------------------V---------------EIPDISVQ  394 (473)
Q Consensus       385 -----------------~--------------------------------------~---------------~~pee~le  394 (473)
                                       .                                      .               ..|++.++
T Consensus       133 ~~~~~~~~~~~~~l~~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~~~p~~~~~  212 (284)
T PRK06596        133 RKLFFNLRKAKKRLGWLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLE  212 (284)
T ss_pred             HHHHHHHHHHHHHhccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCCCCchHHHH
Confidence                             0                                      0               01111222


Q ss_pred             HH----HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          395 KQ----LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       395 ~~----el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      ..    +....|..+|+.||++||.||.+||+. + +++|++|||+.||||.++|+|++++|++|||..+..
T Consensus       213 ~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~-~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~  282 (284)
T PRK06596        213 EDNWEDQRRALLADALEGLDERSRDIIEARWLD-D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA  282 (284)
T ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            22    246678999999999999999999962 2 689999999999999999999999999999998764

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=99.90  E-value=8.5e-23  Score=205.48  Aligned_cols=168  Identities=31%  Similarity=0.517  Sum_probs=142.1

Q ss_pred             hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (473)
Q Consensus       256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~  335 (473)
                      ..+.|+....+.|+||+++|.+|+++++.                                       .++..|++.||.
T Consensus         7 ~~~~y~~~~~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~Lv~   47 (289)
T PRK07500          7 ADRSMIRSAMKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRIIS   47 (289)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHH
Confidence            46779999999999999999999887643                                       134589999999


Q ss_pred             HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC-------------------------------
Q 011992          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT-------------------------------  384 (473)
Q Consensus       336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~-------------------------------  384 (473)
                      .|.++|+++|++|.+++.+++||+|||++|||+++++||+.+|.+|+|+                               
T Consensus        48 ~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~  127 (289)
T PRK07500         48 AHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKAL  127 (289)
T ss_pred             HhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHHHH
Confidence            9999999999999999999999999999999999999999999889880                               


Q ss_pred             -----------------------------------------------------------CC-------------CCchHH
Q 011992          385 -----------------------------------------------------------GV-------------EIPDIS  392 (473)
Q Consensus       385 -----------------------------------------------------------~~-------------~~pee~  392 (473)
                                                                                 ..             ..|++.
T Consensus       128 ~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~~pe~~  207 (289)
T PRK07500        128 FFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPDEQ  207 (289)
T ss_pred             HHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCCCchHH
Confidence                                                                       00             011222


Q ss_pred             HH----HHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992          393 VQ----KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       393 le----~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      +.    ..+....|..+|+.||++||.||.++|+  +++++|++|||+.||||+++|+|++++|++|||..+....
T Consensus       208 ~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~--~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~~  281 (289)
T PRK07500        208 VESSIDGERRRRWLTQALQTLNERELRIIRERRL--REDGATLEALGEELGISKERVRQIEARALEKLRRALLSQS  281 (289)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhc--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            21    1234567889999999999999999985  2379999999999999999999999999999999998654

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=99.90  E-value=7.8e-23  Score=204.77  Aligned_cols=171  Identities=37%  Similarity=0.590  Sum_probs=148.6

Q ss_pred             hhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHH
Q 011992          255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  334 (473)
Q Consensus       255 ~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li  334 (473)
                      +.++.|+..++..|.||.++|.+|+.+.+.                                        ++..|++.||
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~   52 (285)
T TIGR02394        13 DVTQLYLREIGFKPLLTAEEEIAYARRALA----------------------------------------GDFEARKVMI   52 (285)
T ss_pred             hHHHHHHHHHhccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHH
Confidence            357889999999999999999988877543                                        3458999999


Q ss_pred             HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC-----------------------------
Q 011992          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG-----------------------------  385 (473)
Q Consensus       335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~-----------------------------  385 (473)
                      ..|.++|+++|++|.+++.+++||+|||++|+|+++++||+..|++|.|+.                             
T Consensus        53 ~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~~~~~  132 (285)
T TIGR02394        53 ESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKEL  132 (285)
T ss_pred             HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHHHHHH
Confidence            999999999999999999999999999999999999999999888876400                             


Q ss_pred             -------------------------------------------------------------------CCCchHHHHHHHH
Q 011992          386 -------------------------------------------------------------------VEIPDISVQKQLM  398 (473)
Q Consensus       386 -------------------------------------------------------------------~~~pee~le~~el  398 (473)
                                                                                         ...|+..+...+.
T Consensus       133 ~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~~~~e~  212 (285)
T TIGR02394       133 NVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDL  212 (285)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHHHHHHH
Confidence                                                                               0124455566677


Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992          399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      ...|.++|..||+++|.||.++|||.+.+++|++|||+.||||.++|++++++|+++||+.|...+.
T Consensus       213 ~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~  279 (285)
T TIGR02394       213 KQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV  279 (285)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            7889999999999999999999966666999999999999999999999999999999999986544

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).

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.88  E-value=2.1e-21  Score=188.82  Aligned_cols=167  Identities=26%  Similarity=0.484  Sum_probs=140.4

Q ss_pred             hHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHH
Q 011992          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (473)
Q Consensus       256 ~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~  335 (473)
                      .+..|+-..+..|+||+++|..|+..++.                                        ++..+++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence            37788888888888999888877655432                                        24478999999


Q ss_pred             HHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------C---C---C---
Q 011992          336 ANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------T---G---V---  386 (473)
Q Consensus       336 ~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~---~---~---  386 (473)
                      .|.++|+++|.++.+++.+++|++||+++++|+++++|++..+..|.+                    .   .   .   
T Consensus        57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~~~~~~~~~~~  136 (233)
T PRK05803         57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIGV  136 (233)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccccCCCccccccC
Confidence            999999999999999999999999999999999999999987878877                    0   0   0   


Q ss_pred             -----------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992          387 -----------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  449 (473)
Q Consensus       387 -----------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~  449 (473)
                                       ..++..+...+..+.|.++|..||+++|+||.++|++.+.+++|++|||+.||+|.++|++++
T Consensus       137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~  216 (233)
T PRK05803        137 DKEGNEISLIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIE  216 (233)
T ss_pred             CCCcCcccHHHHccCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence                             012333445566678999999999999999999996555599999999999999999999999


Q ss_pred             HHHHHHHHHHhcc
Q 011992          450 SRALYRLKQSLGG  462 (473)
Q Consensus       450 ~RAL~KLR~~L~~  462 (473)
                      ++|+++||+.+..
T Consensus       217 ~rA~~kLr~~l~~  229 (233)
T PRK05803        217 KRALKKLFKELYR  229 (233)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998864

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=99.87  E-value=5.8e-22  Score=197.00  Aligned_cols=178  Identities=21%  Similarity=0.306  Sum_probs=140.9

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG  300 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG  300 (473)
                      |+++.+|++|+|||.|||+     |+|+++   +|...|   .|++.              .+...+++++..+|.+.+|
T Consensus        84 rFDp~~G~~FsTYA~~~Ir-----g~I~~~---lr~~~~~ir~Pr~~--------------~~~~~~i~~~~~~l~~~lg  141 (264)
T PRK07122         84 RFDVETGSDFVSFAVPTIM-----GEVRRH---FRDNSWSVKVPRRL--------------KELHLRLGRATAELSQRLG  141 (264)
T ss_pred             HcCCCCCCChHHHHHHHHH-----HHHHHH---HHHcCCccccCHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence            6789999999999999999     999994   888777   55544              4567788999999999999


Q ss_pred             CCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCc
Q 011992          301 REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR  380 (473)
Q Consensus       301 RePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~  380 (473)
                      ++||.+|||+.+|++.+++...+....                     .....++++.+.++.-+.             .
T Consensus       142 ~~pt~~eiA~~lg~~~~~v~~~~~~~~---------------------~~~~~SLd~~~~~~~~~~-------------~  187 (264)
T PRK07122        142 RAPTASELAAELGMDREEVVEGLVAGS---------------------AYNTLSIDSGGGSGDDDA-------------R  187 (264)
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHhh---------------------cCCCCcccccccCCCCCc-------------c
Confidence            999999999999999999887654221                     112455665543211000             0


Q ss_pred             cccCCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          381 FANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       381 FsT~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ...+....++..++..+....|..+|..||+++|.||.++|+    +++|++|||+.||||.++|++++++|+.+||..+
T Consensus       188 ~~~d~~~~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l  263 (264)
T PRK07122        188 AIADTLGDVDAGLDQIENREALRPLLAALPERERTVLVLRFF----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL  263 (264)
T ss_pred             cchhccCCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence            000112345556677778889999999999999999999998    9999999999999999999999999999999976


Q ss_pred             c
Q 011992          461 G  461 (473)
Q Consensus       461 ~  461 (473)
                      +
T Consensus       264 ~  264 (264)
T PRK07122        264 E  264 (264)
T ss_pred             C
Confidence            3

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=99.87  E-value=9.3e-22  Score=194.64  Aligned_cols=184  Identities=25%  Similarity=0.350  Sum_probs=144.0

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe  302 (473)
                      .+.++.+|+.|+||+.+||+     |+|+|   .+|+..|.|++.              .+...++..+...|.+.+||+
T Consensus        69 ~~fd~~~g~~F~tya~~~Ir-----~~i~~---~lr~~~~~pr~~--------------~~~~~~l~~~~~~l~~~~gr~  126 (257)
T PRK05911         69 ERFDPEKSRRFEGYALFLIK-----AAIID---DLRKQDWVPRSV--------------HQKANKLADAMDSLRQSLGKE  126 (257)
T ss_pred             HhcCCccCCCHHHHHHHHHH-----HHHHH---HHHhcCCCCHHH--------------HHHHHHHHHHHHHHHHHHCcC
Confidence            46688999999999999999     99999   499999988877              567788999999999999999


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhh---hhHHHHHHHhhhhCccCCC
Q 011992          303 PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ---EGSMGLMKSVEKFKPQAGC  379 (473)
Q Consensus       303 PT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQ---Eg~lgL~kAiekFDp~kg~  379 (473)
                      ||.+|+|+.+|++.+++...+.....+                     ...++++.+.   ++..+.  .+..+      
T Consensus       127 pt~~eiA~~l~i~~~~v~~~~~~~~~~---------------------~~~Sld~~~~~~~~~~~~~--~l~~~------  177 (257)
T PRK05911        127 PTDGELCEYLNISQQELSGWFSSARPA---------------------LILSLNEEFPCQSDDEAGL--ALEER------  177 (257)
T ss_pred             CCHHHHHHHhCcCHHHHHHHHHHhhcc---------------------ceeeccccCCCCCCCcccc--chhhh------
Confidence            999999999999999987665432110                     1233333221   110000  00011      


Q ss_pred             ccccCCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          380 RFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       380 ~FsT~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                       +.......|+..+...+....|..+|+.||+++|.||.++|+    +++|++|||+.||+|.++|++++.+|+++||+.
T Consensus       178 -l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~  252 (257)
T PRK05911        178 -IADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYY----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT  252 (257)
T ss_pred             -ccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence             011112356777788888899999999999999999999999    999999999999999999999999999999998


Q ss_pred             hcc
Q 011992          460 LGG  462 (473)
Q Consensus       460 L~~  462 (473)
                      +..
T Consensus       253 l~~  255 (257)
T PRK05911        253 LSA  255 (257)
T ss_pred             HHh
Confidence            864

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=99.86  E-value=9.4e-21  Score=186.97  Aligned_cols=154  Identities=31%  Similarity=0.512  Sum_probs=128.8

Q ss_pred             ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHH
Q 011992          263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV  342 (473)
Q Consensus       263 ~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~  342 (473)
                      .+...|+|+++|+..|+.+++.                                        ++..+++.||..|.++|+
T Consensus        12 ~~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~   51 (258)
T PRK08215         12 NTSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVL   51 (258)
T ss_pred             cCCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHH
Confidence            3667889999999888776442                                        345789999999999999


Q ss_pred             HHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC--------------------------------------
Q 011992          343 HVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT--------------------------------------  384 (473)
Q Consensus       343 sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~--------------------------------------  384 (473)
                      ++|++|.+++.+++|++|||++|+|+++++||+.+|.+|.|.                                      
T Consensus        52 ~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~~vrip~~~~~~~~~~~~~~~~  131 (258)
T PRK08215         52 SVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVREK  131 (258)
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCCceEecHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999998889880                                      


Q ss_pred             ------------------------------------CCCCc------------------hHHHHHHHHHHHHHHHHhhCC
Q 011992          385 ------------------------------------GVEIP------------------DISVQKQLMRQHVRNLLTLLN  410 (473)
Q Consensus       385 ------------------------------------~~~~p------------------ee~le~~el~e~L~~aL~~Lp  410 (473)
                                                          ....|                  +...+.......|..+|+.||
T Consensus       132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~  211 (258)
T PRK08215        132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKNKDENWLEEIALKEAMKKLN  211 (258)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccccHHHHHhHHHHHHHHHcCC
Confidence                                                00000                  000112223446888999999


Q ss_pred             HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ++++.||.++|+    +++|++|||+.||+|.++|++++++|+++||+.|
T Consensus       212 ~~er~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l  257 (258)
T PRK08215        212 DREKLILNLRFF----QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI  257 (258)
T ss_pred             HHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            999999999998    8999999999999999999999999999999876

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=99.86  E-value=1.1e-20  Score=186.18  Aligned_cols=153  Identities=32%  Similarity=0.509  Sum_probs=127.5

Q ss_pred             cCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHH
Q 011992          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (473)
Q Consensus       264 pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~s  343 (473)
                      ..+.|+||++||.+|+.+++.                                        ++..+++.||..|+++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence            356789999999888766442                                        2447899999999999999


Q ss_pred             HHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------------------------
Q 011992          344 VAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------------------------  383 (473)
Q Consensus       344 IA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------------------------  383 (473)
                      +|++|.+++.+++||+|||++|||+++++|++.+|.+|.|                                        
T Consensus        50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~~ir~p~~~~~~~~~~~~~~~~l  129 (254)
T TIGR02850        50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRDKL  129 (254)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCCCccCchHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999989988                                        


Q ss_pred             ----------------------------------CCCCCc----------------h--HHHHHHHHHHHHHHHHhhCCH
Q 011992          384 ----------------------------------TGVEIP----------------D--ISVQKQLMRQHVRNLLTLLNP  411 (473)
Q Consensus       384 ----------------------------------~~~~~p----------------e--e~le~~el~e~L~~aL~~Lpe  411 (473)
                                                        .+...+                +  ...........|..+|..||+
T Consensus       130 ~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~l~~~l~~L~~  209 (254)
T TIGR02850       130 ISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKNKDSQWLEGIALKEAMKRLNE  209 (254)
T ss_pred             HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccccHHHHHhHHHHHHHHHcCCH
Confidence                                              000000                0  000122234568899999999


Q ss_pred             HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ++|.||.++|+    +++|++|||+.||+|.++|++++++|++|||..+
T Consensus       210 rer~vi~~~~~----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~  254 (254)
T TIGR02850       210 REKMILNMRFF----EGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV  254 (254)
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence            99999999998    8999999999999999999999999999999854

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.

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=99.85  E-value=3e-20  Score=182.81  Aligned_cols=131  Identities=24%  Similarity=0.410  Sum_probs=114.6

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC---------------CC----
Q 011992          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT---------------GV----  386 (473)
Q Consensus       326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~---------------~~----  386 (473)
                      +..|++.||..|.++|+++|++|.+++.+++|++||||+++|+++++|++..|..|.++               ..    
T Consensus        27 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~ir  106 (255)
T TIGR02941        27 NGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVH  106 (255)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcC
Confidence            34799999999999999999999999999999999999999999999999888888660               00    


Q ss_pred             -----------------------------------------------------------------------------CCc
Q 011992          387 -----------------------------------------------------------------------------EIP  389 (473)
Q Consensus       387 -----------------------------------------------------------------------------~~p  389 (473)
                                                                                                   ..|
T Consensus       107 i~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~  186 (255)
T TIGR02941       107 VPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARLDSVGEV  186 (255)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccccccCCc
Confidence                                                                                         012


Q ss_pred             hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          390 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       390 ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ++.+...+....+..+|+.||+++|.||.++|+    +++|++|||+.||+|.++|++++++|+++||..+
T Consensus       187 ~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~~----~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~  253 (255)
T TIGR02941       187 EDGYDQTERRMVLEKILPILSEREKSIIHCTFE----ENLSQKETGERLGISQMHVSRLQRQAISKLKEAA  253 (255)
T ss_pred             chHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            333444556667899999999999999999998    9999999999999999999999999999999875

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

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=99.85  E-value=1.8e-20  Score=185.25  Aligned_cols=133  Identities=26%  Similarity=0.381  Sum_probs=114.7

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcC-CcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGR-GISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------  383 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~-~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------  383 (473)
                      ..|+++||..|+++|+++|++|.+. +.+++||+|+|++|||+++++|||.+|++|+|                      
T Consensus        24 ~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr  103 (256)
T PRK07408         24 IALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVR  103 (256)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeee
Confidence            3899999999999999999999775 66799999999999999999999999999999                      


Q ss_pred             ----------------------------------------------------------CC------C---------CCch
Q 011992          384 ----------------------------------------------------------TG------V---------EIPD  390 (473)
Q Consensus       384 ----------------------------------------------------------~~------~---------~~pe  390 (473)
                                                                                +.      .         ..++
T Consensus       104 ~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d~~  183 (256)
T PRK07408        104 IPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPDPR  183 (256)
T ss_pred             eCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCCcc
Confidence                                                                      00      0         0111


Q ss_pred             H--HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992          391 I--SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       391 e--~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~  463 (473)
                      .  .....+....|..+|..||+++|.||.++|+    +++|++|||+.||+|.++|++++++|+++||..+..+
T Consensus       184 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~  254 (256)
T PRK07408        184 YRSFQLAQEDRIRLQQALAQLEERTREVLEFVFL----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE  254 (256)
T ss_pred             cchhhhhHHHHHHHHHHHHcCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence            1  1123345667999999999999999999999    9999999999999999999999999999999998765

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=99.85  E-value=3.9e-20  Score=182.15  Aligned_cols=133  Identities=23%  Similarity=0.366  Sum_probs=114.6

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC---------------CC----
Q 011992          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT---------------GV----  386 (473)
Q Consensus       326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~---------------~~----  386 (473)
                      +..|++.||..|.++|+++|++|.++..+++|++||||+++|+++++|++..|..|.|+               ..    
T Consensus        27 d~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~  106 (257)
T PRK08583         27 DEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVH  106 (257)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcC
Confidence            44899999999999999999999999999999999999999999999999877777540               00    


Q ss_pred             -----------------------------------------------------------------------------CCc
Q 011992          387 -----------------------------------------------------------------------------EIP  389 (473)
Q Consensus       387 -----------------------------------------------------------------------------~~p  389 (473)
                                                                                                   ..|
T Consensus       107 i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~  186 (257)
T PRK08583        107 VPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIVGQQ  186 (257)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhhhcCCc
Confidence                                                                                         011


Q ss_pred             hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          390 DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       390 ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      +..+...+....+..+|..||+++|.||.++|+    +|+|++|||+.||||+++|++++++|+++||..+..
T Consensus       187 e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~  255 (257)
T PRK08583        187 EDGYELTEQRMILEKILPVLSDREKSIIQCTFI----ENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL  255 (257)
T ss_pred             chhHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence            222333455667889999999999999999999    999999999999999999999999999999998864

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=99.84  E-value=5.5e-20  Score=182.62  Aligned_cols=158  Identities=23%  Similarity=0.396  Sum_probs=133.0

Q ss_pred             ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHH
Q 011992          263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV  342 (473)
Q Consensus       263 ~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~  342 (473)
                      ..+..|+||.++|.+|+.+++.                                       .++..+++.|+..|.++|+
T Consensus         5 ~~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~   45 (268)
T PRK06288          5 MSGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVK   45 (268)
T ss_pred             ccCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHH
Confidence            3567899999999998887543                                       1344789999999999999


Q ss_pred             HHHHHhh-c--CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------CC-------------------
Q 011992          343 HVAKQYQ-G--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------TG-------------------  385 (473)
Q Consensus       343 sIA~ry~-~--~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------~~-------------------  385 (473)
                      .+|+++. +  .+.+++|++|||++|||+++++||+.+|.+|.|               ..                   
T Consensus        46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~~~p~~~~~~~~~i~~~~~  125 (268)
T PRK06288         46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRSVRQKARQIERAIA  125 (268)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCccCHHHHHHHHHHHHHHH
Confidence            9999986 3  467899999999999999999999988888888               00                   


Q ss_pred             ----------------------------------------------------------------CCCchHHHHHHHHHHH
Q 011992          386 ----------------------------------------------------------------VEIPDISVQKQLMRQH  401 (473)
Q Consensus       386 ----------------------------------------------------------------~~~pee~le~~el~e~  401 (473)
                                                                                      ...|+..+...+....
T Consensus       126 ~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~~~  205 (268)
T PRK06288        126 MLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRV  205 (268)
T ss_pred             HHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHHHH
Confidence                                                                            0112333445566678


Q ss_pred             HHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992          402 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       402 L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~  463 (473)
                      |..+|..||+++|.||.++|+    +++|++|||+.||+|.++|++++.+|+++||..+...
T Consensus       206 l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~  263 (268)
T PRK06288        206 IVEAIKTLPEREKKVLILYYY----EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEI  263 (268)
T ss_pred             HHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999    9999999999999999999999999999999998643

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.84  E-value=7.7e-20  Score=170.75  Aligned_cols=147  Identities=18%  Similarity=0.274  Sum_probs=126.0

Q ss_pred             CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------  383 (473)
Q Consensus       314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------  383 (473)
                      ++.+.|...+..|+ .+++.||..|.++|+++|+++.++..+++|++||+|+++|+++.+|++. +..|.+         
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            55666766666666 9999999999999999999999999999999999999999999999875 345666         


Q ss_pred             --------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHH
Q 011992          384 --------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE  443 (473)
Q Consensus       384 --------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~  443 (473)
                                          .....++..+...+....+..+|..||+++|.||.|+|+    +|+|++|||+.||+|.+
T Consensus        84 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~  159 (186)
T PRK05602         84 CYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYY----QGLSNIEAAAVMDISVD  159 (186)
T ss_pred             HHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHh----cCCCHHHHHHHhCcCHH
Confidence                                011234445555566778999999999999999999999    99999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhccCch
Q 011992          444 RVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       444 rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      +|+++++||+++||+.+...+.
T Consensus       160 tV~~~l~Rar~~Lr~~l~~~~~  181 (186)
T PRK05602        160 ALESLLARGRRALRAQLADLPG  181 (186)
T ss_pred             HHHHHHHHHHHHHHHHHHhccc
Confidence            9999999999999999987654

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.84  E-value=1.4e-19  Score=175.50  Aligned_cols=136  Identities=33%  Similarity=0.625  Sum_probs=114.8

Q ss_pred             hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------C-
Q 011992          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------T-  384 (473)
Q Consensus       325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~-  384 (473)
                      ++..+++.||..|.+.|+++|.++.++..+++|++||+|+++|+++++|+++.+..|.+                   . 
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            34489999999999999999999999999999999999999999999999887777766                   0 


Q ss_pred             -C-----C--------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992          385 -G-----V--------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF  438 (473)
Q Consensus       385 -~-----~--------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L  438 (473)
                       .     .                    ..++..+...+..+.|.++|+.||+++|+||.++|+++..+++|++|||++|
T Consensus       125 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~l  204 (227)
T TIGR02846       125 GEVSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKIL  204 (227)
T ss_pred             cceeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHH
Confidence             0     0                    0112223344455679999999999999999999965444899999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHh
Q 011992          439 GLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       439 GIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      |+|.++|++++++|+++||+.|
T Consensus       205 gis~~tV~~~~~rAl~~Lr~~~  226 (227)
T TIGR02846       205 GISRSYVSRIEKRALMKLYKEL  226 (227)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999875

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.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=99.82  E-value=2.7e-19  Score=175.93  Aligned_cols=143  Identities=24%  Similarity=0.424  Sum_probs=120.4

Q ss_pred             CHHHHHHH-Hhhcc-hHHHHHHHHHHHHHHHHHHHhhc---CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------
Q 011992          315 SCRDLKSE-LHSGN-SSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------  383 (473)
Q Consensus       315 s~eeL~~~-l~~g~-~A~e~Li~~yl~lV~sIA~ry~~---~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------  383 (473)
                      ++..|... ..+|+ .|++.||..|.++|+++|++|.+   +..+++|++|||++|||+++++|++.+|.+|.|      
T Consensus         7 ~e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~i   86 (251)
T PRK07670          7 EEQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRI   86 (251)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHH
Confidence            34455555 34444 89999999999999999999965   688999999999999999999999999889988      


Q ss_pred             ---------CCC--------------------------------------------------------------------
Q 011992          384 ---------TGV--------------------------------------------------------------------  386 (473)
Q Consensus       384 ---------~~~--------------------------------------------------------------------  386 (473)
                               ...                                                                    
T Consensus        87 rn~~~d~lR~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~  166 (251)
T PRK07670         87 RGAIIDGLRKEDWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDD  166 (251)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCC
Confidence                     000                                                                    


Q ss_pred             -------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          387 -------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       387 -------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                                   ..++..+...+....|..+|..||+++|.||.++|+    +++|++|||++||+|.++|++++++|+
T Consensus       167 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~lgis~~tV~~~~~ra~  242 (251)
T PRK07670        167 GENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSKAL  242 (251)
T ss_pred             cchhhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence                         012233344555667899999999999999999999    999999999999999999999999999


Q ss_pred             HHHHHHhc
Q 011992          454 YRLKQSLG  461 (473)
Q Consensus       454 ~KLR~~L~  461 (473)
                      ++||..+.
T Consensus       243 ~~Lr~~l~  250 (251)
T PRK07670        243 FKLKKLLE  250 (251)
T ss_pred             HHHHHHhh
Confidence            99999875

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.82  E-value=3.6e-19  Score=167.89  Aligned_cols=143  Identities=20%  Similarity=0.238  Sum_probs=118.6

Q ss_pred             HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------  383 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------  383 (473)
                      .+++...+..|+ .+++.||..|.+.|+++|.++.++..+++|++||+|+++|+++++|++..+..+.+           
T Consensus        17 ~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~~~~~wl~~ia~n~~~d   96 (194)
T PRK09646         17 LDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHRRAVD   96 (194)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccccHHHHHHHHHHHHHHH
Confidence            344555555555 99999999999999999999999999999999999999999999998765422222           


Q ss_pred             -----------C----------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992          384 -----------T----------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK  442 (473)
Q Consensus       384 -----------~----------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~  442 (473)
                                 .          ....+++.+...+..+.|..+|..||+++|.||.|+|+    ++++++|||+.||+|.
T Consensus        97 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~EIA~~Lgis~  172 (194)
T PRK09646         97 RVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYY----GGLTYREVAERLAVPL  172 (194)
T ss_pred             HHHhhccccccccccccccccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCh
Confidence                       0          00122333444556678999999999999999999999    9999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhcc
Q 011992          443 ERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       443 ~rVrqi~~RAL~KLR~~L~~  462 (473)
                      ++|+++++||+++||+.+..
T Consensus       173 ~tVk~~l~ra~~~Lr~~l~~  192 (194)
T PRK09646        173 GTVKTRMRDGLIRLRDCLGV  192 (194)
T ss_pred             HhHHHHHHHHHHHHHHHhcc
Confidence            99999999999999998854

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.81  E-value=6e-19  Score=171.20  Aligned_cols=147  Identities=31%  Similarity=0.593  Sum_probs=119.6

Q ss_pred             HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------  383 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------  383 (473)
                      ...+...+..|+ .+++.++..|.+.|+++|+++.+++.+++|++||+|+++|+++++|++..+++|.+           
T Consensus        39 ~~~L~~~~~~gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~  118 (234)
T PRK08301         39 EEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEIL  118 (234)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH
Confidence            445555555555 99999999999999999999999999999999999999999999999877667766           


Q ss_pred             --------C----CCCC------------------c-----hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCC
Q 011992          384 --------T----GVEI------------------P-----DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKP  428 (473)
Q Consensus       384 --------~----~~~~------------------p-----ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~  428 (473)
                              .    ....                  +     ...+........|..+|+.||+++|.||.|+|++...+|
T Consensus       119 d~lRk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg  198 (234)
T PRK08301        119 MYLRRNNKVKAEVSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEE  198 (234)
T ss_pred             HHHHHHhccccccccccccccccCCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCC
Confidence                    0    0000                  0     011223334567999999999999999999994333389


Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          429 KSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       429 lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      +|++|||+.||||+++|+++++||+++||+.+..
T Consensus       199 ~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~  232 (234)
T PRK08301        199 KTQKEVADMLGISQSYISRLEKRIIKRLKKEINK  232 (234)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999998753

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.81  E-value=1e-18  Score=170.21  Aligned_cols=147  Identities=34%  Similarity=0.613  Sum_probs=120.9

Q ss_pred             HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------  383 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------  383 (473)
                      ++.+...+..|+ .+++.|+..|.+.|+++|++|.+++.+++|++||+|+++|+++++|++..++.|.+           
T Consensus        39 ~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~  118 (234)
T TIGR02835        39 EEALLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEIL  118 (234)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence            344555555555 99999999999999999999999999999999999999999999999877667766           


Q ss_pred             ---------C-C--CCC------------------ch-----HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCC
Q 011992          384 ---------T-G--VEI------------------PD-----ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKP  428 (473)
Q Consensus       384 ---------~-~--~~~------------------pe-----e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~  428 (473)
                               . .  ...                  ++     ..+........|..+|+.||+++|.|+.|+|++.++++
T Consensus       119 d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg  198 (234)
T TIGR02835       119 MYLRRNNKTRSEVSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTE  198 (234)
T ss_pred             HHHHHhccccCcccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCC
Confidence                     0 0  000                  00     11233345567999999999999999999996554589


Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          429 KSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       429 lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      +|++|||+.||+|+++|++++++|+++||+.+..
T Consensus       199 ~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~  232 (234)
T TIGR02835       199 KTQKEVADMLGISQSYISRLEKRILKRLKKEINR  232 (234)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999999999999998764

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.

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.81  E-value=1.1e-18  Score=163.37  Aligned_cols=139  Identities=25%  Similarity=0.347  Sum_probs=117.0

Q ss_pred             HHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcC----CcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR----GISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------  383 (473)
Q Consensus       318 eL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~----~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------  383 (473)
                      .+...+..|+ .+++.|+..|.+.|+++|.++.++    ..+++|++||+|+++|+++.+|+.. +..|.+         
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            3555555555 999999999999999999998765    3689999999999999999999753 345655         


Q ss_pred             -----------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992          384 -----------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL  440 (473)
Q Consensus       384 -----------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI  440 (473)
                                             .....|+..+...+..+.|..+|..||+++|+||.++|+    +|+|++|||+.||+
T Consensus        92 ~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgi  167 (189)
T PRK09648         92 VADAHRAAGRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLPEKQREILILRVV----VGLSAEETAEAVGS  167 (189)
T ss_pred             HHHHHHHhCCCccccccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCC
Confidence                                   011234555556667778999999999999999999999    99999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhc
Q 011992          441 SKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       441 S~~rVrqi~~RAL~KLR~~L~  461 (473)
                      |.++|++.++||+++||+.+.
T Consensus       168 s~~tV~~~l~Ra~~~Lr~~l~  188 (189)
T PRK09648        168 TPGAVRVAQHRALARLRAEIE  188 (189)
T ss_pred             CHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999874

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=99.80  E-value=7.8e-19  Score=170.92  Aligned_cols=134  Identities=25%  Similarity=0.494  Sum_probs=117.5

Q ss_pred             hcchHHHHHHHHHHHHHHHHHHHhh---cCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------CCC
Q 011992          325 SGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------TGV  386 (473)
Q Consensus       325 ~g~~A~e~Li~~yl~lV~sIA~ry~---~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------~~~  386 (473)
                      .|.-++++||..|.++|+++|++|.   ++..+++|++||||+|+|+++++|++..|.+|.|               ...
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            3556889999999999999999997   6789999999999999999999999988888988               000


Q ss_pred             ------------------------------------------------------------------------------CC
Q 011992          387 ------------------------------------------------------------------------------EI  388 (473)
Q Consensus       387 ------------------------------------------------------------------------------~~  388 (473)
                                                                                                    ..
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~  164 (236)
T PRK06986         85 WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQDED  164 (236)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccccccCCCCCC
Confidence                                                                                          12


Q ss_pred             chHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       389 pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      |+..+...+....|..+|..||+++|.||.++|+    +++|++|||+.||||.++|++++++|+++||+.+..
T Consensus       165 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  234 (236)
T PRK06986        165 PLQQLEDEELREALVEAIESLPEREQLVLSLYYQ----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE  234 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            2344455566778999999999999999999999    999999999999999999999999999999998864

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=7e-19  Score=165.35  Aligned_cols=145  Identities=19%  Similarity=0.268  Sum_probs=122.6

Q ss_pred             CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------  383 (473)
Q Consensus       315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------  383 (473)
                      +.+.+...+..|+ .+++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++++|++..  .|.+          
T Consensus        12 ~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~~   89 (194)
T PRK12513         12 SDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNLL   89 (194)
T ss_pred             CHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHHH
Confidence            4555666666565 99999999999999999999999999999999999999999999998643  4554          


Q ss_pred             -------------C------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992          384 -------------T------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF  438 (473)
Q Consensus       384 -------------~------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L  438 (473)
                                   .            ....|+..++..+....+..+|+.||+++|.||.|+|+    +|+|++|||+.|
T Consensus        90 ~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~l  165 (194)
T PRK12513         90 IDHWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREH----GDLELEEIAELT  165 (194)
T ss_pred             HHHHHHhccccccccccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehc----cCCCHHHHHHHH
Confidence                         0            01123344455667788999999999999999999998    999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992          439 GLSKERVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       439 GIS~~rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      |+|.++|+++++||+++||+.+...+.
T Consensus       166 gis~~tV~~~l~ra~~~Lr~~l~~~~~  192 (194)
T PRK12513        166 GVPEETVKSRLRYALQKLRELLAEEVA  192 (194)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999876543

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

Probab=99.80  E-value=1.3e-18  Score=158.81  Aligned_cols=132  Identities=21%  Similarity=0.357  Sum_probs=114.7

Q ss_pred             hhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------
Q 011992          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------  383 (473)
Q Consensus       324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------  383 (473)
                      .++..+++.|+..|.+.+++++.++.++..+++|++||+|+++|+++++|+...+ .|.+                    
T Consensus         7 ~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~   85 (170)
T TIGR02952         7 DREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRH   85 (170)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCC
Confidence            3455999999999999999999999999999999999999999999999986433 5655                    


Q ss_pred             ------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          384 ------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       384 ------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                                  .....|++.+...+..+.+..+|..||+++|.||.++|+    +|+|++|||+.||+|+++|++.++|
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~l~is~~tv~~~l~r  161 (170)
T TIGR02952        86 PLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFG----QNLPIAEVARILGKTEGAVKILQFR  161 (170)
T ss_pred             CCCcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence                        011244555566667788999999999999999999999    9999999999999999999999999


Q ss_pred             HHHHHHHHh
Q 011992          452 ALYRLKQSL  460 (473)
Q Consensus       452 AL~KLR~~L  460 (473)
                      |+++||+.|
T Consensus       162 a~~~Lr~~l  170 (170)
T TIGR02952       162 AIKKLARQM  170 (170)
T ss_pred             HHHHHHHhC
Confidence            999999864

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.

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

Probab=99.80  E-value=1e-18  Score=168.68  Aligned_cols=130  Identities=35%  Similarity=0.565  Sum_probs=114.2

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC---------------C-----
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG---------------V-----  386 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~---------------~-----  386 (473)
                      ..|++.|+..|.++|+++|++|.+++.+++||+|||++|+|+++++|++.+|.+|.|+.               .     
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            36899999999999999999999999999999999999999999999999888888800               0     


Q ss_pred             ---------------------------------------------------------------------------CCchH
Q 011992          387 ---------------------------------------------------------------------------EIPDI  391 (473)
Q Consensus       387 ---------------------------------------------------------------------------~~pee  391 (473)
                                                                                                 ..++.
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~~~~  161 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDEDD  161 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCCcch
Confidence                                                                                       01123


Q ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       392 ~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      .++..+....|..+|..||++++.||.++|+    +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus       162 ~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l  226 (227)
T TIGR02980       162 ALETVEDRLALKPLLAALPERERRILLLRFF----EDKTQSEIAERLGISQMHVSRLLRRALKKLREQL  226 (227)
T ss_pred             HHHhHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            3344456678999999999999999999998    9999999999999999999999999999999865

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.

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=1.3e-18  Score=161.32  Aligned_cols=142  Identities=15%  Similarity=0.149  Sum_probs=118.6

Q ss_pred             CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------  383 (473)
Q Consensus       315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------  383 (473)
                      +...+...+..|+ .++..|+..|.+.|+++|.++.++..+++|++||+|+++|+++++|++..+ .|.+          
T Consensus         5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~   83 (179)
T PRK12514          5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHA   83 (179)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHH
Confidence            3445555555555 899999999999999999999999999999999999999999999985432 3433          


Q ss_pred             ---------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992          384 ---------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK  442 (473)
Q Consensus       384 ---------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~  442 (473)
                                           .....|+..+...+....|..+|..||++++.||.++|+    +|+|++|||+.||+|+
T Consensus        84 ~d~~R~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~  159 (179)
T PRK12514         84 IDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL----EGLSYKELAERHDVPL  159 (179)
T ss_pred             HHHHHhcCCcccccccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCh
Confidence                                 001234445555555567899999999999999999999    9999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhc
Q 011992          443 ERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       443 ~rVrqi~~RAL~KLR~~L~  461 (473)
                      ++|++.++||+++||+++.
T Consensus       160 ~tV~~~l~Rar~~Lr~~l~  178 (179)
T PRK12514        160 NTMRTWLRRSLLKLRECLS  178 (179)
T ss_pred             HHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999875

>PRK05572 sporulation sigma factor SigF; Validated

Probab=99.80  E-value=1.8e-18  Score=170.18  Aligned_cols=132  Identities=33%  Similarity=0.535  Sum_probs=111.7

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCC-----------------C-
Q 011992          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGV-----------------E-  387 (473)
Q Consensus       326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~-----------------~-  387 (473)
                      +..+++.||..|.++|+++|++|.++..+++|++|||++++|+++++|++..+.+|.|...                 . 
T Consensus        30 d~~a~~~L~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~~~r~  109 (252)
T PRK05572         30 DQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKV  109 (252)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCCCCCC
Confidence            4489999999999999999999999999999999999999999999999987778877000                 0 


Q ss_pred             ------------------------Cch------------------------------------------------HHHHH
Q 011992          388 ------------------------IPD------------------------------------------------ISVQK  395 (473)
Q Consensus       388 ------------------------~pe------------------------------------------------e~le~  395 (473)
                                              .|.                                                .....
T Consensus       110 ~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~~~  189 (252)
T PRK05572        110 SRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSEED  189 (252)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCchhh
Confidence                                    000                                                00011


Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          396 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       396 ~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      ......|..+|+.||++++.||.++|+    +++|++|||+.+|+|.++|++++++|+++||..+.
T Consensus       190 ~~~~~~l~~~l~~L~~~~~~v~~l~~~----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~  251 (252)
T PRK05572        190 WFDKIALKEAIRELDERERLIVYLRYF----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD  251 (252)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            123456889999999999999999998    99999999999999999999999999999998875

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=99.80  E-value=3.5e-19  Score=173.85  Aligned_cols=169  Identities=20%  Similarity=0.338  Sum_probs=130.0

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP  303 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP  303 (473)
                      +..+..+ .|++|+.+||+     |+|+|   .+|+.+|.|++.              .....+++++...|.+++|++|
T Consensus        62 ~fd~~~~-~F~tYa~~~Ir-----~~il~---~lr~~~~~~r~v--------------r~~~~~i~~~~~~l~~~~g~~p  118 (231)
T PRK12427         62 RYGHPDE-QFAAYAVHRIR-----GAILD---ELRELDWRPRRL--------------RQKTHKTNDAIREIAKRLGHEP  118 (231)
T ss_pred             hcCCCCC-ChHHHHHHHHH-----HHHHH---HHHhcCCCCHHH--------------HHHHHHHHHHHHHHHHHHCCCC
Confidence            4444344 79999999999     99998   599999998877              3556788899999999999999


Q ss_pred             CHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992          304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN  383 (473)
Q Consensus       304 T~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT  383 (473)
                      |.+|+|+.||++.+++...+....                     .....++++.+.+.-.+     +         +  
T Consensus       119 t~~eiA~~lg~~~~~v~~~~~~~~---------------------~~~~~SLd~~~~~~~~~-----~---------~--  161 (231)
T PRK12427        119 NFEEISAELNLTAEEYQEYLLLEN---------------------AGTLESLDELLALEAHN-----D---------I--  161 (231)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHhc---------------------cCCceeccCcccCCCcc-----c---------c--
Confidence            999999999999999876554211                     11235555554221100     0         0  


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          384 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       384 ~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      .....+++   .......|..+|..||+++|.||.++|+    +++|++|||+.||||.++|+|++++|+++||..
T Consensus       162 ~~~~~~~~---~~~~~~~l~~~l~~L~~~er~vi~l~~~----~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~  230 (231)
T PRK12427        162 LQSRDLEE---NIIIEDNLKQALSQLDEREQLILHLYYQ----HEMSLKEIALVLDLTEARICQLNKKIAQKIKSF  230 (231)
T ss_pred             cCCCCHHH---HHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            00112222   2235667999999999999999999998    999999999999999999999999999999964

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=99.80  E-value=1.2e-18  Score=168.84  Aligned_cols=133  Identities=32%  Similarity=0.544  Sum_probs=112.4

Q ss_pred             hhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------CC-
Q 011992          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------TG-  385 (473)
Q Consensus       324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------~~-  385 (473)
                      .++..+++.||..|.++|+++|++|.+++.+++|++|||++|+|+++++|++..|.+|.|                 .. 
T Consensus         7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~~i   86 (231)
T TIGR02885         7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDGII   86 (231)
T ss_pred             cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCCCe
Confidence            344589999999999999999999999999999999999999999999999988888988                 00 


Q ss_pred             ------------------------CCCc--hH------------------------------------------------
Q 011992          386 ------------------------VEIP--DI------------------------------------------------  391 (473)
Q Consensus       386 ------------------------~~~p--ee------------------------------------------------  391 (473)
                                              ...|  ++                                                
T Consensus        87 ~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~  166 (231)
T TIGR02885        87 KVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKGS  166 (231)
T ss_pred             ECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCCc
Confidence                                    0001  00                                                


Q ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       392 ~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ..........+.++|+.||++++.||.++|+    +++|++|||+.||+|+++|++++++|+++||..|
T Consensus       167 ~~~~~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l  231 (231)
T TIGR02885       167 EDSDWLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL  231 (231)
T ss_pred             cHHhHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence            0011123456888999999999999999998    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.

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=1.5e-18  Score=169.56  Aligned_cols=146  Identities=14%  Similarity=0.212  Sum_probs=122.2

Q ss_pred             CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------  383 (473)
Q Consensus       314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------  383 (473)
                      .+.++|...+..|+ .+++.||..|.+.|+++++++.++..+++|++||+|+++|+++++|++..+ .|.+         
T Consensus        48 ~~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~  126 (233)
T PRK12538         48 DEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNR  126 (233)
T ss_pred             ccHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHH
Confidence            34556666666665 899999999999999999999999999999999999999999999975332 4544         


Q ss_pred             -----------C---------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHH
Q 011992          384 -----------T---------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE  443 (473)
Q Consensus       384 -----------~---------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~  443 (473)
                                 .         ....++..+...+....|..+|..||+++|+||.|+|+    +|+|++|||+.||+|.+
T Consensus       127 ~id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~----eg~s~~EIA~~Lgis~~  202 (233)
T PRK12538        127 CIDLRRKPRTENVDAVPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYH----ENMSNGEIAEVMDTTVA  202 (233)
T ss_pred             HHHHHHhhcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----cCCCHHHHHHHHCcCHH
Confidence                       0         01123344555666678999999999999999999999    99999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhccCc
Q 011992          444 RVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       444 rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      +|+++++||+++||+.+...+
T Consensus       203 tVk~~l~RAr~kLr~~l~~~~  223 (233)
T PRK12538        203 AVESLLKRGRQQLRDLLRRHE  223 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999997554

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=1.9e-18  Score=163.25  Aligned_cols=146  Identities=18%  Similarity=0.195  Sum_probs=122.7

Q ss_pred             CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------  383 (473)
Q Consensus       314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------  383 (473)
                      ++...++..+..|+ .+++.||..|.+.|+++|.++.++..+++|++||+++++|+++.+|++.. ..|.+         
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            45566666666665 99999999999999999999999999999999999999999999997422 23444         


Q ss_pred             ---------------C-------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCC
Q 011992          384 ---------------T-------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS  441 (473)
Q Consensus       384 ---------------~-------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS  441 (473)
                                     .       ....+++.+...+....|..+|+.||+++|.||.|+|+    ++++++|||+.||||
T Consensus        90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~eIA~~lgis  165 (196)
T PRK12524         90 CTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHI----EGLSNPEIAEVMEIG  165 (196)
T ss_pred             HHHHHHhhcCCCCCccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcC
Confidence                           0       01123344555666778999999999999999999999    999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhccCc
Q 011992          442 KERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       442 ~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      .++|+++++||+++||..+....
T Consensus       166 ~~tV~~~l~Ra~~~Lr~~l~~~~  188 (196)
T PRK12524        166 VEAVESLTARGKRALAALLAGQR  188 (196)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999999987543

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.79  E-value=2.2e-18  Score=160.04  Aligned_cols=143  Identities=17%  Similarity=0.296  Sum_probs=121.1

Q ss_pred             CCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------
Q 011992          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------  383 (473)
Q Consensus       313 Gms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------  383 (473)
                      .+..+.+...+..|+ .+++.++..|.+.|+++|+++.++..+++|++||+++++|+++++|++..  .|.+        
T Consensus         2 ~~~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn   79 (187)
T PRK09641          2 DLLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATN   79 (187)
T ss_pred             chHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHH
Confidence            344556666666666 99999999999999999999999999999999999999999999998743  4555        


Q ss_pred             ----------------C---C-------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCH
Q 011992          384 ----------------T---G-------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSL  431 (473)
Q Consensus       384 ----------------~---~-------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTl  431 (473)
                                      .   .             ...|+..+...+....+..+|+.||+++++||.++|+    +|+++
T Consensus        80 ~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~----~~~s~  155 (187)
T PRK09641         80 LTIDRLRKRKPDYYLDAEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYI----EDLSL  155 (187)
T ss_pred             HHHHHHHhcCccccccccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHh----hCCCH
Confidence                            0   0             0123344455666678999999999999999999998    99999


Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          432 SEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       432 kEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      +|||+.||||.++|++.++||+++||+.+.
T Consensus       156 ~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~  185 (187)
T PRK09641        156 KEISEILDLPVGTVKTRIHRGREALRKQLR  185 (187)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999999875

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.79  E-value=2.4e-18  Score=161.66  Aligned_cols=145  Identities=16%  Similarity=0.254  Sum_probs=122.4

Q ss_pred             CCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcC---CcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----
Q 011992          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----  383 (473)
Q Consensus       313 Gms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~---~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----  383 (473)
                      .++++.|...+..|+ .+++.|+..|.+.|++++.++.++   ..+++|++||+++++|+++++|++..+ .|.+     
T Consensus         2 ~~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~i   80 (189)
T PRK06811          2 KINEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAI   80 (189)
T ss_pred             CCcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHH
Confidence            466777777777777 899999999999999999999875   357999999999999999999986433 4655     


Q ss_pred             --------------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHH
Q 011992          384 --------------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI  437 (473)
Q Consensus       384 --------------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~  437 (473)
                                                .....+++.+...+....|..+|..||+++|.||.|+|+    +|+|++|||+.
T Consensus        81 arn~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~  156 (189)
T PRK06811         81 SKYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYL----LGEKIEEIAKK  156 (189)
T ss_pred             HHHHHHHHHHHhccccccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHH
Confidence                                      011244455566667778999999999999999999998    99999999999


Q ss_pred             HCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          438 FGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       438 LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      ||+|.++|++.++||+++||...-.
T Consensus       157 lgis~~~V~~~l~Ra~~~Lr~~~~~  181 (189)
T PRK06811        157 LGLTRSAIDNRLSRGRKKLQKNKLN  181 (189)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHcccC
Confidence            9999999999999999999986543

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.79  E-value=2.2e-18  Score=159.93  Aligned_cols=140  Identities=19%  Similarity=0.293  Sum_probs=117.7

Q ss_pred             HHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------
Q 011992          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------  383 (473)
Q Consensus       317 eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------  383 (473)
                      +++...+..|+ .++..|+..|.+.|+++|.++.++..+++|++||+|+++|+++..|++..  .|.+            
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            34555555555 99999999999999999999999999999999999999999999998754  4655            


Q ss_pred             -----------CC-----------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHH
Q 011992          384 -----------TG-----------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVG  435 (473)
Q Consensus       384 -----------~~-----------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIA  435 (473)
                                 ..                 ...++..+...+....+.++|..||+++|.||.++|+    +|+|++|||
T Consensus        84 ~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA  159 (187)
T TIGR02948        84 RLRKRKPDFYLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYM----EDLSLKEIS  159 (187)
T ss_pred             HHHhhcccccccccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHH
Confidence                       00                 0122334444555677999999999999999999998    999999999


Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          436 NIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       436 e~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      +.||+|.++|++.++||+++||..+..
T Consensus       160 ~~lgis~~~v~~~l~Rar~~Lr~~l~~  186 (187)
T TIGR02948       160 EILDLPVGTVKTRIHRGREALRKQLRH  186 (187)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999998763

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

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.79  E-value=3.1e-18  Score=159.32  Aligned_cols=141  Identities=18%  Similarity=0.215  Sum_probs=119.8

Q ss_pred             CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------  383 (473)
Q Consensus       315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------  383 (473)
                      +.+.+...+..|+ .+++.||..|.+.|+++|+++.++..+++|++||+|+++|+++++|++..  .|.+          
T Consensus         6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~~--~~~~wl~~iarn~~   83 (190)
T TIGR02939         6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGDS--AFYTWLYRIAVNTA   83 (190)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCCC--ccHhHHHHHHHHHH
Confidence            3455666666655 89999999999999999999999999999999999999999999998642  3544          


Q ss_pred             ----------C-----C---------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHH
Q 011992          384 ----------T-----G---------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSE  433 (473)
Q Consensus       384 ----------~-----~---------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkE  433 (473)
                                .     .               ...|+..+...+....|..+|..||+++|.||.++|+    ++++++|
T Consensus        84 ~~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~E  159 (190)
T TIGR02939        84 KNHLVAQGRRPPTSDVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLREL----EGLSYED  159 (190)
T ss_pred             HHHHHHhccCCCcccccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhh----cCCCHHH
Confidence                      0     0               0123444555666778999999999999999999999    9999999


Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          434 VGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       434 IAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      ||+.||+|.++|++.++||+++||+.+.
T Consensus       160 IA~~lgis~~tv~~~l~rar~~Lr~~l~  187 (190)
T TIGR02939       160 IARIMDCPVGTVRSRIFRAREAIAIRLR  187 (190)
T ss_pred             HHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999999999986

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.

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=2.6e-18  Score=160.34  Aligned_cols=141  Identities=13%  Similarity=0.142  Sum_probs=116.7

Q ss_pred             CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------  383 (473)
Q Consensus       315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------  383 (473)
                      +.+.+...+..|+ .+++.||..|.+.+++++.++.++..+++|++||+|+.+|+.+++|++.. ..|.+          
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            3345566665555 99999999999999999999999999999999999999999999997532 24544          


Q ss_pred             -------------C-C-------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992          384 -------------T-G-------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK  442 (473)
Q Consensus       384 -------------~-~-------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~  442 (473)
                                   . .       ...++...+..+....+.++|+.||+++|+||.++|+    +|++++|||+.||||.
T Consensus        88 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~eIA~~lgis~  163 (182)
T PRK12537         88 LNVLRDTRREVVLDDDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYV----DGCSHAEIAQRLGAPL  163 (182)
T ss_pred             HHHHHhccccCccccchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCh
Confidence                         0 0       0112233334445667999999999999999999999    9999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHh
Q 011992          443 ERVRQLESRALYRLKQSL  460 (473)
Q Consensus       443 ~rVrqi~~RAL~KLR~~L  460 (473)
                      ++|+..++||+++||.++
T Consensus       164 ~tV~~~l~ra~~~Lr~~l  181 (182)
T PRK12537        164 GTVKAWIKRSLKALRECM  181 (182)
T ss_pred             hhHHHHHHHHHHHHHHHh
Confidence            999999999999999986

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.79  E-value=4e-18  Score=161.29  Aligned_cols=149  Identities=20%  Similarity=0.271  Sum_probs=121.5

Q ss_pred             HcCCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------
Q 011992          311 AIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------  383 (473)
Q Consensus       311 ~lGms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------  383 (473)
                      ...++.+.+...+..|+ .+++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++.+|++.++.+|.|      
T Consensus         6 ~~~~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~   85 (208)
T PRK08295          6 YDELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCI   85 (208)
T ss_pred             ccCCChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHH
Confidence            44566667766666665 99999999999999999999999999999999999999999999999887667776      


Q ss_pred             -------------C-C--------C----------------------CCchHHHHHHHHHHHH-HHHHhhCCHHHHHHHH
Q 011992          384 -------------T-G--------V----------------------EIPDISVQKQLMRQHV-RNLLTLLNPKERCIVR  418 (473)
Q Consensus       384 -------------~-~--------~----------------------~~pee~le~~el~e~L-~~aL~~LperER~VL~  418 (473)
                                   . .        .                      ..|+..+...+....+ ..++..||+++|.||.
T Consensus        86 ~n~~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~  165 (208)
T PRK08295         86 TRQIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLE  165 (208)
T ss_pred             HHHHHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence                         0 0        0                      1222222223333444 4567999999999999


Q ss_pred             HHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992          419 LRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       419 LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      + |+    +++|++|||+.||+|.++|+..++||+++||+++....
T Consensus       166 l-~~----e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~  206 (208)
T PRK08295        166 L-YL----DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENRE  206 (208)
T ss_pred             H-HH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            9 77    89999999999999999999999999999999987653

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.79  E-value=2e-18  Score=155.67  Aligned_cols=127  Identities=20%  Similarity=0.282  Sum_probs=109.9

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------  383 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------  383 (473)
                      ..+|+.|+..|.++|+++++++ ++..++||++||+++++|+++++|++..+ .|.+                       
T Consensus         3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~~   80 (154)
T PRK06759          3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQEK   80 (154)
T ss_pred             cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhccc
Confidence            4689999999999999999886 56779999999999999999999987555 4655                       


Q ss_pred             -CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          384 -TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       384 -~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                       ...+.|++.+...+....|..+|..||+++|.||.++|+    +|+|++|||+.||+|.++|+++++||+++||+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~  153 (154)
T PRK06759         81 CVCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFF----VGKTMGEIALETEMTYYQVRWIYRQALEKMRNS  153 (154)
T ss_pred             ccccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence             112344555555666788999999999999999999999    999999999999999999999999999999974

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.79  E-value=3.4e-18  Score=159.26  Aligned_cols=143  Identities=22%  Similarity=0.308  Sum_probs=116.3

Q ss_pred             CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------  383 (473)
Q Consensus       315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------  383 (473)
                      +..++...+..|+ .+++.|+..|.+.|+++++++.++..+++|++||+|+++|+++++|++..+ .|.+          
T Consensus         9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~   87 (186)
T PRK13919          9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAA   87 (186)
T ss_pred             CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHH
Confidence            4455656555555 999999999999999999999999999999999999999999999986432 3433          


Q ss_pred             ----------C-C------C------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992          384 ----------T-G------V------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL  440 (473)
Q Consensus       384 ----------~-~------~------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI  440 (473)
                                . .      .      ..+............|.++|..||+++|.||.++|+    ++++++|||+.||+
T Consensus        88 ~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgi  163 (186)
T PRK13919         88 VDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYY----QGYTHREAAQLLGL  163 (186)
T ss_pred             HHHHHhhhcccccccccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCc
Confidence                      0 0      0      011112222334567999999999999999999999    99999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcc
Q 011992          441 SKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       441 S~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      |.++|+..++||+++||..+..
T Consensus       164 s~~~V~~~l~ra~~~Lr~~l~~  185 (186)
T PRK13919        164 PLGTLKTRARRALSRLKEVLRE  185 (186)
T ss_pred             CHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999999998864

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=1.5e-18  Score=162.09  Aligned_cols=141  Identities=19%  Similarity=0.223  Sum_probs=117.7

Q ss_pred             hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------
Q 011992          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------  383 (473)
Q Consensus       325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------  383 (473)
                      ++..+++.||..|.+.++++|.++.++..+++|++||+|+.+|+++++|+...+..|.+                     
T Consensus         6 gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~   85 (185)
T PRK12542          6 NDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHE   85 (185)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            44589999999999999999999999999999999999999999999997543345655                     


Q ss_pred             ---CCC---------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          384 ---TGV---------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       384 ---~~~---------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                         ...         ..++......+....|..+|..||+++|+||.|+|+    +|+|++|||+.||+|.++|+..+.|
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tVk~~l~R  161 (185)
T PRK12542         86 TFLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVF----YNLTYQEISSVMGITEANVRKQFER  161 (185)
T ss_pred             hhhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence               000         011111222334467999999999999999999999    9999999999999999999999999


Q ss_pred             HHHHHHHHhccCchhhhh
Q 011992          452 ALYRLKQSLGGKASYGYA  469 (473)
Q Consensus       452 AL~KLR~~L~~~~l~~yl  469 (473)
                      |+++||+.+.......|+
T Consensus       162 ar~~Lr~~l~~~~~~~~~  179 (185)
T PRK12542        162 ARKRVQNMIGGIQHDEFK  179 (185)
T ss_pred             HHHHHHHHHcccchHHHH
Confidence            999999999888777775

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=3.6e-18  Score=159.44  Aligned_cols=140  Identities=17%  Similarity=0.183  Sum_probs=116.3

Q ss_pred             HHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------
Q 011992          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------  383 (473)
Q Consensus       317 eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------  383 (473)
                      ..+...+..|+ .+++.|+..|.+.|+++|+++.++..+++|++||+|+++|+++++|++..+ .|.+            
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            33444444454 999999999999999999999999999999999999999999999987543 2323            


Q ss_pred             -------C--------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992          384 -------T--------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK  442 (473)
Q Consensus       384 -------~--------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~  442 (473)
                             .              ....++......+....|..+|..||++++.|+.++|+    +|++++|||+.||+|+
T Consensus        92 ~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~  167 (187)
T PRK12534         92 HLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFF----EGITYEELAARTDTPI  167 (187)
T ss_pred             HHHhcccccccccccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCh
Confidence                   0              00122333444566778999999999999999999999    9999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhc
Q 011992          443 ERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       443 ~rVrqi~~RAL~KLR~~L~  461 (473)
                      ++|+++++||+++||..+.
T Consensus       168 ~~v~~~l~Rar~~Lr~~l~  186 (187)
T PRK12534        168 GTVKSWIRRGLAKLKACLE  186 (187)
T ss_pred             hHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999875

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=4.7e-18  Score=159.28  Aligned_cols=146  Identities=21%  Similarity=0.304  Sum_probs=122.8

Q ss_pred             CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------  383 (473)
Q Consensus       314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------  383 (473)
                      ++.+++...+..|+ .+++.|+..|.+.++.++.++.++..+++|++||+|+.+|+++++|++.  ..|.+         
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            45556666666555 8999999999999999999999999999999999999999999999863  24544         


Q ss_pred             ----------------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCC
Q 011992          384 ----------------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS  441 (473)
Q Consensus       384 ----------------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS  441 (473)
                                            .....++..+...+....+..+|+.||+++|.||.++|+    ++++++|||+.||+|
T Consensus        85 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis  160 (189)
T PRK12515         85 ALSALRRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYY----HEKSVEEVGEIVGIP  160 (189)
T ss_pred             HHHHHHccCCCCCccccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcC
Confidence                                  001123444455566778999999999999999999999    999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhccCch
Q 011992          442 KERVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       442 ~~rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      .++|+.++.||+++||+.+...+.
T Consensus       161 ~~tV~~~l~Rar~~Lr~~l~~~~~  184 (189)
T PRK12515        161 ESTVKTRMFYARKKLAELLKAAGV  184 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcc
Confidence            999999999999999999886543

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

Probab=99.77  E-value=2.3e-18  Score=166.28  Aligned_cols=181  Identities=27%  Similarity=0.449  Sum_probs=141.4

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP  303 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP  303 (473)
                      +..+..|..|.||+.++|+     +.++|   .+|+..|.|++.              .+...++..+..+|.+.+|++|
T Consensus        43 ~fd~~~~~~f~t~~~~~i~-----~~~~~---~lr~~~~~p~~~--------------~~~~~~l~~~~~~l~~~~~~~~  100 (224)
T TIGR02479        43 RYDPSRGAKFETYAVQRIR-----GAMLD---ELRRLDWVPRSL--------------RQKARKLERAIRELEARLGREP  100 (224)
T ss_pred             hcCCccCCCHHHHHHHHHH-----HHHHH---HHHHcCccCHHH--------------HHHHHHHHHHHHHHHHHHCcCC
Confidence            4567788899999999999     99988   588887877765              4667789999999999999999


Q ss_pred             CHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992          304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN  383 (473)
Q Consensus       304 T~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT  383 (473)
                      +.+|+|+.+|++.+.+..++....                     .+...++++.+.++--+.  .+..+       +.+
T Consensus       101 ~~~ela~~l~~~~~~v~~~~~~~~---------------------~~~~~sl~~~~~~~~~~~--~~~~~-------~~~  150 (224)
T TIGR02479       101 TEEEIAEELGMDLKEYRQALNEIN---------------------ALSLVSLDELLESGDDGG--SLIDR-------IED  150 (224)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHh---------------------cCCccccCCcccCCCccc--hhhhh-------ccc
Confidence            999999999999998877654211                     112334555443211000  00000       111


Q ss_pred             CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          384 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       384 ~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      +....|+..+...+....|.++|+.||+++|.||.++|+    +++|++|||+.||+|.++|++++++|+++||+.+
T Consensus       151 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l  223 (224)
T TIGR02479       151 DKSEDPEEELEREELREALAEAIESLSEREQLVLSLYYY----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL  223 (224)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence            224467778888888899999999999999999999999    9999999999999999999999999999999876

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.

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.77  E-value=4.9e-18  Score=155.71  Aligned_cols=132  Identities=20%  Similarity=0.251  Sum_probs=114.5

Q ss_pred             hhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------
Q 011992          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------  383 (473)
Q Consensus       324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------  383 (473)
                      .++..|++.|+..|.+.|+++++++.+++.+++|++||+++++|++++.|+  .+..|.+                    
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            445589999999999999999999999999999999999999999999998  3445655                    


Q ss_pred             ---C-----------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHH
Q 011992          384 ---T-----------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE  443 (473)
Q Consensus       384 ---~-----------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~  443 (473)
                         .                 ....|+..+...+....+..+|..||++++.||.++|+    +++|++|||+.||+|++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~lgis~~  159 (182)
T PRK09652         84 PPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREI----EGLSYEEIAEIMGCPIG  159 (182)
T ss_pred             CCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHH
Confidence               0                 00124445555566788999999999999999999998    99999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhc
Q 011992          444 RVRQLESRALYRLKQSLG  461 (473)
Q Consensus       444 rVrqi~~RAL~KLR~~L~  461 (473)
                      +|++.+++|+++||+.+.
T Consensus       160 tV~~~l~ra~~~Lr~~l~  177 (182)
T PRK09652        160 TVRSRIFRAREALRAKLQ  177 (182)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999999876

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.77  E-value=1e-17  Score=157.09  Aligned_cols=141  Identities=15%  Similarity=0.210  Sum_probs=118.8

Q ss_pred             HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------  383 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------  383 (473)
                      .+.+...+..|+ .+++.||..|.+.|+++++++.++..+++|++||+|+++|+++.+|++..+  |.+           
T Consensus         7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~~--~~~wl~~ia~n~~~   84 (193)
T PRK11923          7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSA--FYTWLYRIAINTAK   84 (193)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCCc--cHhHHHHHHHHHHH
Confidence            344555555555 899999999999999999999999999999999999999999999987542  333           


Q ss_pred             ---------C--------------------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHH
Q 011992          384 ---------T--------------------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV  434 (473)
Q Consensus       384 ---------~--------------------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEI  434 (473)
                               .                    ....|+..+...+....+..+|..||+++|.||.++|+    +|++++||
T Consensus        85 d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eI  160 (193)
T PRK11923         85 NHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREF----DGLSYEDI  160 (193)
T ss_pred             HHHHHhcCCCccccccccchhhhcccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHh----cCCCHHHH
Confidence                     0                    01223444555666788999999999999999999998    99999999


Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          435 GNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       435 Ae~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      |+.||+|.++|++.++||+++||++++.
T Consensus       161 A~~lgis~~tv~~~l~Rar~~Lr~~l~~  188 (193)
T PRK11923        161 ASVMQCPVGTVRSRIFRAREAIDKALQP  188 (193)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999998863

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=6.5e-18  Score=158.59  Aligned_cols=140  Identities=22%  Similarity=0.300  Sum_probs=115.7

Q ss_pred             HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------  383 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------  383 (473)
                      ..++...+..|+ .+++.|+..|.+.|+++++++.++..+++|++||+|+++|.. ..|++..+ .|.+           
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            445555555555 999999999999999999999999999999999999999975 56775443 5655           


Q ss_pred             -------------C----------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992          384 -------------T----------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL  440 (473)
Q Consensus       384 -------------~----------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI  440 (473)
                                   .          ....++..+...+....|..+|..||+++++||.|+|+    +|+|++|||+.||+
T Consensus        94 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~----~g~s~~EIA~~lgi  169 (194)
T PRK12519         94 DRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYY----EGLSQSEIAKRLGI  169 (194)
T ss_pred             HHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhh----cCCCHHHHHHHhCC
Confidence                         0          00123344445555677899999999999999999998    99999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhc
Q 011992          441 SKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       441 S~~rVrqi~~RAL~KLR~~L~  461 (473)
                      |.++|+++++||+++||+.+.
T Consensus       170 s~~tV~~~l~Ra~~~Lr~~l~  190 (194)
T PRK12519        170 PLGTVKARARQGLLKLRELLQ  190 (194)
T ss_pred             CHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999875

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.77  E-value=6.4e-18  Score=155.87  Aligned_cols=144  Identities=14%  Similarity=0.228  Sum_probs=119.0

Q ss_pred             cCCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------
Q 011992          312 IGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------  383 (473)
Q Consensus       312 lGms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------  383 (473)
                      |.|+...+......|+ .+++.|+..|.+.|+++|+++.++..+++|++||+|+++|++++.|++.  ..|.+       
T Consensus         1 ~~~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~   78 (176)
T PRK09638          1 MQMDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIAS   78 (176)
T ss_pred             CCccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHH
Confidence            3455666666666666 9999999999999999999999999999999999999999999999764  35555       


Q ss_pred             -----------------C----CCCCch--HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992          384 -----------------T----GVEIPD--ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL  440 (473)
Q Consensus       384 -----------------~----~~~~pe--e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI  440 (473)
                                       .    ....++  ...........|..+|..||+++|+||.++|+    +|++++|||+.||+
T Consensus        79 n~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~i  154 (176)
T PRK09638         79 RLYKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHY----YGYTYEEIAKMLNI  154 (176)
T ss_pred             HHHHHHHHHhccccchhhhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhh----cCCCHHHHHHHHCC
Confidence                             0    001111  22233345567899999999999999999998    99999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhc
Q 011992          441 SKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       441 S~~rVrqi~~RAL~KLR~~L~  461 (473)
                      |.++|++.+.||+++||+.+.
T Consensus       155 s~~~V~~~l~ra~~~l~~~l~  175 (176)
T PRK09638        155 PEGTVKSRVHHGIKQLRKEWG  175 (176)
T ss_pred             ChhHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999874

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.77  E-value=1.5e-17  Score=156.88  Aligned_cols=145  Identities=17%  Similarity=0.183  Sum_probs=122.4

Q ss_pred             CCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------
Q 011992          313 GLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------  383 (473)
Q Consensus       313 Gms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------  383 (473)
                      .++.+.+...+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|++..  .|.+        
T Consensus        11 ~~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn   88 (192)
T PRK09643         11 ERSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVN   88 (192)
T ss_pred             CcCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHH
Confidence            355666666666665 99999999999999999999999999999999999999999999998643  3555        


Q ss_pred             ------------C--C-------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992          384 ------------T--G-------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK  442 (473)
Q Consensus       384 ------------~--~-------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~  442 (473)
                                  .  .       ...+++.+...+....|..+|..||+++|.||.|+|+    ++++++|||+.||+|.
T Consensus        89 ~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~----~g~s~~EIA~~lg~s~  164 (192)
T PRK09643         89 ACLDRLRRAKARPTVPLDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDM----QGYSVADAARMLGVAE  164 (192)
T ss_pred             HHHHHHHccccCCCCCccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCH
Confidence                        0  0       0112334455566778999999999999999999999    9999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhccC
Q 011992          443 ERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       443 ~rVrqi~~RAL~KLR~~L~~~  463 (473)
                      ++|+..+.||+++||+.+...
T Consensus       165 ~tV~~rl~rar~~Lr~~l~~~  185 (192)
T PRK09643        165 GTVKSRCARGRARLAELLGYL  185 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999998754

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

Probab=99.76  E-value=1.3e-17  Score=153.34  Aligned_cols=141  Identities=21%  Similarity=0.269  Sum_probs=115.5

Q ss_pred             CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------  383 (473)
Q Consensus       314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------  383 (473)
                      |+++++...+..|+ .+++.++..|.+.|++++.++.++..+++|++||+|+.+|+++++|++..  .|.+         
T Consensus         1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~   78 (169)
T TIGR02954         1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE   78 (169)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence            34555655555555 99999999999999999999999999999999999999999999998643  4555         


Q ss_pred             -----------C---C---CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992          384 -----------T---G---VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR  446 (473)
Q Consensus       384 -----------~---~---~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr  446 (473)
                                 .   .   ...++.... .+....+..+|..||+++|+||.++|+    +|+|++|||+.||||.++|+
T Consensus        79 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eiA~~lgis~~tv~  153 (169)
T TIGR02954        79 CIDLLKKKKKVIPFDPNTSIEKGECETH-ADSRLDLYKAIDTLNDKYQTAIILRYY----HDLTIKEIAEVMNKPEGTVK  153 (169)
T ss_pred             HHHHHHhcCCcCccccccccccchhhhc-hHHHHHHHHHHHhCCHHHhHHHHHHHH----cCCCHHHHHHHHCCCHHHHH
Confidence                       0   0   001111111 122347899999999999999999999    99999999999999999999


Q ss_pred             HHHHHHHHHHHHHhc
Q 011992          447 QLESRALYRLKQSLG  461 (473)
Q Consensus       447 qi~~RAL~KLR~~L~  461 (473)
                      .+++||+++||+.+.
T Consensus       154 ~~l~Ra~~~Lr~~l~  168 (169)
T TIGR02954       154 TYLHRALKKLKKRLE  168 (169)
T ss_pred             HHHHHHHHHHHHHhc
Confidence            999999999999875

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.

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.76  E-value=2e-17  Score=155.15  Aligned_cols=142  Identities=23%  Similarity=0.287  Sum_probs=115.9

Q ss_pred             CCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------
Q 011992          314 LSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------  383 (473)
Q Consensus       314 ms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------  383 (473)
                      |+..++...+..|+ .|++.||..|.+.|+++|+++.++..+++|++||+|+++|+++++|++..+..|.|         
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            45666777776766 99999999999999999999999999999999999999999999999876556655         


Q ss_pred             -----------CC------------------------------CCCchHHHHHHHHHHHHHHHHhhC-CHHHHHHHHHHh
Q 011992          384 -----------TG------------------------------VEIPDISVQKQLMRQHVRNLLTLL-NPKERCIVRLRF  421 (473)
Q Consensus       384 -----------~~------------------------------~~~pee~le~~el~e~L~~aL~~L-perER~VL~LrY  421 (473)
                                 ..                              ...|+..+...+..+.|.++|+.| ++.++.|+. +|
T Consensus        84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~  162 (198)
T TIGR02859        84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SY  162 (198)
T ss_pred             HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HH
Confidence                       00                              012333344455566788999995 566666664 57


Q ss_pred             hccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          422 GIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       422 ~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      +    +++|++|||+.||+|.++|+..++||+++||+.+
T Consensus       163 ~----~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l  197 (198)
T TIGR02859       163 L----DGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYL  197 (198)
T ss_pred             H----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence            7    8999999999999999999999999999999876

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.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=1e-17  Score=155.99  Aligned_cols=132  Identities=17%  Similarity=0.212  Sum_probs=114.9

Q ss_pred             hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------
Q 011992          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------  383 (473)
Q Consensus       325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------  383 (473)
                      ++..+++.||..|.+.|+++++.+.++..+++|++||+|+.+|+++.+|++..  .|.+                     
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            34489999999999999999999999999999999999999999999998764  3443                     


Q ss_pred             -------C-----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          384 -------T-----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       384 -------~-----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                             .     ....|+. +...+....|..+|..||+++|.||.|+|+    +++|++|||+.||||.++|+..++|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~----e~~s~~EIA~~lgis~~tV~~~l~r  156 (179)
T PRK12543         82 RIFEKAEEQRKPVSIDFSED-VLSKESNQELIELIHKLPYKLRQVIILRYL----HDYSQEEIAQLLQIPIGTVKSRIHA  156 (179)
T ss_pred             ccccccccccccccccChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence                   0     0112333 556667788999999999999999999999    9999999999999999999999999


Q ss_pred             HHHHHHHHhccC
Q 011992          452 ALYRLKQSLGGK  463 (473)
Q Consensus       452 AL~KLR~~L~~~  463 (473)
                      |+++||+.+...
T Consensus       157 a~~~Lr~~l~~~  168 (179)
T PRK12543        157 ALKKLRQKEQIE  168 (179)
T ss_pred             HHHHHHHHHHHH
Confidence            999999998754

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=1.6e-17  Score=151.94  Aligned_cols=134  Identities=18%  Similarity=0.217  Sum_probs=118.4

Q ss_pred             hhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------
Q 011992          324 HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------  383 (473)
Q Consensus       324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------  383 (473)
                      .++..+++.|+..|++.|+++|+++.++..+++|++||+++++|.+++.|+  .+..|.+                    
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            344499999999999999999999999999999999999999999999997  2334554                    


Q ss_pred             ------------C--CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992          384 ------------T--GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  449 (473)
Q Consensus       384 ------------~--~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~  449 (473)
                                  .  ....|+..+...+....+..+|+.||++++.||.++|+    ++++++|||+.||+|+++|++++
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~~~~~~eIA~~lgis~~tv~~~~  162 (179)
T PRK11924         87 KAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYV----EGLSYREIAEILGVPVGTVKSRL  162 (179)
T ss_pred             cccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHH
Confidence                        0  23456667777888889999999999999999999998    99999999999999999999999


Q ss_pred             HHHHHHHHHHhccC
Q 011992          450 SRALYRLKQSLGGK  463 (473)
Q Consensus       450 ~RAL~KLR~~L~~~  463 (473)
                      ++|+++||+.+...
T Consensus       163 ~ra~~~lr~~l~~~  176 (179)
T PRK11924        163 RRARQLLRECLEAQ  176 (179)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999988754

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.76  E-value=1.7e-17  Score=154.68  Aligned_cols=130  Identities=18%  Similarity=0.199  Sum_probs=114.2

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------  383 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------  383 (473)
                      ..|++.||..|.+.|++++.++.++..+++|++||+|+.+|+++++|+...  .|.+                       
T Consensus        15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n~~~d~~Rk~~~~~~~   92 (179)
T PRK09415         15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAINHCKDYLKSWHNKKVI   92 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHHHHHHHHHhhcccccc
Confidence            389999999999999999999999999999999999999999999997642  4554                       


Q ss_pred             --C--------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          384 --T--------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       384 --~--------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                        .        ....++..+...+....|..+|+.||+++|+||.|+|+    +|+|++|||+.||||.++|++++.||+
T Consensus        93 ~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tv~~~l~Ra~  168 (179)
T PRK09415         93 VTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYY----EELSIKEIAEVTGVNENTVKTRLKKAK  168 (179)
T ss_pred             ccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence              0        11234555566667788999999999999999999999    999999999999999999999999999


Q ss_pred             HHHHHHhcc
Q 011992          454 YRLKQSLGG  462 (473)
Q Consensus       454 ~KLR~~L~~  462 (473)
                      ++||+.+..
T Consensus       169 ~~Lr~~l~~  177 (179)
T PRK09415        169 ELLKKGLEE  177 (179)
T ss_pred             HHHHHHHhc
Confidence            999998864

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.75  E-value=9.6e-18  Score=157.26  Aligned_cols=144  Identities=22%  Similarity=0.345  Sum_probs=118.4

Q ss_pred             CCCHHHHHHHHhh----cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----
Q 011992          313 GLSCRDLKSELHS----GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----  383 (473)
Q Consensus       313 Gms~eeL~~~l~~----g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----  383 (473)
                      +++.+++...++.    +..|++.||..|.+.|+++|.++.++..+++|++||+|+++|+++++|++.  ..|.+     
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            4566666666653    348999999999999999999999999999999999999999999999853  35655     


Q ss_pred             --------------C-CC---------CCch-HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992          384 --------------T-GV---------EIPD-ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF  438 (473)
Q Consensus       384 --------------~-~~---------~~pe-e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L  438 (473)
                                    . ..         ..+. ......+....|..+|+.||+++|.||.|+|+    +|++++|||+.|
T Consensus        85 a~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l  160 (188)
T PRK09640         85 TYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFV----AELEFQEIADIM  160 (188)
T ss_pred             HHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHh----cCCCHHHHHHHH
Confidence                          0 00         0111 11123345577999999999999999999999    999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          439 GLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       439 GIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      |||.++|+..+.||+++||+.+..
T Consensus       161 gis~~tV~~~l~Ra~~~Lr~~l~~  184 (188)
T PRK09640        161 HMGLSATKMRYKRALDKLREKFAG  184 (188)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999998753

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=2e-17  Score=160.69  Aligned_cols=142  Identities=22%  Similarity=0.309  Sum_probs=120.4

Q ss_pred             CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------  383 (473)
Q Consensus       315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------  383 (473)
                      +.+.+...+..|+ .+++.|+..|.+.|++++.++.++..+++|++||+|+++|+++++|++..  .|.+          
T Consensus        16 ~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~~--~~~~wL~~iarn~~   93 (231)
T PRK11922         16 SDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDA--SLSTWLSRIVLNEA   93 (231)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCCc--hhHHHHHHHHHHHH
Confidence            3445555555455 99999999999999999999999999999999999999999999998753  4444          


Q ss_pred             --------------C--C---------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHH
Q 011992          384 --------------T--G---------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLS  432 (473)
Q Consensus       384 --------------~--~---------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlk  432 (473)
                                    .  .               ...|+..+...+..+.|..+|..||+++|+||.++|+    +++|++
T Consensus        94 ~d~~Rk~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~  169 (231)
T PRK11922         94 LGRLRRRRRLVNLAEMVMASTIAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVV----EELSVE  169 (231)
T ss_pred             HHHHHhhcccccchhcccccccccccccccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehh----cCCCHH
Confidence                          0  0               0134455566677788999999999999999999998    999999


Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          433 EVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       433 EIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      |||+.||+|.++|++++.||+++||+.+..
T Consensus       170 EIAe~lgis~~tVk~~l~Rar~kLr~~l~~  199 (231)
T PRK11922        170 ETAQALGLPEETVKTRLHRARRLLRESLAR  199 (231)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999875

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=2e-17  Score=155.97  Aligned_cols=141  Identities=13%  Similarity=0.195  Sum_probs=114.8

Q ss_pred             HHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------
Q 011992          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------  383 (473)
Q Consensus       319 L~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------  383 (473)
                      +...+..|+ .+++.||..|.+.|+.+|.++.++..+++|++||+|+.+|+.+++|++..+ .|.+              
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            444455555 899999999999999999999999999999999999999999999986432 4555              


Q ss_pred             ---C--C------CCCch----------HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992          384 ---T--G------VEIPD----------ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK  442 (473)
Q Consensus       384 ---~--~------~~~pe----------e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~  442 (473)
                         .  .      ...++          ...+.......+..+|..||+++|.||.|+|+    ++++++|||+.||||.
T Consensus        96 Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----eg~s~~EIA~~lgis~  171 (194)
T PRK12531         96 RKQKGKDLHIHADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYL----EELPHQQVAEMFDIPL  171 (194)
T ss_pred             HHhcccccccchhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCH
Confidence               0  0      00000          01112234467899999999999999999999    9999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhccCc
Q 011992          443 ERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       443 ~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      ++|+..+++|+++||..+..+.
T Consensus       172 ~tVk~rl~ra~~~Lr~~l~~~~  193 (194)
T PRK12531        172 GTVKSRLRLAVEKLRHSMDAES  193 (194)
T ss_pred             HHHHHHHHHHHHHHHHHhhhcc
Confidence            9999999999999999987654

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

Probab=99.75  E-value=2.3e-17  Score=148.09  Aligned_cols=127  Identities=20%  Similarity=0.205  Sum_probs=111.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------  383 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------  383 (473)
                      .|++.|+..|.+.|+++++++.++..+++|++||+++++|+++.+|++..  .|.+                        
T Consensus         1 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~~~~   78 (161)
T TIGR02985         1 KAFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEEKYQ   78 (161)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHhHHH
Confidence            37899999999999999999999999999999999999999999997643  5655                        


Q ss_pred             ----------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          384 ----------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       384 ----------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                                .....++..+...+....|..++..||++++.||.++|.    +|+|.+|||+.||+|+++|++++.+|+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~----~~~~~~eIA~~lgis~~tv~~~~~ra~  154 (161)
T TIGR02985        79 EEILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRF----EGKSYKEIAEELGISVKTVEYHISKAL  154 (161)
T ss_pred             HHHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence                      011234555666777788999999999999999999998    999999999999999999999999999


Q ss_pred             HHHHHHh
Q 011992          454 YRLKQSL  460 (473)
Q Consensus       454 ~KLR~~L  460 (473)
                      ++||+.|
T Consensus       155 ~~Lr~~l  161 (161)
T TIGR02985       155 KELRKEL  161 (161)
T ss_pred             HHHHhhC
Confidence            9999864

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.75  E-value=2.2e-17  Score=152.09  Aligned_cols=134  Identities=16%  Similarity=0.171  Sum_probs=112.4

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------  383 (473)
Q Consensus       326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------  383 (473)
                      +..+++.||..|.+.++++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+                      
T Consensus         7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~   85 (173)
T PRK09645          7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPV   85 (173)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhccccc
Confidence            4589999999999999999999999999999999999999999999996422 23444                      


Q ss_pred             ----C----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992          384 ----T----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  455 (473)
Q Consensus       384 ----~----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K  455 (473)
                          .    ....++..+...+....|..+|+.||+++|+||.|+|+    +|+|++|||+.||+|+++|+.+++||+++
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~  161 (173)
T PRK09645         86 EGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYY----RGWSTAQIAADLGIPEGTVKSRLHYALRA  161 (173)
T ss_pred             ccccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence                0    01122333444445567999999999999999999999    99999999999999999999999999999


Q ss_pred             HHHHhccCc
Q 011992          456 LKQSLGGKA  464 (473)
Q Consensus       456 LR~~L~~~~  464 (473)
                      ||+.+...+
T Consensus       162 Lr~~l~~~~  170 (173)
T PRK09645        162 LRLALQERG  170 (173)
T ss_pred             HHHHhhccc
Confidence            999987543

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

Probab=99.75  E-value=3.1e-17  Score=161.61  Aligned_cols=148  Identities=18%  Similarity=0.233  Sum_probs=121.9

Q ss_pred             HcCCCHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHH-------HhhhhCccCCCccc
Q 011992          311 AIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMK-------SVEKFKPQAGCRFA  382 (473)
Q Consensus       311 ~lGms~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~k-------AiekFDp~kg~~Fs  382 (473)
                      .|+.++..+...+..|+ .||..|+..|.+.|+.++.++.++..+++|++||+|+.+|.       ++.+|++..  .|.
T Consensus        21 ~~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~--~~~   98 (244)
T TIGR03001        21 QLHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRG--PLL   98 (244)
T ss_pred             cccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCC--chH
Confidence            35567777888777777 89999999999999999999999999999999999999995       677787532  454


Q ss_pred             c------------------------CC---------CCCchHHHHH----HHHHHHHHHHHhhCCHHHHHHHHHHhhccC
Q 011992          383 N------------------------TG---------VEIPDISVQK----QLMRQHVRNLLTLLNPKERCIVRLRFGIED  425 (473)
Q Consensus       383 T------------------------~~---------~~~pee~le~----~el~e~L~~aL~~LperER~VL~LrY~L~~  425 (473)
                      +                        ..         ...|+..+..    .+..+.|.++|+.||+++|+||.|+|+   
T Consensus        99 tWL~~Ia~N~~id~lRk~~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~---  175 (244)
T TIGR03001        99 SWVRIVATRIALELQAQERRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFV---  175 (244)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHH---
Confidence            4                        00         0122333322    235567999999999999999999999   


Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992          426 GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       426 ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                       +|+|++|||++||||.++|+..++||+++||+.+....
T Consensus       176 -eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~  213 (244)
T TIGR03001       176 -DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRL  213 (244)
T ss_pred             -cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence             99999999999999999999999999999999987653

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.

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.74  E-value=6.4e-17  Score=154.45  Aligned_cols=134  Identities=13%  Similarity=0.154  Sum_probs=110.7

Q ss_pred             hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------C-
Q 011992          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------T-  384 (473)
Q Consensus       325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~-  384 (473)
                      ++..+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++..|++.++ .|.+                   . 
T Consensus        35 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~~  113 (206)
T PRK12526         35 RDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAKK  113 (206)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhcccc
Confidence            444999999999999999999999999999999999999999999999986544 2443                   0 


Q ss_pred             -CC----C-----------CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 011992          385 -GV----E-----------IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL  448 (473)
Q Consensus       385 -~~----~-----------~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi  448 (473)
                       ..    .           .+............|..+|..||+++|.||.++|+    +++|++|||+.||+|.++|+.+
T Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~  189 (206)
T PRK12526        114 EQNLGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYF----QELSQEQLAQQLNVPLGTVKSR  189 (206)
T ss_pred             ccccccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHH
Confidence             00    0           00111112223457899999999999999999999    9999999999999999999999


Q ss_pred             HHHHHHHHHHHhccC
Q 011992          449 ESRALYRLKQSLGGK  463 (473)
Q Consensus       449 ~~RAL~KLR~~L~~~  463 (473)
                      ++||+++||+.+...
T Consensus       190 l~Ra~~~Lr~~l~~~  204 (206)
T PRK12526        190 LRLALAKLKVQMGEQ  204 (206)
T ss_pred             HHHHHHHHHHHHhhc
Confidence            999999999998653

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.74  E-value=4.3e-17  Score=151.97  Aligned_cols=134  Identities=10%  Similarity=0.008  Sum_probs=111.8

Q ss_pred             hhcchHHHHHHHHHHHHHHHHHHHhhc--CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------
Q 011992          324 HSGNSSREKLINANLRLVVHVAKQYQG--RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------  383 (473)
Q Consensus       324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~--~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------  383 (473)
                      .++..+|+.||..|.+.|++++..+.+  +..+++|++||+|+.+|+.++.|+......|.+                  
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            445589999999999999998766665  467899999999999999999886433334554                  


Q ss_pred             --------------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992          384 --------------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  449 (473)
Q Consensus       384 --------------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~  449 (473)
                                    .....|++.+...+....|..+|..||+++|.||.|+|+    +|+|++|||+.||+|+++|+.++
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~l  164 (178)
T PRK12529         89 LELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATL----DGMKQKDIAQALDIALPTVKKYI  164 (178)
T ss_pred             HHhhhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHH
Confidence                          011245555555666778999999999999999999999    99999999999999999999999


Q ss_pred             HHHHHHHHHHhc
Q 011992          450 SRALYRLKQSLG  461 (473)
Q Consensus       450 ~RAL~KLR~~L~  461 (473)
                      ++|+.+|++.+.
T Consensus       165 ~rAl~~~~~~~~  176 (178)
T PRK12529        165 HQAYVTCLSLMP  176 (178)
T ss_pred             HHHHHHHHHhCC
Confidence            999999998764

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=3.7e-17  Score=153.53  Aligned_cols=130  Identities=15%  Similarity=0.131  Sum_probs=111.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------CC
Q 011992          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------TG  385 (473)
Q Consensus       329 A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~~  385 (473)
                      +|+.|+..|.+.|+++|++++++..+++|++||.|+.+|+++++|+...  .|.+                       ..
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            6889999999999999999999999999999999999999999997543  3544                       00


Q ss_pred             C----------------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHH
Q 011992          386 V----------------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI  437 (473)
Q Consensus       386 ~----------------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~  437 (473)
                      .                            ..|+..+...+....|..+|..||+++|.||.|+|+    +|+|++|||+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~  156 (191)
T PRK12520         81 DDADEQSDDDLFDALFAADGHYREPPSDWGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREW----LELETEEICQE  156 (191)
T ss_pred             cccccchhhhhhhhhcccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHH
Confidence            0                            123333445556677999999999999999999999    99999999999


Q ss_pred             HCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992          438 FGLSKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       438 LGIS~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      ||+|+++|++.+.||+++||+.+....
T Consensus       157 lgis~~tV~~~l~Rar~~Lr~~l~~~~  183 (191)
T PRK12520        157 LQITATNAWVLLYRARMRLRECLDLHW  183 (191)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999998765

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

Probab=99.73  E-value=5.1e-17  Score=147.08  Aligned_cols=127  Identities=19%  Similarity=0.247  Sum_probs=107.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------CC-C-
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------TG-V-  386 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~~-~-  386 (473)
                      ++++.++..|.+.|+++|+++.++..++||++||+++.+|+++++|++..  .|.+                   .. . 
T Consensus         1 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~   78 (159)
T TIGR02989         1 EAFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVF   78 (159)
T ss_pred             CHHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            37899999999999999999999999999999999999999999998653  4555                   00 0 


Q ss_pred             -----------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992          387 -----------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  455 (473)
Q Consensus       387 -----------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K  455 (473)
                                 ..+.......+....|..+|+.||++++.||.++|+    +|++++|||+.||||.++|+..++||+++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~----~g~~~~eIA~~l~is~~tv~~~l~Rar~~  154 (159)
T TIGR02989        79 DDELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQ----RGVSLTALAEQLGRTVNAVYKALSRLRVR  154 (159)
T ss_pred             CHHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence                       011122223444567899999999999999999998    99999999999999999999999999999


Q ss_pred             HHHHh
Q 011992          456 LKQSL  460 (473)
Q Consensus       456 LR~~L  460 (473)
                      ||+++
T Consensus       155 Lr~~~  159 (159)
T TIGR02989       155 LRDCV  159 (159)
T ss_pred             HHhcC
Confidence            99864

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=99.73  E-value=1.1e-16  Score=149.68  Aligned_cols=142  Identities=17%  Similarity=0.171  Sum_probs=114.8

Q ss_pred             HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHH----HhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------
Q 011992          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAK----QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------  383 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~----ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------  383 (473)
                      ...+...+..|+ .+|+.||..|.+.|+++++    ++.++..+++|++||+++.+|++++.|++..  .|.+       
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            344555555555 9999999999999999986    4557889999999999999999999998753  4555       


Q ss_pred             -----------C---C-----CC--CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCH
Q 011992          384 -----------T---G-----VE--IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSK  442 (473)
Q Consensus       384 -----------~---~-----~~--~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~  442 (473)
                                 .   .     ..  .+.......+....|..+|..||+++|.||.|+|+    +|++++|||+.||+|.
T Consensus        86 n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~  161 (184)
T PRK12539         86 YKLIDHLRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKL----EGLSVAEAATRSGMSE  161 (184)
T ss_pred             HHHHHHHHHHhccccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCcHHHHHHHHCcCH
Confidence                       0   0     00  01122233445677999999999999999999999    9999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhccC
Q 011992          443 ERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       443 ~rVrqi~~RAL~KLR~~L~~~  463 (473)
                      ++|+.+++||+++||+.+...
T Consensus       162 ~tV~~~l~ra~~~Lr~~l~~~  182 (184)
T PRK12539        162 SAVKVSVHRGLKALAALIGRE  182 (184)
T ss_pred             HHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999988654

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=8.4e-17  Score=148.62  Aligned_cols=129  Identities=16%  Similarity=0.196  Sum_probs=110.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------C--C-
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------T--G-  385 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~--~-  385 (473)
                      ..+++|+..|.++|+++|++|.++..+++|++||+++.+|+++++|++..  +|.+                   .  . 
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            45889999999999999999999999999999999999999999998743  4555                   0  0 


Q ss_pred             ----------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992          386 ----------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  449 (473)
Q Consensus       386 ----------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~  449 (473)
                                      ...+.+.....+..+.|..+|..||++++.|+.|+|.    +|++++|||+.||+|.++|+..+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~~~s~~EIA~~lgis~~tV~~~l  156 (173)
T PRK12522         81 LDLFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYY----EQYSYKEMSEILNIPIGTVKYRL  156 (173)
T ss_pred             ccccchhhhhhhccccCCCChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHH
Confidence                            0011122444556678999999999999999999999    99999999999999999999999


Q ss_pred             HHHHHHHHHHhcc
Q 011992          450 SRALYRLKQSLGG  462 (473)
Q Consensus       450 ~RAL~KLR~~L~~  462 (473)
                      +||+++||+.+..
T Consensus       157 ~Ra~~~Lr~~l~~  169 (173)
T PRK12522        157 NYAKKQMREHLEG  169 (173)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998864

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.72  E-value=4.2e-17  Score=148.40  Aligned_cols=123  Identities=13%  Similarity=0.050  Sum_probs=106.0

Q ss_pred             HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C-------
Q 011992          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T-------  384 (473)
Q Consensus       335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~-------  384 (473)
                      ..|.+.++++|.+++++..+++|++||+|+.+|+++++|++.   .|.+                       .       
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~   78 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEELSLCKETE   78 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccccccchhhh
Confidence            468999999999999999999999999999999999999853   3655                       0       


Q ss_pred             ----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          385 ----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       385 ----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                          ....+++.+...+....|..+|+.||+++|.||.|+|+    +|+|++|||+.||+|.++|+++++||+++||+.+
T Consensus        79 ~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  154 (160)
T PRK09642         79 ENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYL----EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW  154 (160)
T ss_pred             hhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence                00123445555666778999999999999999999999    9999999999999999999999999999999999


Q ss_pred             ccCc
Q 011992          461 GGKA  464 (473)
Q Consensus       461 ~~~~  464 (473)
                      ...+
T Consensus       155 ~~~~  158 (160)
T PRK09642        155 KEEE  158 (160)
T ss_pred             hhhc
Confidence            7654

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

Probab=99.72  E-value=1.2e-16  Score=148.41  Aligned_cols=133  Identities=21%  Similarity=0.235  Sum_probs=110.1

Q ss_pred             hcchHHHHHHHHHHHHHHHHHHHhh----cCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------C
Q 011992          325 SGNSSREKLINANLRLVVHVAKQYQ----GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------T  384 (473)
Q Consensus       325 ~g~~A~e~Li~~yl~lV~sIA~ry~----~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------~  384 (473)
                      ++..+++.|+..|.+.|+.+|+++.    ++..+++|++||+++.+|+++.+|+...+..|.+                .
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            3448999999999999999999875    3677899999999999999999997654444554                0


Q ss_pred             ------------C---------------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCH
Q 011992          385 ------------G---------------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSL  431 (473)
Q Consensus       385 ------------~---------------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTl  431 (473)
                                  .                     ...|++.+...+....|..+|..||+++|.||.++|+    +|+++
T Consensus        84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~----~g~s~  159 (189)
T TIGR02984        84 LGAQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHL----EGLSF  159 (189)
T ss_pred             HHHHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCH
Confidence                        0                     0012333444555678999999999999999999998    99999


Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          432 SEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       432 kEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      +|||+.||||.++|++.++||+++||+.++
T Consensus       160 ~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l~  189 (189)
T TIGR02984       160 AEVAERMDRSEGAVSMLWVRGLARLRQILE  189 (189)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHHhC
Confidence            999999999999999999999999998763

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).

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

Probab=99.72  E-value=1.3e-16  Score=148.00  Aligned_cols=139  Identities=19%  Similarity=0.283  Sum_probs=107.0

Q ss_pred             HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCc-----chhhHhhhhHHHHHH-HhhhhCccCCCcccc-----
Q 011992          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-----SLHDLLQEGSMGLMK-SVEKFKPQAGCRFAN-----  383 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~-----saEDLiQEg~lgL~k-AiekFDp~kg~~FsT-----  383 (473)
                      ...+...+..|+ .+++.|+..|.+.++++|+++.++..     +++|++||+|+.+|+ ...+|++..  .|.+     
T Consensus         4 ~~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~~--~~~~wl~~i   81 (183)
T TIGR02999         4 VTELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDRA--HFFAAAAKA   81 (183)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCchH--HHHHHHHHH
Confidence            345556666666 89999999999999999999999887     899999999999998 777786542  2322     


Q ss_pred             ---------------CC-----CC-----CchHHHHHHHHH---HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHH
Q 011992          384 ---------------TG-----VE-----IPDISVQKQLMR---QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVG  435 (473)
Q Consensus       384 ---------------~~-----~~-----~pee~le~~el~---e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIA  435 (473)
                                     ..     ..     .+.......+..   +.+...|+.||+++|.||.|+|+    +|+|++|||
T Consensus        82 ~~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA  157 (183)
T TIGR02999        82 MRRILVDHARRRRAQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFF----AGLTVEEIA  157 (183)
T ss_pred             HHHHHHHHHHHHHHHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHH----cCCCHHHHH
Confidence                           00     00     011111111222   23334456699999999999999    999999999


Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          436 NIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       436 e~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ++||+|+++|+.+++||+++||+.+
T Consensus       158 ~~lgis~~tVk~~l~Rar~~Lr~~l  182 (183)
T TIGR02999       158 ELLGVSVRTVERDWRFARAWLADEL  182 (183)
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999876

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=1.7e-16  Score=147.82  Aligned_cols=139  Identities=19%  Similarity=0.223  Sum_probs=111.8

Q ss_pred             HHHHHhhc-chHHHHHHHHHHHHHHHHHHHhhc----CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------
Q 011992          319 LKSELHSG-NSSREKLINANLRLVVHVAKQYQG----RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------  383 (473)
Q Consensus       319 L~~~l~~g-~~A~e~Li~~yl~lV~sIA~ry~~----~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------  383 (473)
                      +...+..| ..+++.||..|.+.|+++|.++++    +..+++|++||+++.+|...+.|+..  ..|.+          
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            34444444 499999999999999999998875    35689999999999999999999763  34554          


Q ss_pred             ---------C-C-------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992          384 ---------T-G-------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR  446 (473)
Q Consensus       384 ---------~-~-------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr  446 (473)
                               . .       ...+............+..+|+.||+++|+||.++|+    +|+|++|||+.||+|.++|+
T Consensus        90 ~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~l~is~~tV~  165 (184)
T PRK12512         90 IDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISV----EGASIKETAAKLSMSEGAVR  165 (184)
T ss_pred             HHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHH
Confidence                     0 0       0011111122334567899999999999999999999    99999999999999999999


Q ss_pred             HHHHHHHHHHHHHhccC
Q 011992          447 QLESRALYRLKQSLGGK  463 (473)
Q Consensus       447 qi~~RAL~KLR~~L~~~  463 (473)
                      ..+++|+++||+.+..+
T Consensus       166 ~~l~ra~~~Lr~~l~~~  182 (184)
T PRK12512        166 VALHRGLAALAAKFRSE  182 (184)
T ss_pred             HHHHHHHHHHHHHhhcC
Confidence            99999999999998765

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=7.3e-17  Score=148.68  Aligned_cols=135  Identities=18%  Similarity=0.147  Sum_probs=110.7

Q ss_pred             HhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------
Q 011992          323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------  383 (473)
Q Consensus       323 l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------  383 (473)
                      ..++..+++.||..|.+.|+++++++.+ ..+++|++||+|+.+|+.++.|++.  ..|.+                   
T Consensus         6 ~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~   82 (175)
T PRK12518          6 QRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQ   82 (175)
T ss_pred             HcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhc
Confidence            3444599999999999999999999875 5789999999999999999999864  24554                   


Q ss_pred             -------CC------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          384 -------TG------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       384 -------~~------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                             ..      ...++......+....+.++|+.||+++|.||.|+|+    +|+|++|||+.||+|.++|++.++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lg~s~~tv~~~l~  158 (175)
T PRK12518         83 RPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDL----EDLPQKEIAEILNIPVGTVKSRLF  158 (175)
T ss_pred             cccchhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHh----cCCCHHHHHHHHCCCHHHHHHHHH
Confidence                   00      0111222333344467899999999999999999999    999999999999999999999999


Q ss_pred             HHHHHHHHHhccCc
Q 011992          451 RALYRLKQSLGGKA  464 (473)
Q Consensus       451 RAL~KLR~~L~~~~  464 (473)
                      ||+++||+.+...+
T Consensus       159 Rar~~L~~~l~~~~  172 (175)
T PRK12518        159 YARRQLRKFLQQQG  172 (175)
T ss_pred             HHHHHHHHHHHhcc
Confidence            99999999987643

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.71  E-value=1.2e-16  Score=149.86  Aligned_cols=139  Identities=19%  Similarity=0.123  Sum_probs=110.6

Q ss_pred             HHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------
Q 011992          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------  383 (473)
Q Consensus       319 L~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------  383 (473)
                      +...+..|+ .+++.||..|.+.+++++. +.++..+++|++||+|+.+|+.+++|++..  .|.+              
T Consensus        14 l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~~--~~~~Wl~~Iarn~~~d~~   90 (185)
T PRK09649         14 LALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSARS--SARTWLLAIARHVVADHI   90 (185)
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCccc--hHHHHHHHHHHHHHHHHH
Confidence            444444444 8999999999999999995 688889999999999999999999998642  4544              


Q ss_pred             --------CC-CCC------chHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 011992          384 --------TG-VEI------PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL  448 (473)
Q Consensus       384 --------~~-~~~------pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi  448 (473)
                              .. ...      ++......+....|..+|..||+++|.||.|+|+    +++|++|||+.||+|+++|+..
T Consensus        91 Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tVk~~  166 (185)
T PRK09649         91 RHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSR  166 (185)
T ss_pred             HHhccccccccccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHH----cCCCHHHHHHHHCCCHHHHHHH
Confidence                    00 000      1111112233456889999999999999999999    9999999999999999999999


Q ss_pred             HHHHHHHHHHHhccCc
Q 011992          449 ESRALYRLKQSLGGKA  464 (473)
Q Consensus       449 ~~RAL~KLR~~L~~~~  464 (473)
                      ++||+++||+.+...+
T Consensus       167 l~Rar~~Lr~~~~~~~  182 (185)
T PRK09649        167 VARARDALLADAEPDD  182 (185)
T ss_pred             HHHHHHHHHhhCCccc
Confidence            9999999999766544

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

Probab=99.71  E-value=2e-16  Score=147.83  Aligned_cols=137  Identities=22%  Similarity=0.316  Sum_probs=116.1

Q ss_pred             HHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------
Q 011992          321 SELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------  383 (473)
Q Consensus       321 ~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------  383 (473)
                      ....++..++..++..+.+.++++++++.++..+++|++||+|+.+|+++..|.  .+..|.+                 
T Consensus         8 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~~--~~~~~~~wl~~Ia~n~~iD~~R~~   85 (182)
T COG1595           8 EALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSFR--GRSSFKAWLYRIARNLAIDRLRKR   85 (182)
T ss_pred             HHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcC--CCCchHHHHHHHHHHHHHHHHHHh
Confidence            334555689999999999999999999999999999999999999999999992  2335655                 


Q ss_pred             ---------------CCCCCch--HHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992          384 ---------------TGVEIPD--ISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR  446 (473)
Q Consensus       384 ---------------~~~~~pe--e~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr  446 (473)
                                     .....++  ..+...+....|.++|..||+++|.+|.|+|+    +|+|++|||+.||||.++|+
T Consensus        86 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~----~gls~~EIA~~l~i~~~tVk  161 (182)
T COG1595          86 KRRRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYL----EGLSYEEIAEILGISVGTVK  161 (182)
T ss_pred             cccccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhh----cCCCHHHHHHHHCCCHHHHH
Confidence                           0111111  13455677889999999999999999999999    99999999999999999999


Q ss_pred             HHHHHHHHHHHHHhccC
Q 011992          447 QLESRALYRLKQSLGGK  463 (473)
Q Consensus       447 qi~~RAL~KLR~~L~~~  463 (473)
                      ..+++|+.+||+.+...
T Consensus       162 s~l~ra~~~l~~~l~~~  178 (182)
T COG1595         162 SRLHRARKKLREQLEEA  178 (182)
T ss_pred             HHHHHHHHHHHHHHhhc
Confidence            99999999999998764

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.71  E-value=1e-16  Score=151.12  Aligned_cols=133  Identities=21%  Similarity=0.160  Sum_probs=110.3

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------  383 (473)
Q Consensus       326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------  383 (473)
                      +..+|..|+..|.+.++++|++++++..+++|++||+|+.+|+.+++|+...  .|.+                      
T Consensus         8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~~   85 (187)
T PRK12516          8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREVQ   85 (187)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence            3478999999999999999999999999999999999999999999997542  3544                      


Q ss_pred             CCC----C--CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          384 TGV----E--IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       384 ~~~----~--~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ...    .  ..............|..+|+.||+++|+||.|+|+    +|++++|||+.||+|+++|+.+++||+++||
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~----~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr  161 (187)
T PRK12516         86 DTDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGA----SGFAYEEAAEICGCAVGTIKSRVNRARQRLQ  161 (187)
T ss_pred             ccccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            000    0  00111112233467899999999999999999999    9999999999999999999999999999999


Q ss_pred             HHhccCc
Q 011992          458 QSLGGKA  464 (473)
Q Consensus       458 ~~L~~~~  464 (473)
                      +.+....
T Consensus       162 ~~l~~~~  168 (187)
T PRK12516        162 EILQIEG  168 (187)
T ss_pred             HHHHhhc
Confidence            9997653

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.71  E-value=1.4e-16  Score=146.08  Aligned_cols=129  Identities=17%  Similarity=0.097  Sum_probs=112.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------------
Q 011992          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------------  383 (473)
Q Consensus       330 ~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------------  383 (473)
                      |+.||..|.+.|+++|+++.++..+++|++||+|+.+|++++.|++.   .|.+                          
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~~~   79 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVGTD   79 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccchh
Confidence            67899999999999999999999999999999999999999999753   3544                          


Q ss_pred             ----CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          384 ----TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       384 ----~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                          .....+++.+...+....+.++|..||+++|+||.|+|+    +|++++|||+.||+|.++|+.+++||+++||+.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~  155 (165)
T PRK09644         80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDV----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKAL  155 (165)
T ss_pred             HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence                011234555555666788999999999999999999999    999999999999999999999999999999999


Q ss_pred             hccCch
Q 011992          460 LGGKAS  465 (473)
Q Consensus       460 L~~~~l  465 (473)
                      +.....
T Consensus       156 l~~~~~  161 (165)
T PRK09644        156 LKEEKS  161 (165)
T ss_pred             HHhhhh
Confidence            876543

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.71  E-value=1.9e-16  Score=153.31  Aligned_cols=131  Identities=21%  Similarity=0.195  Sum_probs=113.8

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------
Q 011992          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------  383 (473)
Q Consensus       326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------  383 (473)
                      ...+|..||..|.+.++++++++.++..+++|++||+|+.+|+.+++|++.   .|.+                      
T Consensus        16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~   92 (216)
T PRK12533         16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHE   92 (216)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccccc
Confidence            347899999999999999999999999999999999999999999999753   2444                      


Q ss_pred             -C---C-------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992          384 -T---G-------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR  446 (473)
Q Consensus       384 -~---~-------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr  446 (473)
                       .   .             ...|+..+...+....|..+|..||+++|+||.|+|+    +++|++|||+.||||+++|+
T Consensus        93 ~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~----eg~s~~EIAe~LgiS~~tVk  168 (216)
T PRK12533         93 VAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLREL----EDMSYREIAAIADVPVGTVM  168 (216)
T ss_pred             ccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHh----cCCCHHHHHHHHCCCHHHHH
Confidence             0   0             0123444556667788999999999999999999999    99999999999999999999


Q ss_pred             HHHHHHHHHHHHHhccC
Q 011992          447 QLESRALYRLKQSLGGK  463 (473)
Q Consensus       447 qi~~RAL~KLR~~L~~~  463 (473)
                      ++++||+++||+.+...
T Consensus       169 ~~L~RAr~~Lr~~l~~~  185 (216)
T PRK12533        169 SRLARARRRLAALLGGA  185 (216)
T ss_pred             HHHHHHHHHHHHHHccc
Confidence            99999999999999754

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.71  E-value=1.6e-16  Score=146.87  Aligned_cols=130  Identities=16%  Similarity=0.097  Sum_probs=108.8

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------  383 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------  383 (473)
                      ..++..||..|.+.|+++|.++.++..+++|++||+|+.+|+.. .|...  ..|.+                       
T Consensus         9 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~~-~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~~~   85 (172)
T PRK12523          9 SELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRP-ELPTP--REPRAFLAAVAKGLMFDHFRRAALEQAY   85 (172)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHccc-ccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            38999999999999999999999999999999999999999863 45432  23544                       


Q ss_pred             ----C-----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          384 ----T-----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       384 ----~-----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                          .     ....++......+....+..+|..||+++|.||.|+|+    +|++++|||++||+|.++|++++++|++
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~  161 (172)
T PRK12523         86 LAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRL----DGMGHAEIAERLGVSVSRVRQYLAQGLR  161 (172)
T ss_pred             HHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                0     11233444444455567999999999999999999999    9999999999999999999999999999


Q ss_pred             HHHHHhccC
Q 011992          455 RLKQSLGGK  463 (473)
Q Consensus       455 KLR~~L~~~  463 (473)
                      +||..|..+
T Consensus       162 ~~~~~l~~~  170 (172)
T PRK12523        162 QCYIALYGE  170 (172)
T ss_pred             HHHHHhcCC
Confidence            999988754

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

Probab=99.71  E-value=1.2e-16  Score=145.39  Aligned_cols=132  Identities=20%  Similarity=0.209  Sum_probs=111.5

Q ss_pred             hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------C---
Q 011992          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------T---  384 (473)
Q Consensus       325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------~---  384 (473)
                      ++..+++.|+..|.+.|++++..+.++..+++|++||+|+.+|.++++|+..  ..|.+                 .   
T Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~rk~~~~~   80 (162)
T TIGR02983         3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDP--DAPDAYVRRVLVNLARSRWRRRRLLE   80 (162)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence            4458999999999999999999999999999999999999999999999542  34544                 0   


Q ss_pred             ------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          385 ------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       385 ------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                            ....+.......+..+.|..+|..||+++|.||.|+|+    +|+|++|||+.||+|.++|++++.||+++||+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~  156 (162)
T TIGR02983        81 LPTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYY----EDLSEAQVAEALGISVGTVKSRLSRALARLRE  156 (162)
T ss_pred             ccccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHH----hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence                  00112222334556678999999999999999999999    99999999999999999999999999999999


Q ss_pred             Hhcc
Q 011992          459 SLGG  462 (473)
Q Consensus       459 ~L~~  462 (473)
                      .+..
T Consensus       157 ~l~~  160 (162)
T TIGR02983       157 LLEE  160 (162)
T ss_pred             HhcC
Confidence            8764

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.

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.70  E-value=2.3e-16  Score=147.11  Aligned_cols=138  Identities=14%  Similarity=0.142  Sum_probs=111.3

Q ss_pred             HHHHhhcchHHHHHHHHHHHHHHHHHHHhhc-CCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------
Q 011992          320 KSELHSGNSSREKLINANLRLVVHVAKQYQG-RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------  383 (473)
Q Consensus       320 ~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~-~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------  383 (473)
                      .....++..+++.||..|.+.|+.++.++.+ +..+++|++||+|+.+|++++.|++..  .|.+               
T Consensus        13 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~~--~~~~wl~~iarN~~~d~~R   90 (181)
T PRK12536         13 LRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRADQ--PLTAWVHAIARYKLMDFLR   90 (181)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHH
Confidence            3344445599999999999999999988764 578999999999999999999998643  4544               


Q ss_pred             -----C--CCCCc-------hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992          384 -----T--GVEIP-------DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  449 (473)
Q Consensus       384 -----~--~~~~p-------ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~  449 (473)
                           .  .....       .......+....+.++|+.||++++.||.++|.    +|++++|||+.||+|+++|+..+
T Consensus        91 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~l~is~~tV~~~l  166 (181)
T PRK12536         91 SRARREALHDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKL----EGLSVAETAQLTGLSESAVKVGI  166 (181)
T ss_pred             HHhccccccCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHH
Confidence                 0  00000       000112345567999999999999999999999    99999999999999999999999


Q ss_pred             HHHHHHHHHHhccC
Q 011992          450 SRALYRLKQSLGGK  463 (473)
Q Consensus       450 ~RAL~KLR~~L~~~  463 (473)
                      ++|+++||+.+..+
T Consensus       167 ~rar~~Lr~~l~~~  180 (181)
T PRK12536        167 HRGLKALAAKIRGE  180 (181)
T ss_pred             HHHHHHHHHHhcCC
Confidence            99999999988754

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.70  E-value=2.9e-16  Score=150.27  Aligned_cols=131  Identities=22%  Similarity=0.287  Sum_probs=114.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------  383 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------  383 (473)
                      .+++.|+..|++.+++++.++.++..+++|++||+|+.+|++..+|++.   .|.+                        
T Consensus        28 ~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~~---~~~~wL~~iarn~~~d~~Rk~~~~~~~~  104 (203)
T PRK09647         28 PSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPG---TFEGWLHRITTNLFLDMVRRRARIRMEA  104 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc---ccHHHHHHHHHHHHHHHHHhcccCcccc
Confidence            8999999999999999999999999999999999999999999999752   3544                        


Q ss_pred             ---------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          384 ---------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       384 ---------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                               .....|+..+...+....|..+|..||++++.||.|+|+    +|++++|||+.||+|.++|++.++||++
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RArk  180 (203)
T PRK09647        105 LPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDI----EGLSYEEIAATLGVKLGTVRSRIHRGRQ  180 (203)
T ss_pred             ccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                     001233445556667788999999999999999999999    9999999999999999999999999999


Q ss_pred             HHHHHhccCch
Q 011992          455 RLKQSLGGKAS  465 (473)
Q Consensus       455 KLR~~L~~~~l  465 (473)
                      +||+.+....-
T Consensus       181 ~Lr~~l~~~~~  191 (203)
T PRK09647        181 QLRAALAAHAP  191 (203)
T ss_pred             HHHHHHHHhch
Confidence            99999976543

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

Probab=99.69  E-value=4.4e-16  Score=136.53  Aligned_cols=127  Identities=27%  Similarity=0.438  Sum_probs=110.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------C------
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------T------  384 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------~------  384 (473)
                      .+++.++..|.++|+++++++.++..+++|++||+++++|++++.|++.  ..|.+                 .      
T Consensus         1 ~a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~~~~~~   78 (158)
T TIGR02937         1 EAFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRREL   78 (158)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhccCCcch
Confidence            3688999999999999999999999999999999999999999999887  45655                 1      


Q ss_pred             --------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992          385 --------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  456 (473)
Q Consensus       385 --------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL  456 (473)
                              ....++...........|.++|+.||++++.||.++|+    .|++..|||+.+|+|+++|+++..+++++|
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl  154 (158)
T TIGR02937        79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKL  154 (158)
T ss_pred             hhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                    01234444555667778999999999999999999988    899999999999999999999999999999


Q ss_pred             HHHh
Q 011992          457 KQSL  460 (473)
Q Consensus       457 R~~L  460 (473)
                      |+.+
T Consensus       155 ~~~l  158 (158)
T TIGR02937       155 RELL  158 (158)
T ss_pred             HhhC
Confidence            9864

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

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

Probab=99.69  E-value=1.5e-16  Score=149.60  Aligned_cols=130  Identities=19%  Similarity=0.169  Sum_probs=108.6

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------C-C
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------T-G  385 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~-~  385 (473)
                      ..+|+.|+..|.+.|+++|.++.++..+++|++||+|+.+|+++.+|++..  .|.+                    . .
T Consensus        10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~~--~~~~wL~~iarN~~~d~~Rk~~~~~~~   87 (193)
T TIGR02947        10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGT--NLKAWLYRILTNTYINSYRKAQRRPQQ   87 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCCC--cchHHHHHHHHHHHHHHHHHhcCCccc
Confidence            478999999999999999999999999999999999999999999997542  4554                    0 0


Q ss_pred             C--C-------------------CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHH
Q 011992          386 V--E-------------------IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKER  444 (473)
Q Consensus       386 ~--~-------------------~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~r  444 (473)
                      .  .                   .++......+....|..+|..||+++|.||.|+|+    +|+|++|||+.||+|.++
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~----~g~s~~EIA~~lgis~~t  163 (193)
T TIGR02947        88 SDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADV----EGFAYKEIAEIMGTPIGT  163 (193)
T ss_pred             ccchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhh----cCCCHHHHHHHHCCCHHH
Confidence            0  0                   00011111223467899999999999999999999    999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcc
Q 011992          445 VRQLESRALYRLKQSLGG  462 (473)
Q Consensus       445 Vrqi~~RAL~KLR~~L~~  462 (473)
                      |+.+++||+++||+.+..
T Consensus       164 Vk~~l~Rar~~Lr~~l~~  181 (193)
T TIGR02947       164 VMSRLHRGRKQLRKQLVD  181 (193)
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999999999999999864

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.

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.69  E-value=4.2e-16  Score=143.10  Aligned_cols=131  Identities=18%  Similarity=0.130  Sum_probs=108.6

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------C
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------T  384 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------~  384 (473)
                      ...|..+|..|.+.|+++|+++.++..++||++||+|+.+|+.++.|+...  .|.+                      .
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~   82 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQD   82 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            357889999999999999999999999999999999999999999997533  3544                      0


Q ss_pred             C------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          385 G------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       385 ~------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .      ...+............+..+|..||+++|+||.|+|+    +|++++|||+.||+|.++|++.++||+++||.
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~  158 (164)
T PRK12547         83 SDGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGA----SGFSYEDAAAICGCAVGTIKSRVSRARNRLQE  158 (164)
T ss_pred             ccccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            0      0001111122334567899999999999999999999    99999999999999999999999999999999


Q ss_pred             HhccC
Q 011992          459 SLGGK  463 (473)
Q Consensus       459 ~L~~~  463 (473)
                      .+...
T Consensus       159 ~l~~~  163 (164)
T PRK12547        159 LLKVD  163 (164)
T ss_pred             HHhcc
Confidence            88643

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.68  E-value=6.8e-16  Score=140.81  Aligned_cols=125  Identities=16%  Similarity=0.077  Sum_probs=104.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------  383 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------  383 (473)
                      .+++.|+..|.+.|+++|.++.++..+++|++||+|+.+|+..+.|++.   .|.+                        
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~~   80 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLERAYL   80 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            5889999999999999999999999999999999999999998877542   2433                        


Q ss_pred             ---CC-----CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992          384 ---TG-----VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  455 (473)
Q Consensus       384 ---~~-----~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K  455 (473)
                         ..     ...++......+....|..+|..||+++|.||.|+|+    +|++++|||+.||+|.++|+..+++|+++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----~g~s~~EIA~~l~is~~tV~~~l~ra~~~  156 (161)
T PRK12528         81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQV----DGLGYGEIATELGISLATVKRYLNKAAMR  156 (161)
T ss_pred             HHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence               00     0112222333344568899999999999999999999    99999999999999999999999999999


Q ss_pred             HHHH
Q 011992          456 LKQS  459 (473)
Q Consensus       456 LR~~  459 (473)
                      |+..
T Consensus       157 ~~~~  160 (161)
T PRK12528        157 CYFA  160 (161)
T ss_pred             HHhc
Confidence            9975

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=8.9e-16  Score=140.01  Aligned_cols=126  Identities=17%  Similarity=0.139  Sum_probs=105.4

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------  383 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------  383 (473)
                      ..+++.++..|.+.|+++|.++.++..+++|++||+|+.+|+.+++|++.   .|.+                       
T Consensus         4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~   80 (161)
T PRK12541          4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT   80 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc
Confidence            36899999999999999999999999999999999999999999999753   3655                       


Q ss_pred             --CC-----CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992          384 --TG-----VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  456 (473)
Q Consensus       384 --~~-----~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL  456 (473)
                        ..     ...++...........+..+|..||+++|.||.|+|.    ++++++|||+.||+|.++|++.++||+++|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L  156 (161)
T PRK12541         81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDY----YGFSYKEIAEMTGLSLAKVKIELHRGRKET  156 (161)
T ss_pred             chhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence              00     0112222222233345668999999999999999999    999999999999999999999999999999


Q ss_pred             HHH
Q 011992          457 KQS  459 (473)
Q Consensus       457 R~~  459 (473)
                      |+.
T Consensus       157 ~~~  159 (161)
T PRK12541        157 KSI  159 (161)
T ss_pred             Hhh
Confidence            975

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.67  E-value=1.3e-15  Score=139.12  Aligned_cols=128  Identities=20%  Similarity=0.200  Sum_probs=108.7

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------  383 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------  383 (473)
                      ..+++.|+..|.+.|+++|+++.++..+++|++||+|+.+|++  .|+.  +..|.+                       
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            3579999999999999999999999999999999999999998  5653  234554                       


Q ss_pred             ----------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          384 ----------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       384 ----------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                                .....|++.....+....+..+|..||+++|.||.++|     +|++++|||+.||+|.++|+..+.||+
T Consensus        78 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~  152 (166)
T PRK09639         78 ILGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAK  152 (166)
T ss_pred             ccchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence                      01123455555566677899999999999999999998     599999999999999999999999999


Q ss_pred             HHHHHHhccC
Q 011992          454 YRLKQSLGGK  463 (473)
Q Consensus       454 ~KLR~~L~~~  463 (473)
                      ++||+.+...
T Consensus       153 ~~Lr~~l~~~  162 (166)
T PRK09639        153 KKFRKIYEQM  162 (166)
T ss_pred             HHHHHHHHHh
Confidence            9999988743

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=7.8e-16  Score=145.10  Aligned_cols=135  Identities=21%  Similarity=0.181  Sum_probs=111.9

Q ss_pred             HhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------
Q 011992          323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------  383 (473)
Q Consensus       323 l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------  383 (473)
                      +..+..+|+.+|..|.+.|+++|+++.++..+++|++||+|+.+|+.++.|.+..  .|.+                   
T Consensus        18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~~~~~~r~~~~   95 (188)
T PRK12517         18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRENARRFERKQF   95 (188)
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHHHHHHHHHhcc
Confidence            3445689999999999999999999999999999999999999999999997542  3433                   


Q ss_pred             --CCC-----C-CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992          384 --TGV-----E-IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  455 (473)
Q Consensus       384 --~~~-----~-~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K  455 (473)
                        ...     . .+....+.....+.|..+|..||+++|.||.++|+    +|++++|||+.||||+++|+.+++||+++
T Consensus        96 ~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Rar~~  171 (188)
T PRK12517         96 DLVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVI----GGFSGEEIAEILDLNKNTVMTRLFRARNQ  171 (188)
T ss_pred             CccCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence              000     0 01111223334567999999999999999999999    99999999999999999999999999999


Q ss_pred             HHHHhccC
Q 011992          456 LKQSLGGK  463 (473)
Q Consensus       456 LR~~L~~~  463 (473)
                      ||+.+...
T Consensus       172 Lr~~l~~~  179 (188)
T PRK12517        172 LKEALEKP  179 (188)
T ss_pred             HHHHHHHH
Confidence            99998754

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=1.5e-15  Score=144.31  Aligned_cols=139  Identities=17%  Similarity=0.145  Sum_probs=111.4

Q ss_pred             HHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------
Q 011992          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------  383 (473)
Q Consensus       319 L~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------  383 (473)
                      +...+..++ .+++.||..|.+.++.++. +.++..+++|++||.|+.+|+..++|++..  .|.+              
T Consensus        15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~   91 (196)
T PRK12535         15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAARS--SARTWLLSLARRVWVDNI   91 (196)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCcc--cHHHHHHHHHHHHHHHHH
Confidence            433444444 8999999999999999975 578888999999999999999999997632  3444              


Q ss_pred             ------CC------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHH
Q 011992          384 ------TG------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERV  445 (473)
Q Consensus       384 ------~~------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rV  445 (473)
                            ..            ...++.. ...+....+..+|+.||+++|+||.|+|+    +|+|++|||+.||+|.++|
T Consensus        92 Rk~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIAe~lgis~~tV  166 (196)
T PRK12535         92 RHDMARPRKSATEYEDAAATTASNETT-GSWSEWIDVRTLIDALPPERREALILTQV----LGYTYEEAAKIADVRVGTI  166 (196)
T ss_pred             HhhccCCCcccccccccccccCCcchh-HHHHHHHHHHHHHHcCCHHHHHHhhhHHH----hCCCHHHHHHHhCCCHHHH
Confidence                  00            0111211 12223457899999999999999999999    9999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhccCch
Q 011992          446 RQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       446 rqi~~RAL~KLR~~L~~~~l  465 (473)
                      ++.++||+++||+.+.....
T Consensus       167 ~~~l~Rar~~Lr~~l~~~~~  186 (196)
T PRK12535        167 RSRVARARADLIAATATGQA  186 (196)
T ss_pred             HHHHHHHHHHHHHHhccccc
Confidence            99999999999999987643

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.67  E-value=5.6e-16  Score=143.52  Aligned_cols=134  Identities=16%  Similarity=0.088  Sum_probs=107.5

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHH--hhhhCccCCCcccc---------------------
Q 011992          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKS--VEKFKPQAGCRFAN---------------------  383 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kA--iekFDp~kg~~FsT---------------------  383 (473)
                      ..+++.++..|.+.+++++.++.++..+++|++||.|+.+|+.  +..+++.+++-|..                     
T Consensus         9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~~~~~~~~~~~~wL~~iarn~~~d~~R~~~~~~~~~~~   88 (172)
T PRK09651          9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEM   88 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhhcccccccCHHHHHHHHHHHHHHHHHHHHHHHhhhhhH
Confidence            4789999999999999999999999999999999999999987  33332212111111                     


Q ss_pred             ------CCCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          384 ------TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       384 ------~~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                            .....|+......+....+..+|+.||+++|.||.|+|+    +|+|++|||+.||+|.++|+..++||+.+|+
T Consensus        89 ~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~  164 (172)
T PRK09651         89 LALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQL----DGLTYSEIAHKLGVSVSSVKKYVAKATEHCL  164 (172)
T ss_pred             HhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhc----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence                  001233334444455678999999999999999999999    9999999999999999999999999999999


Q ss_pred             HHhccCc
Q 011992          458 QSLGGKA  464 (473)
Q Consensus       458 ~~L~~~~  464 (473)
                      ...-..+
T Consensus       165 ~~~~~~~  171 (172)
T PRK09651        165 LFRLEYG  171 (172)
T ss_pred             HHHHHcC
Confidence            8765543

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.66  E-value=4.5e-16  Score=140.17  Aligned_cols=121  Identities=22%  Similarity=0.212  Sum_probs=103.4

Q ss_pred             HHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------C---------
Q 011992          334 INANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------T---------  384 (473)
Q Consensus       334 i~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~---------  384 (473)
                      |..|.+.|+++++++.++..+++|++||+|+.+|+++++|++   ..|.+                    .         
T Consensus         1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~   77 (154)
T TIGR02950         1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGD   77 (154)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccHhhhhh
Confidence            357899999999999999999999999999999999999986   35655                    0         


Q ss_pred             ----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          385 ----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       385 ----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                          ....|+..+...+....|..+|+.||++++.||.++|+    +|++++|||+.||+|+++|++.++||+++||+.+
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~----~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l  153 (154)
T TIGR02950        78 LEQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREF----KEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL  153 (154)
T ss_pred             ccccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhh----ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence                01123444444555678999999999999999999998    9999999999999999999999999999999876


Q ss_pred             c
Q 011992          461 G  461 (473)
Q Consensus       461 ~  461 (473)
                      +
T Consensus       154 ~  154 (154)
T TIGR02950       154 E  154 (154)
T ss_pred             C
Confidence            3

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.

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

Probab=99.66  E-value=1.1e-15  Score=154.44  Aligned_cols=132  Identities=17%  Similarity=0.213  Sum_probs=110.3

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------C-
Q 011992          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------T-  384 (473)
Q Consensus       326 g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~-  384 (473)
                      +..+++.||..|.+.|+++|++++++..+++|++||.|+.+|+++++|+...  .|.+                    . 
T Consensus         3 d~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~   80 (324)
T TIGR02960         3 DGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRS--SVRTWLYRIATNACLDALEARQRRPR   80 (324)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCccc--chHHHHHHHHHHHHHHHHHhccCCcC
Confidence            4489999999999999999999999999999999999999999999997532  3444                    0 


Q ss_pred             --C--C---------------------------------CCchHHHHHHH-HHHHHHHHHhhCCHHHHHHHHHHhhccCC
Q 011992          385 --G--V---------------------------------EIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLRFGIEDG  426 (473)
Q Consensus       385 --~--~---------------------------------~~pee~le~~e-l~e~L~~aL~~LperER~VL~LrY~L~~g  426 (473)
                        .  .                                 ..|+..+...+ ....+..+|..||+++|.||.|+|+    
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~----  156 (324)
T TIGR02960        81 PVGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDV----  156 (324)
T ss_pred             ccccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHH----
Confidence              0  0                                 01222222233 3456889999999999999999999    


Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~  463 (473)
                      ++++++|||++||+|+++|+++++||+++||+.+...
T Consensus       157 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  193 (324)
T TIGR02960       157 LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSA  193 (324)
T ss_pred             hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999999999999999999998743

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.

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

Probab=99.66  E-value=1.3e-15  Score=143.48  Aligned_cols=127  Identities=13%  Similarity=0.097  Sum_probs=107.8

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C---C
Q 011992          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T---G  385 (473)
Q Consensus       332 ~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~---~  385 (473)
                      +.+..|.+.|+++|+++.++..+++|++||+|+.+|+..++|++.  ..|.+                       .   .
T Consensus         6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~~   83 (188)
T TIGR02943         6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLDD   83 (188)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccccc
Confidence            567789999999999999999999999999999999999999754  24443                       0   0


Q ss_pred             C-------------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCC
Q 011992          386 V-------------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGL  440 (473)
Q Consensus       386 ~-------------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGI  440 (473)
                      .                         ..|+..+...+....+..+|..||+++|+||.|+|+    ++++++|||+.||+
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~EIA~~lgi  159 (188)
T TIGR02943        84 ELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREV----LGFESDEICQELEI  159 (188)
T ss_pred             ccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHhCC
Confidence            0                         122344555566678999999999999999999999    99999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHhccCc
Q 011992          441 SKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       441 S~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      |.++|++++.||+++||+++....
T Consensus       160 s~~tvk~rl~Rar~~Lr~~l~~~~  183 (188)
T TIGR02943       160 STSNCHVLLYRARLSLRACLSINW  183 (188)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999987543

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.

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=1.5e-15  Score=142.63  Aligned_cols=129  Identities=21%  Similarity=0.219  Sum_probs=107.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------C--
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------T--  384 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------~--  384 (473)
                      .++..++..|++.|+++|.++.++..+++|++||+|+.+|+++++|++..  .|.+                     .  
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~   82 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVEDA   82 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhcccccccc
Confidence            46778999999999999999999999999999999999999999997543  3444                     0  


Q ss_pred             -C------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          385 -G------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       385 -~------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                       .      ...++.  ........|..+|+.||+++|+||.|+|+    +|+|++|||+.||+|.++|++.++||+++||
T Consensus        83 ~~~~~~~~~~~~~~--~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr  156 (182)
T PRK12540         83 DGSYAKTLKSQPGQ--NAHLEFEEFRAALDKLPQDQREALILVGA----SGFSYEDAAAICGCAVGTIKSRVNRARSKLS  156 (182)
T ss_pred             cccccccccCCCch--HHHHHHHHHHHHHHhCCHHHHHHhhHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence             0      011111  11223456899999999999999999999    9999999999999999999999999999999


Q ss_pred             HHhccCc
Q 011992          458 QSLGGKA  464 (473)
Q Consensus       458 ~~L~~~~  464 (473)
                      +.+....
T Consensus       157 ~~l~~~~  163 (182)
T PRK12540        157 ALLYVDG  163 (182)
T ss_pred             HHHHhcc
Confidence            9998654

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=1.5e-15  Score=142.95  Aligned_cols=126  Identities=17%  Similarity=0.104  Sum_probs=104.4

Q ss_pred             HHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------CC-----C
Q 011992          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------TG-----V  386 (473)
Q Consensus       333 Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------~~-----~  386 (473)
                      -|..|.+.++++|.++.++..+++|++||+|+.+|++++.|++..  .|.+                     ..     .
T Consensus        12 ~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~~~   89 (189)
T PRK12530         12 EIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNESELIEE   89 (189)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCccccccc
Confidence            356788899999999999999999999999999999999997643  3443                     00     0


Q ss_pred             -----------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHH
Q 011992          387 -----------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE  443 (473)
Q Consensus       387 -----------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~  443 (473)
                                             ..++..+...+....|..+|+.||+++|+||.|+|+    +|+|++|||+.||+|++
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----~g~s~~EIA~~lgis~~  165 (189)
T PRK12530         90 DSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREY----LELSSEQICQECDISTS  165 (189)
T ss_pred             ccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHH----cCCCHHHHHHHHCCCHH
Confidence                                   011223334455667899999999999999999999    99999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhccCc
Q 011992          444 RVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       444 rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      +|+.+++||+++||+++....
T Consensus       166 tVk~~l~RAr~~Lr~~l~~~~  186 (189)
T PRK12530        166 NLHVLLYRARLQLQACLSKNW  186 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999987543

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.65  E-value=1.6e-15  Score=138.16  Aligned_cols=122  Identities=13%  Similarity=0.104  Sum_probs=104.9

Q ss_pred             HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------------C--
Q 011992          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------------T--  384 (473)
Q Consensus       335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------------~--  384 (473)
                      ..|++.++.++.+++++..+++|++||+|+.+|+..+.|++.   .|.+                            .  
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~~   78 (159)
T PRK12527          2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEE   78 (159)
T ss_pred             hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhcccccchhhhhcc
Confidence            568889999999999999999999999999999999888642   4444                            0  


Q ss_pred             ---CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          385 ---GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       385 ---~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                         ....|+..+..++....|..+|..||++++.||.|+|+    +++|++|||+.||+|+++|+..+.||+++||+.+.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~  154 (159)
T PRK12527         79 ERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKL----EGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR  154 (159)
T ss_pred             ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence               01234555566666778999999999999999999999    99999999999999999999999999999999987


Q ss_pred             cC
Q 011992          462 GK  463 (473)
Q Consensus       462 ~~  463 (473)
                      ..
T Consensus       155 ~~  156 (159)
T PRK12527        155 QW  156 (159)
T ss_pred             hc
Confidence            54

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=1.5e-15  Score=144.41  Aligned_cols=127  Identities=17%  Similarity=0.140  Sum_probs=105.3

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------------C-CC-----
Q 011992          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------------T-GV-----  386 (473)
Q Consensus       332 ~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------------~-~~-----  386 (473)
                      .++..|.+.++++|++++++..+++|++||+|+.+|+++++|++..  .|.+                   . ..     
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~   89 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALDA   89 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            3588899999999999999999999999999999999999998653  3444                   0 00     


Q ss_pred             ----------------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992          387 ----------------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF  438 (473)
Q Consensus       387 ----------------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L  438 (473)
                                                  ..++......+....+..+|..||+++|.||.|+|+    +|++++|||+.|
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----eg~s~~EIA~~l  165 (201)
T PRK12545         90 ELDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREF----LDFEIDDICTEL  165 (201)
T ss_pred             ccchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHH
Confidence                                        011222233344457889999999999999999999    999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992          439 GLSKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       439 GIS~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      |+|+++|+..+.||+++||+.+...+
T Consensus       166 gis~~tVk~~l~RAr~~Lr~~l~~~~  191 (201)
T PRK12545        166 TLTANHCSVLLYRARTRLRTCLSEKG  191 (201)
T ss_pred             CcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999996543

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.65  E-value=1.6e-15  Score=138.21  Aligned_cols=125  Identities=15%  Similarity=0.185  Sum_probs=104.7

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------C---
Q 011992          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------T---  384 (473)
Q Consensus       332 ~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------~---  384 (473)
                      .++..|.+.++++|.++.++..+++|++||+++++|+....|++..   |.+                        .   
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~---~~~wl~~iarn~~~d~~R~~~~~~~~~~~~~   78 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQ---PVAYLFRIVRNLAIDHYRRQALENKYHGDEE   78 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCccc---HHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            3677899999999999999999999999999999999887775432   222                        0   


Q ss_pred             -------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          385 -------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       385 -------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                             ....++..+...+..+.+..+|..||+++|.||.++|+    +++|++|||+.||+|.++|+..+.||+++||
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr  154 (163)
T PRK07037         79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRL----HGETQKDIARELGVSPTLVNFMIRDALVHCR  154 (163)
T ss_pred             cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence                   01233444455566678899999999999999999999    9999999999999999999999999999999


Q ss_pred             HHhccC
Q 011992          458 QSLGGK  463 (473)
Q Consensus       458 ~~L~~~  463 (473)
                      +.+...
T Consensus       155 ~~l~~~  160 (163)
T PRK07037        155 KCLDAC  160 (163)
T ss_pred             HHHhcc
Confidence            998654

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.65  E-value=2.1e-15  Score=153.93  Aligned_cols=136  Identities=19%  Similarity=0.192  Sum_probs=110.8

Q ss_pred             HHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-------------
Q 011992          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-------------  383 (473)
Q Consensus       318 eL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-------------  383 (473)
                      +|...+..|+ .+++.||..|.+.|+++|+++.++..+++|++||+|+.+|+.+++|++.  ..|.+             
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            3444444444 9999999999999999999999999999999999999999999999743  23443             


Q ss_pred             --------C---CC-------------------------------CCchHHHHHHH-HHHHHHHHHhhCCHHHHHHHHHH
Q 011992          384 --------T---GV-------------------------------EIPDISVQKQL-MRQHVRNLLTLLNPKERCIVRLR  420 (473)
Q Consensus       384 --------~---~~-------------------------------~~pee~le~~e-l~e~L~~aL~~LperER~VL~Lr  420 (473)
                              .   ..                               ..|+..+...+ ....|..+|..||+++|.||.|+
T Consensus        86 ~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~  165 (339)
T PRK08241         86 LEGRARRPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILR  165 (339)
T ss_pred             HHhhccccCccccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhH
Confidence                    0   00                               01222223223 34568899999999999999999


Q ss_pred             hhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          421 FGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       421 Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      |+    +++|++|||++||+|.++|+++++||+++||+.
T Consensus       166 ~~----~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~  200 (339)
T PRK08241        166 DV----LGWSAAEVAELLDTSVAAVNSALQRARATLAER  200 (339)
T ss_pred             Hh----hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence            99    999999999999999999999999999999994

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=1.6e-15  Score=142.83  Aligned_cols=128  Identities=18%  Similarity=0.178  Sum_probs=107.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCcc-hhhHhhhhHHHHHHHhhhhCccCCCcccc---------------------CC---
Q 011992          331 EKLINANLRLVVHVAKQYQGRGIS-LHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------------TG---  385 (473)
Q Consensus       331 e~Li~~yl~lV~sIA~ry~~~~~s-aEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------------~~---  385 (473)
                      +..+..|.+.|+++|+++.++..+ ++|++||+|+.+|+++++|+..  ..|.+                     ..   
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            355678899999999999999888 9999999999999999999753  24544                     00   


Q ss_pred             ----------------------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHH
Q 011992          386 ----------------------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI  437 (473)
Q Consensus       386 ----------------------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~  437 (473)
                                                  ...|+..+...+....+..+|..||+++|+||.|+|+    +|+|++|||+.
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~----~g~s~~EIA~~  161 (195)
T PRK12532         86 LDDELLDEAFESHFSQNGHWTPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEI----LGFSSDEIQQM  161 (195)
T ss_pred             ccccccchhhhhhhccccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHH----hCCCHHHHHHH
Confidence                                        0123344445566678999999999999999999999    99999999999


Q ss_pred             HCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992          438 FGLSKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       438 LGIS~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      ||+|.++|+++++||+++||+++....
T Consensus       162 lgis~~tVk~~l~Rar~~Lr~~l~~~~  188 (195)
T PRK12532        162 CGISTSNYHTIMHRARESLRQCLQIKW  188 (195)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999997554

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.65  E-value=2.8e-15  Score=140.54  Aligned_cols=128  Identities=18%  Similarity=0.127  Sum_probs=109.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------------
Q 011992          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------------  383 (473)
Q Consensus       330 ~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------------  383 (473)
                      ++.|+..|.+.|++++.++.++..+++|++||+++.+|+.+..|+..  ..|.+                          
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~   80 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELPDD   80 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence            67899999999999999999999999999999999999999999753  35655                          


Q ss_pred             C-CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          384 T-GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       384 ~-~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      . ....++......+....+..+|+.||+++|.||.|+|+    +|+++.|||++||+|.++|+.++.||+++||+.+..
T Consensus        81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~----~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  156 (181)
T PRK09637         81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTEL----EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG  156 (181)
T ss_pred             hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            0 01122333444556678999999999999999999999    999999999999999999999999999999998875


Q ss_pred             C
Q 011992          463 K  463 (473)
Q Consensus       463 ~  463 (473)
                      .
T Consensus       157 ~  157 (181)
T PRK09637        157 C  157 (181)
T ss_pred             c
Confidence            3

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=2.8e-15  Score=143.73  Aligned_cols=127  Identities=19%  Similarity=0.202  Sum_probs=108.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc--------------------CC----C
Q 011992          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN--------------------TG----V  386 (473)
Q Consensus       331 e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT--------------------~~----~  386 (473)
                      ..++..|.+.|+++|+++.++...++|++||+|+.+|+.+.+|+..  ..|.+                    ..    .
T Consensus        21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~~   98 (206)
T PRK12544         21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSLL   98 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccccccc
Confidence            4688899999999999999999999999999999999999999754  23544                    00    0


Q ss_pred             ----------------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH
Q 011992          387 ----------------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF  438 (473)
Q Consensus       387 ----------------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~L  438 (473)
                                                  ..|+..+...+....+..+|..||+++|+||.|+|+    ++++++|||+.|
T Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~----~g~s~~EIAe~l  174 (206)
T PRK12544         99 RDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREF----IELETNEICHAV  174 (206)
T ss_pred             cccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHH
Confidence                                        123334445555567899999999999999999999    999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhccC
Q 011992          439 GLSKERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       439 GIS~~rVrqi~~RAL~KLR~~L~~~  463 (473)
                      |+|.++|++.++||+++||+.+...
T Consensus       175 gis~~tV~~~l~RAr~~Lr~~l~~~  199 (206)
T PRK12544        175 DLSVSNLNVLLYRARLRLRECLENK  199 (206)
T ss_pred             CcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999998753

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=5.8e-15  Score=136.08  Aligned_cols=127  Identities=14%  Similarity=0.078  Sum_probs=107.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------  383 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------  383 (473)
                      ..+..++..|++.++++|.++.++..+++|++||+|+.+|+....++.   ..|.+                        
T Consensus         9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~~   85 (168)
T PRK12525          9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAYL   85 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678899999999999999999999999999999999999986554432   13433                        


Q ss_pred             ---C-----CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992          384 ---T-----GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  455 (473)
Q Consensus       384 ---~-----~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K  455 (473)
                         .     ....|+..+...+....|..+|..||+++|.||.|+|+    +|+|++|||+.||+|+++|+..+.+|+++
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~----eg~s~~EIA~~l~is~~tV~~~l~ra~~~  161 (168)
T PRK12525         86 QSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQL----EGLTYVEIGERLGVSLSRIHQYMVEAFKC  161 (168)
T ss_pred             HHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence               0     01244444555566778999999999999999999999    99999999999999999999999999999


Q ss_pred             HHHHhc
Q 011992          456 LKQSLG  461 (473)
Q Consensus       456 LR~~L~  461 (473)
                      ||..+.
T Consensus       162 ~~~~~~  167 (168)
T PRK12525        162 CYQGFQ  167 (168)
T ss_pred             HHHhhc
Confidence            998764

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.62  E-value=4.8e-15  Score=137.18  Aligned_cols=122  Identities=17%  Similarity=0.152  Sum_probs=103.8

Q ss_pred             HHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------------------C---CCC
Q 011992          335 NANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------------------T---GVE  387 (473)
Q Consensus       335 ~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------------------~---~~~  387 (473)
                      ..|.+.++.+++++.++..+++|++||+|+.+|+++++|+..  ..|.+                        .   ...
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~   79 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD   79 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence            468889999999999999999999999999999999999853  35655                        0   011


Q ss_pred             CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          388 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       388 ~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      .+++.....+....|..+|..||+++|.||.|+|+    ++++++|||+.||+|.++|++.++||+++||..+..
T Consensus        80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  150 (170)
T TIGR02959        80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTEL----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET  150 (170)
T ss_pred             CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            23333444556678999999999999999999999    999999999999999999999999999999999864

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=99.61  E-value=7.6e-15  Score=138.74  Aligned_cols=129  Identities=18%  Similarity=0.176  Sum_probs=103.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------CC
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------TG  385 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------~~  385 (473)
                      ..++.|+. |.+.|+++|+.++++..+++|++||+|+.+|+++..|+..  ..|.+                      ..
T Consensus         8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~~   84 (188)
T PRK12546          8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPDP   84 (188)
T ss_pred             hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccCc
Confidence            34555544 7799999999999999999999999999999999999753  24544                      00


Q ss_pred             CC------CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          386 VE------IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       386 ~~------~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      ..      ..............+..+|..||+++|.||.|+|+    +|++++|||+.||||.++|++++.||+++||+.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~  160 (188)
T PRK12546         85 EGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGA----SGFSYEEAAEMCGVAVGTVKSRANRARARLAEL  160 (188)
T ss_pred             ccccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHh----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            00      00001112233457899999999999999999999    999999999999999999999999999999999


Q ss_pred             hccC
Q 011992          460 LGGK  463 (473)
Q Consensus       460 L~~~  463 (473)
                      +...
T Consensus       161 l~~~  164 (188)
T PRK12546        161 LQLE  164 (188)
T ss_pred             Hhcc
Confidence            8753

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.61  E-value=1e-14  Score=137.13  Aligned_cols=128  Identities=13%  Similarity=0.124  Sum_probs=104.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------CC---
Q 011992          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------TG---  385 (473)
Q Consensus       331 e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------~~---  385 (473)
                      ...+..+++.|+.+|.++.++..+++|++||+|+.+|+++..|+...  .|.+                      ..   
T Consensus         7 ~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~~~~~   84 (182)
T PRK12511          7 RFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSGG--NLRTWLMSILHNAFIDELRRRRVEARRADEL   84 (182)
T ss_pred             hhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHhhccccccccch
Confidence            44577899999999999999999999999999999999999997532  4544                      00   


Q ss_pred             ----CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          386 ----VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       386 ----~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                          ...+............|..+|..||+++|.||.|+|+    +|+|++|||+.||||.++|++.++||+++||+.+.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~  160 (182)
T PRK12511         85 AVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAI----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE  160 (182)
T ss_pred             hhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence                0011111222334567889999999999999999999    99999999999999999999999999999999987


Q ss_pred             cCc
Q 011992          462 GKA  464 (473)
Q Consensus       462 ~~~  464 (473)
                      ..+
T Consensus       161 ~~~  163 (182)
T PRK12511        161 GTG  163 (182)
T ss_pred             hcC
Confidence            543

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.56  E-value=2.4e-14  Score=140.05  Aligned_cols=132  Identities=18%  Similarity=0.157  Sum_probs=103.2

Q ss_pred             HHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------
Q 011992          319 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------  383 (473)
Q Consensus       319 L~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------  383 (473)
                      +.+.+..+..+++.++..| +.++++|.++.++..++||++||+|+.+|+..+..+     .|.+               
T Consensus         9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~~~~~~-----~~~~WL~~IarN~~id~~R   82 (228)
T PRK06704          9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQKYSNKD-----ICMTLVYKIARNRWLDQIK   82 (228)
T ss_pred             HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCccc-----cHHHHHHHHHHHHHHHHHh
Confidence            3444444556777777766 789999999999999999999999999998643322     2333               


Q ss_pred             --C---------CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          384 --T---------GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       384 --~---------~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                        .         ....+..  ...+..+.+..+|+.||+++|.||.|+|+    +++|++|||+.||+|+++|+.++.||
T Consensus        83 k~k~~~~~~~~~~~~~~~~--~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~----eg~S~~EIAe~LgiS~~tVksrL~Ra  156 (228)
T PRK06704         83 SKSVHEKIRDQITFEEPHE--KIADLHEMVGKVLSSLNVQQSAILLLKDV----FQYSIADIAKVCSVSEGAVKASLFRS  156 (228)
T ss_pred             ccccccccccccccCChHH--HHHHHHHHHHHHHHhCCHHHhhHhhhHHh----hCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence              0         0011111  12234567899999999999999999999    99999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q 011992          453 LYRLKQSLGG  462 (473)
Q Consensus       453 L~KLR~~L~~  462 (473)
                      +++||+.+..
T Consensus       157 rk~Lr~~l~~  166 (228)
T PRK06704        157 RNRLKTVSEE  166 (228)
T ss_pred             HHHHHHHHHh
Confidence            9999999865

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.55  E-value=5.3e-14  Score=141.34  Aligned_cols=127  Identities=19%  Similarity=0.156  Sum_probs=103.3

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T  384 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~  384 (473)
                      ..+..++..|.+.++++|++++++..++||++||+|+. |.....|+.   ..|.+                       .
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~   79 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRETY   79 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhcccccc
Confidence            34678999999999999999999999999999999999 666666642   23444                       0


Q ss_pred             -C----------CCCchHHH-HHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          385 -G----------VEIPDISV-QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       385 -~----------~~~pee~l-e~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                       .          ...|++.. ...+....+..+|+.||+++|.||.|+|+    ++++++|||++||+|+++|+++++||
T Consensus        80 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVk~~l~RA  155 (293)
T PRK09636         80 VGPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDV----FGVPFDEIASTLGRSPAACRQLASRA  155 (293)
T ss_pred             cCCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence             0          01122222 23444567899999999999999999999    99999999999999999999999999


Q ss_pred             HHHHHHHhcc
Q 011992          453 LYRLKQSLGG  462 (473)
Q Consensus       453 L~KLR~~L~~  462 (473)
                      +++||+.+..
T Consensus       156 r~~Lr~~~~~  165 (293)
T PRK09636        156 RKHVRAARPR  165 (293)
T ss_pred             HHHHHhhCCC
Confidence            9999998753

>PRK09191 two-component response regulator; Provisional

Probab=99.50  E-value=1.8e-13  Score=132.39  Aligned_cols=124  Identities=16%  Similarity=0.130  Sum_probs=103.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc------------C--CCCCchHHHH
Q 011992          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN------------T--GVEIPDISVQ  394 (473)
Q Consensus       329 A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT------------~--~~~~pee~le  394 (473)
                      ++..+|..|.+.++++|.++.++..+++|++||+|+.+|+....|++..  .|.+            .  ....+..   
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~~~~~~~~~~~~~---   76 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLWSSAGANDPEPGS---   76 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHhccccccCCCCCC---
Confidence            5788999999999999999999999999999999999999999997632  2333            0  0000110   


Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992          395 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       395 ~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~  463 (473)
                        .....+..+|..||+++|.||.|+|+    +++|++|||+.||+|+++|+.++.+|+++||..+...
T Consensus        77 --~~~~~l~~~l~~L~~~~r~v~~l~~~----~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~~  139 (261)
T PRK09191         77 --PFEARAERRLAGLTPLPRQAFLLTAL----EGFSVEEAAEILGVDPAEAEALLDDARAEIARQVATR  139 (261)
T ss_pred             --CchHHHHHHHHhCCHHHhHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCCe
Confidence              01127899999999999999999999    9999999999999999999999999999999877643

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.48  E-value=2.5e-13  Score=137.17  Aligned_cols=126  Identities=18%  Similarity=0.095  Sum_probs=103.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T  384 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~  384 (473)
                      ..+..+|..|.+.++++|++++++..++||++||+|+.+|++...+.    ..|.+                       .
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~~----~~~~aWL~~Ia~n~~id~lRk~~~rr~~~   80 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDI----DDERGWLIVVTSRLCLDHIKSASTRRERP   80 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCcccc----ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence            56788999999999999999999999999999999999998765421    12222                       0


Q ss_pred             --C-C----------CCchH-HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          385 --G-V----------EIPDI-SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       385 --~-~----------~~pee-~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                        . .          ..|++ .....+....+..+|+.|||++|.||.|+|+    .+++++|||++||+|+++|+++++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~----~g~s~~EIA~~Lgis~~tVr~~l~  156 (290)
T PRK09635         81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEI----FGLPYQQIATTIGSQASTCRQLAH  156 (290)
T ss_pred             ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHH----hCCCHHHHHHHHCcCHHHHHHHHH
Confidence              0 0          11222 2334555678999999999999999999999    999999999999999999999999


Q ss_pred             HHHHHHHHHhc
Q 011992          451 RALYRLKQSLG  461 (473)
Q Consensus       451 RAL~KLR~~L~  461 (473)
                      ||+++||....
T Consensus       157 RAr~~Lr~~~~  167 (290)
T PRK09635        157 RARRKINESRI  167 (290)
T ss_pred             HHHHHHHhhCC
Confidence            99999998654

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

Probab=99.48  E-value=3.2e-13  Score=135.21  Aligned_cols=122  Identities=25%  Similarity=0.193  Sum_probs=97.9

Q ss_pred             HHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------C-C--
Q 011992          332 KLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------T-G--  385 (473)
Q Consensus       332 ~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------~-~--  385 (473)
                      ++|..|.+.++++|+++.++..++||++||+|+.+++.  .|+..  ..|.+                       . .  
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~   76 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREVYVGPW   76 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence            36889999999999999999999999999999997764  34321  23433                       0 0  


Q ss_pred             --------CCCchHHHHH-HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992          386 --------VEIPDISVQK-QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  456 (473)
Q Consensus       386 --------~~~pee~le~-~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL  456 (473)
                              ...|++.+.. +.+...+..+|+.||+++|.||.|+|+    ++++++|||+.||+|+++|+++++||+++|
T Consensus        77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~----~g~s~~EIA~~lg~s~~tVr~~l~RAr~~L  152 (281)
T TIGR02957        77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREV----FDYPYEEIASIVGKSEANCRQLVSRARRHL  152 (281)
T ss_pred             CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                    0123333332 334557888999999999999999999    999999999999999999999999999999


Q ss_pred             HHHhc
Q 011992          457 KQSLG  461 (473)
Q Consensus       457 R~~L~  461 (473)
                      |+...
T Consensus       153 r~~~~  157 (281)
T TIGR02957       153 DARRP  157 (281)
T ss_pred             HhhCC
Confidence            99765

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.

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.47  E-value=3.8e-13  Score=121.97  Aligned_cols=108  Identities=19%  Similarity=0.235  Sum_probs=86.3

Q ss_pred             cCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc----------------------CC---------C------------
Q 011992          350 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN----------------------TG---------V------------  386 (473)
Q Consensus       350 ~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT----------------------~~---------~------------  386 (473)
                      ++..+++|++||+|+.+|+.+..+ +  +..|.+                      ..         .            
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSLFSSFSDDDDDDDFDPLETLD   78 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccccccccccccccccccHHHHhc
Confidence            345678999999999999987763 2  233443                      00         0            


Q ss_pred             ------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          387 ------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       387 ------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                            ..|+..+...+....|..+|..||+++|.||.|+|+    +|+|++|||+.||+|.++|+.++.||+++||+.+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l  154 (161)
T PRK09047         79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKAL  154 (161)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence                  122333444556678999999999999999999999    9999999999999999999999999999999999


Q ss_pred             ccCc
Q 011992          461 GGKA  464 (473)
Q Consensus       461 ~~~~  464 (473)
                      ...+
T Consensus       155 ~~~~  158 (161)
T PRK09047        155 EAKG  158 (161)
T ss_pred             HhcC
Confidence            7654

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=99.46  E-value=2.9e-13  Score=134.80  Aligned_cols=115  Identities=25%  Similarity=0.434  Sum_probs=88.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHHHHHHHH--
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNL--  405 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~e~L~~a--  405 (473)
                      .++++||..|+++|.++|++|.+++++++||+|+|++||++|+++|||.+|++|+|+..++....+     ...|.+.  
T Consensus        40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I-----~~~lr~~~~  114 (264)
T PRK07122         40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEV-----RRHFRDNSW  114 (264)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH-----HHHHHHcCC
Confidence            478999999999999999999999999999999999999999999999999999997766533332     2222221  


Q ss_pred             HhhCCHHHHHHH----------HHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          406 LTLLNPKERCIV----------RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       406 L~~LperER~VL----------~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +=.+|-+-+..+          .-.+    |...|..|||+.||++...|.+++..
T Consensus       115 ~ir~Pr~~~~~~~~i~~~~~~l~~~l----g~~pt~~eiA~~lg~~~~~v~~~~~~  166 (264)
T PRK07122        115 SVKVPRRLKELHLRLGRATAELSQRL----GRAPTASELAAELGMDREEVVEGLVA  166 (264)
T ss_pred             ccccCHHHHHHHHHHHHHHHHHHHHh----CCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            011443332221          1123    48899999999999999999987654

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

Probab=99.39  E-value=1.4e-12  Score=127.50  Aligned_cols=118  Identities=30%  Similarity=0.514  Sum_probs=87.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHHHHHHHHHh-
Q 011992          329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLT-  407 (473)
Q Consensus       329 A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~e~L~~aL~-  407 (473)
                      |+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||.+|++|+|+..++....+.     ..+.+... 
T Consensus         1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~-----~~l~~~~~~   75 (238)
T TIGR02393         1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAIT-----RAIADQART   75 (238)
T ss_pred             CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHH-----HHHHHcCCc
Confidence            578999999999999999999999999999999999999999999999999999977665433322     22211111 


Q ss_pred             -hCCHHHHHH----HHHH--hhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 -LLNPKERCI----VRLR--FGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 -~LperER~V----L~Lr--Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                       .+|..-+..    ....  +.-..|.++|.+|||+.||++...|.++...
T Consensus        76 vrip~~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~  126 (238)
T TIGR02393        76 IRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKI  126 (238)
T ss_pred             EEeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence             133332211    1110  0011248999999999999999999987553

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.

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.30  E-value=1.7e-11  Score=109.68  Aligned_cols=106  Identities=12%  Similarity=0.135  Sum_probs=80.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhh-----hCccCCCcccc-------------------C-
Q 011992          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEK-----FKPQAGCRFAN-------------------T-  384 (473)
Q Consensus       330 ~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiek-----FDp~kg~~FsT-------------------~-  384 (473)
                      |+.||..|.+.++++|+++...    ++ +||.++.+|..+.+     |++.  ..|.+                   . 
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            4679999999999999998652    23 49999999998865     4332  24544                   0 


Q ss_pred             CC----------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHH
Q 011992          385 GV----------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVR  446 (473)
Q Consensus       385 ~~----------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVr  446 (473)
                      ..          ..+.+.+...+....+.++|+.||+++|+||.|+|+    +|+|++|||++||+|.++|+
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~----~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        74 KIIYNSEITDIKLSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKFF----EDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             hhhhhhhhhccccchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHhhc
Confidence            00          011223334445567899999999999999999999    99999999999999999996

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.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=99.30  E-value=2.4e-11  Score=120.56  Aligned_cols=115  Identities=23%  Similarity=0.344  Sum_probs=85.3

Q ss_pred             chHHHHHHHHHHHHHHHHHHHhhc---CCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHHHHHH
Q 011992          327 NSSREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVR  403 (473)
Q Consensus       327 ~~A~e~Li~~yl~lV~sIA~ry~~---~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~e~L~  403 (473)
                      ..|++.||..|+++|+++|++|.+   .+++++||+|+|++|||+++++|||++|++|.|+...+....+.     ..++
T Consensus        22 ~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~-----~~lr   96 (257)
T PRK05911         22 IEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAII-----DDLR   96 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHH-----HHHH
Confidence            389999999999999999999852   35679999999999999999999999999999865544333222     2222


Q ss_pred             HHHhhCCHHHHH----H------HHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          404 NLLTLLNPKERC----I------VRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       404 ~aL~~LperER~----V------L~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +. ..+|..-+.    +      +.-.++    ..+|..|||+.||++.+.|..+...
T Consensus        97 ~~-~~~pr~~~~~~~~l~~~~~~l~~~~g----r~pt~~eiA~~l~i~~~~v~~~~~~  149 (257)
T PRK05911         97 KQ-DWVPRSVHQKANKLADAMDSLRQSLG----KEPTDGELCEYLNISQQELSGWFSS  149 (257)
T ss_pred             hc-CCCCHHHHHHHHHHHHHHHHHHHHHC----cCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            11 123332211    1      222344    8899999999999999999887654

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.24  E-value=2.2e-11  Score=91.38  Aligned_cols=50  Identities=36%  Similarity=0.628  Sum_probs=46.5

Q ss_pred             HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ||+.||++|+.||.++|+    +++|+.|||+.||+|.++|++++.+|++|||+
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            688999999999999999    99999999999999999999999999999995

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 ....

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

Probab=99.21  E-value=5.8e-11  Score=117.51  Aligned_cols=129  Identities=25%  Similarity=0.408  Sum_probs=89.3

Q ss_pred             HHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCc-chhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHH
Q 011992          319 LKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI-SLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQ  396 (473)
Q Consensus       319 L~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~-saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~  396 (473)
                      +......|+ .++ .||.+|+|+|.++|++|.+.+. ..|||+|-|++||++|+++||+.+|.+|+|+........+.+.
T Consensus        14 ~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~   92 (247)
T COG1191          14 LLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDY   92 (247)
T ss_pred             HHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHH
Confidence            444444555 777 9999999999999999987766 9999999999999999999999999999996543322222111


Q ss_pred             HHHH---HHHHHHhhCCHHHH---HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          397 LMRQ---HVRNLLTLLNPKER---CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       397 el~e---~L~~aL~~LperER---~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ....   ++-.-+..+..+-.   .-+...++    .+.|..|||+.|||+..-|.+.+...
T Consensus        93 LR~~~~v~vpR~~~~~~~~i~~~~~~l~~el~----r~pt~~EIA~~L~i~~ee~~~~~~~~  150 (247)
T COG1191          93 LRKNDSVKVPRSLRELGRRIEEAIDELEQELG----REPTDEEIAEELGIDKEEYIEALLAI  150 (247)
T ss_pred             HHhCCCccCcHHHHHHHHHHHHHHHHHHHHhC----CCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence            1110   11111111111111   12334555    99999999999999999888765443

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.10  E-value=1.9e-09  Score=101.81  Aligned_cols=140  Identities=22%  Similarity=0.302  Sum_probs=94.7

Q ss_pred             HHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcC---Ccchhh--HhhhhHHHHHHHhhhhCccCCCcccc-------
Q 011992          317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGR---GISLHD--LLQEGSMGLMKSVEKFKPQAGCRFAN-------  383 (473)
Q Consensus       317 eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~---~~saED--LiQEg~lgL~kAiekFDp~kg~~FsT-------  383 (473)
                      .++...++.|+ .|++.|+..|++.+..+|++++..   ..+.+|  +++|+|+.++......+......|..       
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            34555566666 999999999999999999887643   234554  46777777665222111111111221       


Q ss_pred             ---------------C------C---C--C-CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHH
Q 011992          384 ---------------T------G---V--E-IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGN  436 (473)
Q Consensus       384 ---------------~------~---~--~-~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe  436 (473)
                                     .      .   .  . .........++.+.+..... |+|+++++|.++|+    +|+|.+|||+
T Consensus        85 r~lid~~R~~~a~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~-l~~~~~~~v~l~~~----~Gls~~EIA~  159 (185)
T PF07638_consen   85 RKLIDHARRRQAQKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLA-LDPRQRRVVELRFF----EGLSVEEIAE  159 (185)
T ss_pred             HHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHc-cCHHHHHHHHHHHH----CCCCHHHHHH
Confidence                           0      0   0  0 00111122234444554444 99999999999999    9999999999


Q ss_pred             HHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          437 IFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       437 ~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      .||||+.+|+..+..|..+|+..|.
T Consensus       160 ~lgiS~~tV~r~l~~aR~~l~~~l~  184 (185)
T PF07638_consen  160 RLGISERTVRRRLRRARAWLRRELR  184 (185)
T ss_pred             HHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999998875

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

Probab=99.10  E-value=3.5e-10  Score=109.33  Aligned_cols=114  Identities=25%  Similarity=0.421  Sum_probs=79.5

Q ss_pred             HHHHHHHHHHHHHHHhhc---CCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHHH-----HHHH
Q 011992          333 LINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQ-----HVRN  404 (473)
Q Consensus       333 Li~~yl~lV~sIA~ry~~---~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~e-----~L~~  404 (473)
                      |+..|.++|+++|++|.+   ++.+++|++|||++|+|+++++||+.+|.+|+|+........+.....+.     .+.+
T Consensus         1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~~~p~~~~~   80 (224)
T TIGR02479         1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQ   80 (224)
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcCccCHHHHH
Confidence            578999999999999986   78999999999999999999999999999998854433222221111100     1111


Q ss_pred             HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .+..|....+. +.-.++    ...+.+|||+.||++...|+++...
T Consensus        81 ~~~~l~~~~~~-l~~~~~----~~~~~~ela~~l~~~~~~v~~~~~~  122 (224)
T TIGR02479        81 KARKLERAIRE-LEARLG----REPTEEEIAEELGMDLKEYRQALNE  122 (224)
T ss_pred             HHHHHHHHHHH-HHHHHC----cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            11122111111 222344    7889999999999999999998753

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.

>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=99.00  E-value=1.2e-09  Score=83.00  Aligned_cols=54  Identities=30%  Similarity=0.440  Sum_probs=46.6

Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992          399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  456 (473)
Q Consensus       399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL  456 (473)
                      ++.|.++|..||+++|.||.++|+    +|+|++|||+.+|+|.++|++.+.+|+++|
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            367899999999999999999999    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.

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=98.94  E-value=4.4e-09  Score=102.94  Aligned_cols=116  Identities=22%  Similarity=0.264  Sum_probs=77.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhc---CCcchhhHhhhhHHHHHHHhhhhCccCCCccccCCCCCchHHHHHHHHH-----H
Q 011992          329 SREKLINANLRLVVHVAKQYQG---RGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMR-----Q  400 (473)
Q Consensus       329 A~e~Li~~yl~lV~sIA~ry~~---~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~~~~pee~le~~el~-----e  400 (473)
                      ....|+..|.++|.++|++|..   .+.+++||+|||++|||+++++||+..+ .|+|+........+......     .
T Consensus        16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~~~r   94 (231)
T PRK12427         16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDWRPR   94 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            3457899999999999999874   4679999999999999999999997555 78875444322222111000     0


Q ss_pred             HHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          401 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       401 ~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      .+...+..+. +-..-+.-.++    ...|..|||+.||++.+.|.++..
T Consensus        95 ~vr~~~~~i~-~~~~~l~~~~g----~~pt~~eiA~~lg~~~~~v~~~~~  139 (231)
T PRK12427         95 RLRQKTHKTN-DAIREIAKRLG----HEPNFEEISAELNLTAEEYQEYLL  139 (231)
T ss_pred             HHHHHHHHHH-HHHHHHHHHHC----CCCCHHHHHHHhCCCHHHHHHHHH
Confidence            0111111111 11112222334    889999999999999999988764

>PRK06930 positive control sigma-like factor; Validated

Probab=98.88  E-value=7.8e-08  Score=90.43  Aligned_cols=71  Identities=18%  Similarity=0.285  Sum_probs=63.8

Q ss_pred             chHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992          389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       389 pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~  463 (473)
                      +.......+....|..+|..||+++|.||.|+|+    +|+|++|||+.||+|.++|++++.||+++|+..+...
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            4444555667788999999999999999999998    9999999999999999999999999999999988754

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=98.74  E-value=3.5e-08  Score=96.28  Aligned_cols=60  Identities=23%  Similarity=0.406  Sum_probs=54.3

Q ss_pred             hhcchHHHHHHHHHHHHHHHHHHHhhcCC--cchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992          324 HSGNSSREKLINANLRLVVHVAKQYQGRG--ISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN  383 (473)
Q Consensus       324 ~~g~~A~e~Li~~yl~lV~sIA~ry~~~~--~saEDLiQEg~lgL~kAiekFDp~kg~~FsT  383 (473)
                      +.|+..+++||..|.++|.++|.++.++.  .+.||++|+|++|+|+|+++||+++|..|.+
T Consensus         5 ~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~s   66 (218)
T TIGR02895         5 QPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLS   66 (218)
T ss_pred             hcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHH
Confidence            45665599999999999999999998764  5799999999999999999999999999988

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).

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=98.74  E-value=3.8e-09  Score=108.54  Aligned_cols=80  Identities=20%  Similarity=0.173  Sum_probs=67.5

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhh---cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL---WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF  299 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~---~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l  299 (473)
                      .+..+.+|++|+|||.|||+     |+|.++   ++...   |.|++.              .+.+.++.++..+|.+.+
T Consensus       129 ~~fdp~~G~rFsTYA~~wIr-----~aI~~~---i~~~~r~vrlP~~~--------------~~~~~~l~~~~~~l~~~l  186 (324)
T PRK07921        129 EKFDYTKGFKFSTYATWWIR-----QAITRG---MADQSRTIRLPVHL--------------VEQVNKLARIKRELHQQL  186 (324)
T ss_pred             HHcCCccCCCHHHHHHHHHH-----HHHHHH---HHHcCCCccCCHHH--------------HHHHHHHHHHHHHHHHHh
Confidence            46688999999999999999     999985   66544   455544              466778999999999999


Q ss_pred             CCCCCHHHHHHHcCCCHHHHHHHHh
Q 011992          300 GREPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       300 GRePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      ||+||.+|||+.+|++.+++...+.
T Consensus       187 gr~pt~~EiA~~lgi~~~~v~~~~~  211 (324)
T PRK07921        187 GREATDEELAEESGIPEEKIADLLE  211 (324)
T ss_pred             CCCCCHHHHHHHhCcCHHHHHHHHH
Confidence            9999999999999999999887653

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=98.68  E-value=8.9e-09  Score=111.34  Aligned_cols=79  Identities=19%  Similarity=0.205  Sum_probs=66.0

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhh---cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL---WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG  300 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~---~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG  300 (473)
                      |+.+.+|++|+|||.||||     |+|.++   ++...   |.|++.              .+.+.+|.+++.+|.+.+|
T Consensus       315 kFDp~rG~rFSTYA~wWIR-----qaI~ra---I~d~~r~IRvP~~~--------------~e~i~kl~~~~~~L~~~lg  372 (509)
T PRK05901        315 KFDYTKGYKFSTYATWWIR-----QAITRA---MADQARTIRIPVHM--------------VETINKLGRIERELLQELG  372 (509)
T ss_pred             HhCcccCCCchhhhHHHHH-----HHHHHH---HHHcCCceecCHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence            5688999999999999999     999874   44433   455544              4567788899999999999


Q ss_pred             CCCCHHHHHHHcCCCHHHHHHHHh
Q 011992          301 REPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       301 RePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      |+||.+|||+.||++.+.+..++.
T Consensus       373 r~PT~eELAe~Lgis~e~V~~~~~  396 (509)
T PRK05901        373 REPTPEELAKEMGFTPEKVREIQK  396 (509)
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Confidence            999999999999999999887654

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=98.60  E-value=2.4e-07  Score=91.42  Aligned_cols=69  Identities=23%  Similarity=0.406  Sum_probs=59.1

Q ss_pred             CHHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCc--chhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992          315 SCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGI--SLHDLLQEGSMGLMKSVEKFKPQAGCRFAN  383 (473)
Q Consensus       315 s~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~--saEDLiQEg~lgL~kAiekFDp~kg~~FsT  383 (473)
                      +.+++...+..|+ .|++.|+..|.++|+++|.++.++..  .++|++|++++++|+++++|++.+|..|.+
T Consensus         4 ~~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~a   75 (237)
T PRK08311          4 SLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLS   75 (237)
T ss_pred             cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHH
Confidence            3445555556565 89999999999999999999988775  589999999999999999999988877877

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=98.56  E-value=2.4e-08  Score=104.51  Aligned_cols=80  Identities=19%  Similarity=0.192  Sum_probs=66.9

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF  299 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l  299 (473)
                      .+..+.+|.+|+|||.|||+     |+|.++   ++...|   .|++.              .+.+.++.++...|.+.+
T Consensus       179 ~kFd~~kg~~FsTYA~wWIR-----qaI~~~---I~~~~r~IRlP~~~--------------~~~~~~i~~a~~~l~~~l  236 (373)
T PRK07406        179 EKFDHEKGYKFSTYATWWIR-----QAITRA---IADQSRTIRLPVHL--------------YETISRIKKTTKVLSQEF  236 (373)
T ss_pred             HhcCCccCCCHHHHHHHHHH-----HHHHHH---HHhcCCceeCCHHH--------------HHHHHHHHHHHHHHHHHh
Confidence            35688899999999999999     999885   655444   55544              466778999999999999


Q ss_pred             CCCCCHHHHHHHcCCCHHHHHHHHh
Q 011992          300 GREPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       300 GRePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      ||+||.+|||+.+|++.+++.....
T Consensus       237 gr~Pt~~EIA~~lg~~~e~v~~~~~  261 (373)
T PRK07406        237 GRKPTEEEIAESMEMTIEKLRFIAK  261 (373)
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            9999999999999999999876543

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

Probab=98.56  E-value=2.9e-08  Score=102.27  Aligned_cols=82  Identities=21%  Similarity=0.218  Sum_probs=63.4

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP  303 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP  303 (473)
                      |+++.+|++|+|||+|||+     ++|.++...--++.+.|-+.              ++.+.+|.+++.+|.+.+|++|
T Consensus       146 kFdp~rG~kFsTYA~wWIr-----qaI~raI~~q~rtIRipvh~--------------~e~~nkl~r~~r~l~q~~~r~p  206 (342)
T COG0568         146 KFDPEKGFKFSTYATWWIR-----QAITRAIADQARTIRIPVHQ--------------VELINKLRRVKRELLQELGREP  206 (342)
T ss_pred             hcCcccCCcchhHHHHHHH-----HHHHHHHHHhcchhhHhHHH--------------HHHHHHHHHHHHHHHHHhcCCC
Confidence            5689999999999999999     77776411122233333322              5567778889999999999999


Q ss_pred             CHHHHHHHcCCCHHHHHHHHh
Q 011992          304 TLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       304 T~eEiA~~lGms~eeL~~~l~  324 (473)
                      +.+|||+.+|++.+++.....
T Consensus       207 ~~eeia~~l~~~~~~V~~m~~  227 (342)
T COG0568         207 TPEEIAEELGVSPDKVREMLK  227 (342)
T ss_pred             CHHHHHHHhCCCHHHHHHHHH
Confidence            999999999999988877654

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=98.55  E-value=2.5e-08  Score=110.54  Aligned_cols=79  Identities=19%  Similarity=0.212  Sum_probs=67.4

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG  300 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG  300 (473)
                      |+.+.+|++|+|||.|||+     |+|.++   ++...|   .|++.              ++...++.++...|.+.+|
T Consensus       424 kfd~~~G~~FstYA~~wIr-----~aI~~~---i~~~~r~irip~~~--------------~~~~~k~~~~~~~~~~~~g  481 (619)
T PRK05658        424 KFEYRRGYKFSTYATWWIR-----QAITRS---IADQARTIRIPVHM--------------IETINKLNRISRQMLQEIG  481 (619)
T ss_pred             hcCccCCCchHHHhHHHHH-----HHHHHH---HHHcCCceecCHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence            4688999999999999999     999984   766555   45444              4567788999999999999


Q ss_pred             CCCCHHHHHHHcCCCHHHHHHHHh
Q 011992          301 REPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       301 RePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      |+||.+|||+.||++.+++...+.
T Consensus       482 r~pt~~eiA~~l~~~~~~v~~~~~  505 (619)
T PRK05658        482 REPTPEELAERLGMPEDKVRKVLK  505 (619)
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Confidence            999999999999999999887654

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=98.54  E-value=5e-08  Score=96.78  Aligned_cols=79  Identities=18%  Similarity=0.138  Sum_probs=68.2

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF  299 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l  299 (473)
                      .+..+.+|.+|+||+++||+     |+|+|+   +|...|   .|++.              .+...+++++..+|.+.+
T Consensus        69 ~~fd~~~g~~F~tya~~~Ir-----~~i~~~---lr~~~~~vr~pr~~--------------~~~~~~~~~~~~~l~~~l  126 (256)
T PRK07408         69 ERFDPSKGHAFSSFAIPYIR-----GEIQHY---LRDKSPTVRIPRRW--------------QELQRQAKKVRQELRQEL  126 (256)
T ss_pred             HhcCCCCCCCcHHHHHHHHH-----HHHHHH---HHHcCCeeeeCHHH--------------HHHHHHHHHHHHHHHHHh
Confidence            35688999999999999999     999994   887555   56555              466778999999999999


Q ss_pred             CCCCCHHHHHHHcCCCHHHHHHHH
Q 011992          300 GREPTLIEWAKAIGLSCRDLKSEL  323 (473)
Q Consensus       300 GRePT~eEiA~~lGms~eeL~~~l  323 (473)
                      ||+||.+|||+.+|++.+++....
T Consensus       127 gr~pt~~elA~~lgi~~~~v~~~~  150 (256)
T PRK07408        127 GRQPTDQEIAQALDISLEEWQEIK  150 (256)
T ss_pred             CCCCCHHHHHHHcCCCHHHHHHHH
Confidence            999999999999999999987754

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=98.52  E-value=4.1e-08  Score=102.49  Aligned_cols=81  Identities=17%  Similarity=0.169  Sum_probs=66.7

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhh---cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL---WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF  299 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~---~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l  299 (473)
                      .+..+.+|.+|+|||.|||+     |+|.++   ++...   |.|++.              ...+.++.++..+|.+.+
T Consensus       172 ~~fd~~~g~~FsTyA~~wIr-----~aI~~~---i~~~~r~irip~~~--------------~~~~~~~~~~~~~l~~~l  229 (367)
T PRK09210        172 EKFDYRKGFKFSTYATWWIR-----QAITRA---IADQARTIRIPVHM--------------VETINKLIRVQRQLLQEL  229 (367)
T ss_pred             HhcCCCCCCchHHHHHHHHH-----HHHHHH---HHHcCCceeccHHH--------------HHHHHHHHHHHHHHHHHh
Confidence            35678899999999999999     998874   54444   445444              456778899999999999


Q ss_pred             CCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992          300 GREPTLIEWAKAIGLSCRDLKSELHS  325 (473)
Q Consensus       300 GRePT~eEiA~~lGms~eeL~~~l~~  325 (473)
                      ||+||.+|||+.||++.+++..++..
T Consensus       230 gr~pt~~EiA~~l~~~~~~v~~~~~~  255 (367)
T PRK09210        230 GREPTPEEIAEEMDMPPEKVREILKI  255 (367)
T ss_pred             CCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            99999999999999999998876543

>PRK00118 putative DNA-binding protein; Validated

Probab=98.51  E-value=5e-07  Score=78.65  Aligned_cols=64  Identities=22%  Similarity=0.155  Sum_probs=57.1

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992          398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       398 l~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      +...+.-+...||++++.|+.++|+    +++|++|||+.+|+|+++|+.++.+|+++||+++..-++
T Consensus         7 ~~~l~d~~~~~L~ekqRevl~L~y~----eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~   70 (104)
T PRK00118          7 MNLLFDFYGSLLTEKQRNYMELYYL----DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL   70 (104)
T ss_pred             HHHHHHHHhccCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            3445566778999999999999999    999999999999999999999999999999999876543

>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=98.42  E-value=8.7e-07  Score=64.80  Aligned_cols=54  Identities=37%  Similarity=0.589  Sum_probs=50.1

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..+..++..|++.++.++.++|.    ++++..+||+.+|+|.++|+.++.++..+||
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            35788899999999999999998    8999999999999999999999999988874

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

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=98.40  E-value=1.1e-07  Score=100.58  Aligned_cols=84  Identities=15%  Similarity=0.154  Sum_probs=67.2

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe  302 (473)
                      .|+.+.+|.+|+||++||||     |+|.+......+.++.|.+.              ...+.+|.+++..|.+.+||.
T Consensus       218 ekFDp~rG~rFSTYa~wwIR-----qaI~r~i~~~srtIrlP~~i--------------~e~l~~lrk~~r~L~~~lgR~  278 (415)
T PRK07598        218 EKFDPTKGYRFSTYAYWWIR-----QGITRAIATQSRTIRLPVHI--------------TEKLNKIKKAQRKISQEKGRT  278 (415)
T ss_pred             HHcCcccCCCHHHHHHHHHH-----HHHHHHHHHcCCceehhHHH--------------HHHHHHHHHHHHHHHHHhCCC
Confidence            46788999999999999999     99887411122234455555              355778889999999999999


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHhh
Q 011992          303 PTLIEWAKAIGLSCRDLKSELHS  325 (473)
Q Consensus       303 PT~eEiA~~lGms~eeL~~~l~~  325 (473)
                      ||.+|||+.+||+.+.+..++..
T Consensus       279 pt~~EiA~~l~is~~~vr~~l~~  301 (415)
T PRK07598        279 PTIEDIAQELEMTPTQVREVLLR  301 (415)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Confidence            99999999999999999887653

>PRK05949 RNA polymerase sigma factor; Validated

Probab=98.40  E-value=1.5e-07  Score=96.93  Aligned_cols=84  Identities=18%  Similarity=0.141  Sum_probs=65.8

Q ss_pred             hhccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992          222 KRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR  301 (473)
Q Consensus       222 ~~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR  301 (473)
                      ..+..+.+|.+|+|||.||||     ++|.++.....+.++.|.+.              .+.+.++.++...+...+||
T Consensus       133 ~~kfd~~~G~rFsTYa~wwIr-----q~I~r~i~~~~r~iRlP~~~--------------~~~~~~l~k~~~~l~~~lgr  193 (327)
T PRK05949        133 VEKFDPTRGYKFSTYAYWWIR-----QAITRAIAQQARTIRLPIHI--------------TEKLNKIKKTQRELSQKLGR  193 (327)
T ss_pred             HHhcCCcCCCChhhhhHHHHH-----HHHHHHHHHcCCceeCCHHH--------------HHHHHHHHHHHHHHHHHhCC
Confidence            345688999999999999999     99887422223334455444              35566788888899999999


Q ss_pred             CCCHHHHHHHcCCCHHHHHHHHh
Q 011992          302 EPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       302 ePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      +||.+|+|+.+|++.+++...+.
T Consensus       194 ~pt~~eiA~~l~i~~~~v~~~~~  216 (327)
T PRK05949        194 SATPAEIAKELELEPSQIREYLS  216 (327)
T ss_pred             CCCHHHHHHHhCcCHHHHHHHHH
Confidence            99999999999999999887653

>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=98.26  E-value=1.1e-06  Score=68.88  Aligned_cols=50  Identities=26%  Similarity=0.490  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccc
Q 011992          333 LINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA  382 (473)
Q Consensus       333 Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~Fs  382 (473)
                      ||+.|.++|++++.++.++..+++|++||+++++|+++++|++..+..|.
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~   50 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFR   50 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHH
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHH
Confidence            68899999999999999999999999999999999999999987764444

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 ....

>PRK04217 hypothetical protein; Provisional

Probab=98.19  E-value=3.8e-06  Score=73.88  Aligned_cols=55  Identities=20%  Similarity=0.136  Sum_probs=51.0

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      ..|++.+++++.++|+    +++|++|||+.||||.++|++++.+|+++|++.+.....
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            4699999999999998    999999999999999999999999999999999876543

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=98.17  E-value=8.1e-07  Score=91.10  Aligned_cols=83  Identities=18%  Similarity=0.169  Sum_probs=65.4

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe  302 (473)
                      .+..+.+|.+|.||+.||||     ++|.++.....+.++.|.+.              .+.+.++.++...+...+|++
T Consensus       124 ~~fd~~~g~rf~tYa~~wIR-----~~I~~~i~~~~~~ir~p~~~--------------~~~~~~l~~~~~~l~~~~gr~  184 (317)
T PRK07405        124 EKFDPTKGYRFSTYAYWWIR-----QAITRAIAEKSRTIRLPIHI--------------TEKLNKIKKAQRQLSQQLGRA  184 (317)
T ss_pred             HHhCcCCCCChHHHHHHHHH-----HHHHHHHHhcCCCccCChHH--------------HHHHHHHHHHHHHHHHHhCCC
Confidence            35677789999999999999     99877422222344455544              456678888999999999999


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHh
Q 011992          303 PTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       303 PT~eEiA~~lGms~eeL~~~l~  324 (473)
                      ||.+|||+.+|++.+.+...+.
T Consensus       185 pt~~eiA~~~~~~~~~v~~~~~  206 (317)
T PRK07405        185 ATIGELAEELELTPKQVREYLE  206 (317)
T ss_pred             CCHHHHHHHhCcCHHHHHHHHH
Confidence            9999999999999998887754

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

Probab=98.14  E-value=9.7e-07  Score=89.47  Aligned_cols=83  Identities=18%  Similarity=0.165  Sum_probs=64.1

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe  302 (473)
                      .+..+.+|.+|+||+.|||+     ++|.++...-.+..+.|.+.              .+.+.++.++...+.+.+|++
T Consensus       117 ~kfd~~~g~rFsTya~~wIr-----~~I~r~i~~~~r~vr~p~~~--------------~~~~~~~rk~~~~l~~~~~~~  177 (298)
T TIGR02997       117 EKFDPTRGYKFSTYAYWWIR-----QGITRAIANQSRTIRLPIHI--------------TEKLNKIKKVQRELSQKLGRT  177 (298)
T ss_pred             HHhCccCCCChHHHHHHHHH-----HHHHHHHHhcCCCeeCcHHH--------------HHHHHHHHHHHHHHHHHhCCC
Confidence            35678899999999999999     88876422222333444433              345667888888999999999


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHh
Q 011992          303 PTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       303 PT~eEiA~~lGms~eeL~~~l~  324 (473)
                      ||.+|+|+.+|++.+++.....
T Consensus       178 pt~~eia~~l~~~~~~v~~~~~  199 (298)
T TIGR02997       178 PSEAEIAEALELEPEQVRELLQ  199 (298)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHH
Confidence            9999999999999999887654

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).

>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=98.13  E-value=1.3e-05  Score=69.48  Aligned_cols=57  Identities=26%  Similarity=0.326  Sum_probs=45.0

Q ss_pred             HHHHHHHhh-CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          400 QHVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       400 e~L~~aL~~-LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ..|.+.... |+++++.++.+||.    +++|+.|||+.+|||+..|...++||..+|...=
T Consensus         8 ~~L~d~Yg~LLT~kQ~~~l~lyy~----eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE   65 (101)
T PF04297_consen    8 NLLFDFYGELLTEKQREILELYYE----EDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYE   65 (101)
T ss_dssp             HHHHHHHGGGS-HHHHHHHHHHCT----S---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHc----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            344555544 99999999999999    9999999999999999999999999999997653

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.

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.11  E-value=6.4e-06  Score=75.09  Aligned_cols=53  Identities=19%  Similarity=0.256  Sum_probs=47.1

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      .|+++|++|+.|++     +|+|++|||+.||+|+++|+.++++|+++|+.......+
T Consensus         6 ~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l   58 (137)
T TIGR00721         6 FLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDF   58 (137)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHH
Confidence            59999999999964     799999999999999999999999999999986544333

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=98.11  E-value=7e-06  Score=75.18  Aligned_cols=51  Identities=24%  Similarity=0.399  Sum_probs=46.8

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      ..|+++|++||.+++     +|+|++|||+.||+|+++|++++++|+++||+.+..
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            469999999999954     799999999999999999999999999999987654

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=98.05  E-value=3.1e-06  Score=85.72  Aligned_cols=87  Identities=16%  Similarity=0.104  Sum_probs=60.1

Q ss_pred             hhccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992          222 KRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR  301 (473)
Q Consensus       222 ~~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR  301 (473)
                      -.+..+.+|..|+|||.|||+     |+|.+   .++...|.++.-   +...+..+..+   +++++.....+...+|+
T Consensus        82 ~~~fd~~~~~~f~tya~~~Ir-----~~I~~---~lr~~~~~iR~p---~~~~~~~~~~~---~~~~~~~~~~~~~~l~~  147 (289)
T PRK07500         82 AARFEPDREVRFSTYATWWIR-----ASIQD---YILRNWSIVRGG---TSSAQKALFFN---LRRLRARLAQADEELTK  147 (289)
T ss_pred             HHHcCCCCCCChHHHHHHHHH-----HHHHH---HHHHCCCceecC---ccHHHHHHHHH---HHHHHHHHHhhhcccCC
Confidence            345677889999999999999     99998   488766666532   11222222222   22333333334446899


Q ss_pred             CCCHHHHHHHcCCCHHHHHHH
Q 011992          302 EPTLIEWAKAIGLSCRDLKSE  322 (473)
Q Consensus       302 ePT~eEiA~~lGms~eeL~~~  322 (473)
                      +||.+|||+.+|++.+++...
T Consensus       148 ~pt~~eiA~~l~~~~~~v~~~  168 (289)
T PRK07500        148 QEIHREIATALGVSLSDVEMM  168 (289)
T ss_pred             CCCHHHHHHHhCcCHHHHHHH
Confidence            999999999999999988654

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=98.03  E-value=4.1e-06  Score=84.54  Aligned_cols=81  Identities=10%  Similarity=0.054  Sum_probs=55.5

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh--C
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF--G  300 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l--G  300 (473)
                      .+..+.+|.+|+|||.|||+     |+|.|+   +++. |...+.|  ++          +..+++..+...+.+++  +
T Consensus        91 ~~fd~~~~~~FstYA~~~Ir-----~~i~~~---l~~~-~~~vr~p--~~----------~~~~~~~~~~~~~~~~l~~~  149 (284)
T PRK06596         91 KRFDPEVGVRLVSFAVHWIK-----AEIHEY---ILRN-WRIVKVA--TT----------KAQRKLFFNLRKAKKRLGWL  149 (284)
T ss_pred             HHhCcccCCCHHHHHHHHHH-----HHHHHH---HHHc-CCeeecc--ch----------HHHHHHHHHHHHHHHHhccC
Confidence            35678999999999999999     999984   7765 4222222  11          11122222333333444  4


Q ss_pred             CCCCHHHHHHHcCCCHHHHHHHHh
Q 011992          301 REPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       301 RePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      ++||.+|||+.+|++.+++.....
T Consensus       150 ~~~t~~eiA~~l~~~~~~v~~~~~  173 (284)
T PRK06596        150 NPEEVEMVAEELGVSEEEVREMES  173 (284)
T ss_pred             CCCCHHHHHHHhCcCHHHHHHHHH
Confidence            999999999999999999887643

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=98.01  E-value=5.2e-05  Score=68.61  Aligned_cols=62  Identities=18%  Similarity=0.264  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          397 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       397 el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ...+.|..+|+.|++.+|.||.++|+  .+..+|..+||..||+|+.+|.++..+++.+|...+
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            45678999999999999999999997  112359999999999999999999999999999875

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.

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=97.99  E-value=5.6e-06  Score=81.92  Aligned_cols=81  Identities=20%  Similarity=0.091  Sum_probs=64.9

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhc--ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW--GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG  300 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~--~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG  300 (473)
                      .+..+..|..|.||+.++|+     ++++|+   +|+..+  .|++.              .+...++.++..++.+++|
T Consensus        77 ~~fd~~~~~~f~tyl~~~ir-----n~~~~~---lr~~~~ir~p~~~--------------~~~~~~~~~~~~~l~~~l~  134 (254)
T TIGR02850        77 DNFDLSQNVKFSTYAVPMII-----GEIRRY---LRDNNPIRVSRSL--------------RDIAYKALQVRDKLISENS  134 (254)
T ss_pred             HhcCCCCCCChHHHHHHHHH-----HHHHHH---HHhCCCccCchHH--------------HHHHHHHHHHHHHHHHHhC
Confidence            45677788899999999999     999884   776442  33333              3445678888899999999


Q ss_pred             CCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992          301 REPTLIEWAKAIGLSCRDLKSELHS  325 (473)
Q Consensus       301 RePT~eEiA~~lGms~eeL~~~l~~  325 (473)
                      ++||.+|+|+.+|++.+++...+..
T Consensus       135 ~~pt~~elA~~l~~~~e~v~~~~~~  159 (254)
T TIGR02850       135 KEPTVSEIAKELKVPQEEVVFALDA  159 (254)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            9999999999999999998776554

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.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=97.98  E-value=4.6e-06  Score=83.12  Aligned_cols=80  Identities=26%  Similarity=0.403  Sum_probs=68.8

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe  302 (473)
                      .+..+.+|..|.||+.+||+     ++++|   .+|+..|.|++.              .+...++.++...|++.+|++
T Consensus        77 ~~fd~~~~~~f~ty~~~~ir-----~~i~d---~~R~~~~~p~~~--------------~~~~~~i~~~~~~l~~~~~~~  134 (268)
T PRK06288         77 EKFDPEREIKFKTYAVTRIR-----GAIFD---ELRSIDWIPRSV--------------RQKARQIERAIAMLEARLGRT  134 (268)
T ss_pred             HHcCcccCCCHHHHHHHHHH-----HHHHH---HHHhcCccCHHH--------------HHHHHHHHHHHHHHHHHHCCC
Confidence            34566777899999999999     99998   499988988877              355678889999999999999


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHh
Q 011992          303 PTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       303 PT~eEiA~~lGms~eeL~~~l~  324 (473)
                      ||.+|||+.+|++.+.+...+.
T Consensus       135 pt~~eia~~lg~~~~~v~~~~~  156 (268)
T PRK06288        135 PSDEEIADELGISLEEYNSLLS  156 (268)
T ss_pred             CCHHHHHHHcCCCHHHHHHHHH
Confidence            9999999999999998877654

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.88  E-value=2.9e-05  Score=57.78  Aligned_cols=46  Identities=26%  Similarity=0.420  Sum_probs=41.2

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++++.++.+. .    .+++.+|||+.+|+|+++|+.++.+++.+|+
T Consensus         2 ~~l~~~e~~i~~~~-~----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~   47 (58)
T smart00421        2 ASLTPREREVLRLL-A----EGLTNKEIAERLGISEKTVKTHLSNIMRKLG   47 (58)
T ss_pred             CCCCHHHHHHHHHH-H----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            46899999998774 4    7899999999999999999999999988875

lux regulon (activates the bioluminescence operon

>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=97.87  E-value=2.6e-05  Score=63.31  Aligned_cols=42  Identities=31%  Similarity=0.608  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992          284 DLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS  325 (473)
Q Consensus       284 ~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~  325 (473)
                      ++++|.+++.+|.+++||+||.+|||+.||++.+++..++..
T Consensus         2 ~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~   43 (78)
T PF04539_consen    2 KLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQA   43 (78)
T ss_dssp             HHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence            467899999999999999999999999999999999877653

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 ....

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.87  E-value=3.4e-05  Score=63.10  Aligned_cols=48  Identities=19%  Similarity=0.219  Sum_probs=42.9

Q ss_pred             HHHHHHHhhCCHHHHHHHHHH-hhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          400 QHVRNLLTLLNPKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       400 e~L~~aL~~LperER~VL~Lr-Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ..+.+.|+.||++++.++.|+ |.    +++|++|||+.||+|+++|+.++++
T Consensus         7 ~~~~~~l~~l~~~~r~af~L~R~~----eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879         7 KKLAERLTWVDSLAEAAAALAREE----AGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             hhHHHHHhcCCHHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            346778899999999999995 56    8999999999999999999999875

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.

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=97.78  E-value=2e-05  Score=76.45  Aligned_cols=79  Identities=24%  Similarity=0.181  Sum_probs=63.7

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhh--cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL--WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR  301 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~--~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR  301 (473)
                      +..+..|..|.||+.++|+     ++|+|+   +|...  +.|++.              .+...++..+...|...+|+
T Consensus        55 ~f~~~~~~~f~tyl~~~i~-----~~i~~~---lr~~~~i~~p~~~--------------~~~~~~~~~~~~~l~~~~~r  112 (231)
T TIGR02885        55 KFDLSYDVKFSTYAVPMIM-----GEIKRF---LRDDGIIKVSRSL--------------KELARKIRYMKEELSKELGR  112 (231)
T ss_pred             hcCCCCCCCcHHHHHHHHH-----HHHHHH---HHhCCCeECCHHH--------------HHHHHHHHHHHHHHHHHHCc
Confidence            4456677899999999999     999984   77644  355544              34566788888999999999


Q ss_pred             CCCHHHHHHHcCCCHHHHHHHHh
Q 011992          302 EPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       302 ePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      .||.+|+|+.+|++.+++...+.
T Consensus       113 ~pt~~ela~~l~~~~~~v~~~~~  135 (231)
T TIGR02885       113 EPTINELAEALGVSPEEIVMALE  135 (231)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            99999999999999998876654

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.

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=97.74  E-value=2e-05  Score=78.15  Aligned_cols=79  Identities=19%  Similarity=0.081  Sum_probs=63.4

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhc--ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW--GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR  301 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~--~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR  301 (473)
                      +..+.+|..|.||+.++|+     ++++|+   +|+..+  .|++.              .+...++.++..++.+++|+
T Consensus        81 ~fd~~~~~~f~t~l~~~ir-----~~i~~~---lr~~~~vrip~~~--------------~~~~~~~~~~~~~l~~~~~r  138 (258)
T PRK08215         81 NFDLSQNVKFSTYAVPMII-----GEIRRY---LRDNNPIRVSRSL--------------RDIAYKALQVREKLINENSK  138 (258)
T ss_pred             hcCCCCCCCcHHHHHHHHH-----HHHHHH---HHhCCceEecHHH--------------HHHHHHHHHHHHHHHHHhCC
Confidence            4566778899999999999     999984   776542  33333              34456778888999999999


Q ss_pred             CCCHHHHHHHcCCCHHHHHHHHh
Q 011992          302 EPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       302 ePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      +|+..|+|+.+|++.+++...+.
T Consensus       139 ~p~~~eia~~l~v~~~~v~~~~~  161 (258)
T PRK08215        139 EPTVEEIAKELEVPREEVVFALD  161 (258)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            99999999999999999877553

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=97.72  E-value=0.00019  Score=61.87  Aligned_cols=55  Identities=22%  Similarity=0.439  Sum_probs=50.0

Q ss_pred             HHHHHHHHHhhCC-HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992          398 MRQHVRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  456 (473)
Q Consensus       398 l~e~L~~aL~~Lp-erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL  456 (473)
                      .+..+..+|+.|+ +.+|.||.++|.    .+++..+||+.||+|+.++..++.+|++.|
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            4556888998886 789999999999    899999999999999999999999999876

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.

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

Probab=97.72  E-value=2.7e-05  Score=75.25  Aligned_cols=82  Identities=18%  Similarity=0.235  Sum_probs=64.7

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP  303 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP  303 (473)
                      +..+.+|..|.||+.++|+     ++|+|   .+|+..|..+ .|          -.......++..+...+.+.+|++|
T Consensus        47 ~f~~~~~~~F~ty~~~~i~-----~~~~~---~~r~~~~~~r-i~----------~~~~~~~~~~~~~~~~l~~~~~~~p  107 (227)
T TIGR02980        47 RFDPSYGVKFSTFAVPTIM-----GEIKR---FFRDDTWAVR-VP----------RRLKELGLKINKATEELTQRLGRSP  107 (227)
T ss_pred             hcCcccCCCcHHHHHHHHH-----HHHHH---HHHHcCCcee-cC----------HHHHHHHHHHHHHHHHHHHHHCCCC
Confidence            4456678899999999999     99998   4888777443 22          0013445677888999999999999


Q ss_pred             CHHHHHHHcCCCHHHHHHHHh
Q 011992          304 TLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       304 T~eEiA~~lGms~eeL~~~l~  324 (473)
                      +.+|+|+.+|++.+++...+.
T Consensus       108 ~~~ela~~l~~~~~~v~~~~~  128 (227)
T TIGR02980       108 TIAEIAEELGVSEEEVVEALE  128 (227)
T ss_pred             CHHHHHHHhCCCHHHHHHHHH
Confidence            999999999999998876554

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.

>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=97.70  E-value=9.6e-05  Score=56.99  Aligned_cols=47  Identities=23%  Similarity=0.317  Sum_probs=40.8

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ..|+++|.+|+.+..     .|++.+|||+.||||..+|+....++++||.-
T Consensus         2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~   48 (58)
T PF00196_consen    2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV   48 (58)
T ss_dssp             GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred             CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence            469999999998887     69999999999999999999999999999863

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 ....

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=97.69  E-value=4.2e-05  Score=76.49  Aligned_cols=83  Identities=17%  Similarity=0.191  Sum_probs=53.3

Q ss_pred             hhccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992          222 KRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR  301 (473)
Q Consensus       222 ~~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR  301 (473)
                      -.+..+.+|.+|+|||.|||+     |+|+++   ++.. |...+.|  ++....++      ..++..+...+.  .++
T Consensus        77 ~~~fd~~~~~~FsTYA~~~Ir-----~~i~~~---l~~~-~~~ir~p--~~~~~~~~------~~~~~~~~~~~~--~~~  137 (270)
T TIGR02392        77 VKRFDPERGVRLVSFAVHWIK-----AEIHEY---ILRN-WRLVKVA--TTKAQRKL------FFNLRKMKKRLQ--GWL  137 (270)
T ss_pred             HHHhCcccCCChHHhhHHHHH-----HHHHHH---HHHc-CCceecC--chHHHHHH------HHHHHHHHHHHh--cCC
Confidence            345678999999999999999     999984   7764 5433333  11111111      122333333332  125


Q ss_pred             CC-CHHHHHHHcCCCHHHHHHHH
Q 011992          302 EP-TLIEWAKAIGLSCRDLKSEL  323 (473)
Q Consensus       302 eP-T~eEiA~~lGms~eeL~~~l  323 (473)
                      .| +.+|||+.+|++.+++....
T Consensus       138 ~~~~~~eiA~~l~~~~~~v~~~~  160 (270)
T TIGR02392       138 NPEEVEAIAEELGVSEREVREME  160 (270)
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Confidence            56 69999999999999987753

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.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=97.69  E-value=2.9e-05  Score=76.62  Aligned_cols=81  Identities=21%  Similarity=0.295  Sum_probs=68.8

Q ss_pred             hhccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992          222 KRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR  301 (473)
Q Consensus       222 ~~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR  301 (473)
                      ..+..+.+|..|.+|+.++|+     +.++|+   +|+..|.|++.              .+...+++++...+.+.+|+
T Consensus        67 ~~~f~~~~~~~f~tyl~~~ir-----n~~~d~---lR~~~~~p~~~--------------~~~~~~~~~~~~~~~~~~~~  124 (251)
T PRK07670         67 LEKFDPSRDLKFDTYASFRIR-----GAIIDG---LRKEDWLPRSM--------------REKTKKVEAAIEKLEQRYMR  124 (251)
T ss_pred             HHHcCcccCCCHHHHHHHHHH-----HHHHHH---HHhcCCCCHHH--------------HHHHHHHHHHHHHHHHHHCC
Confidence            345577778899999999999     999984   88877777665              45677788888999999999


Q ss_pred             CCCHHHHHHHcCCCHHHHHHHHh
Q 011992          302 EPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       302 ePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      +|+.+|||+.+|++.+++..++.
T Consensus       125 ~~~~~eia~~l~~~~~~v~~~~~  147 (251)
T PRK07670        125 NVTPKEVAAELGMTEEEVEATMN  147 (251)
T ss_pred             CCCHHHHHHHhCcCHHHHHHHHH
Confidence            99999999999999999887764

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.68  E-value=0.00011  Score=54.86  Aligned_cols=45  Identities=29%  Similarity=0.507  Sum_probs=39.8

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      |+++++.++.++ .    .+++.+|||+.+|+|..+|+..+.+++++|+.
T Consensus         1 l~~~e~~i~~~~-~----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~   45 (57)
T cd06170           1 LTPREREVLRLL-A----EGKTNKEIADILGISEKTVKTHLRNIMRKLGV   45 (57)
T ss_pred             CCHHHHHHHHHH-H----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            689999999875 4    68999999999999999999999998877764

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

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=97.59  E-value=3e-05  Score=79.93  Aligned_cols=82  Identities=15%  Similarity=0.087  Sum_probs=62.7

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP  303 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP  303 (473)
                      +..+.+|..|+||+.|||+     ++|.++.....+..+.|++.              ++++.++.++...|+..+|++|
T Consensus       130 ~fd~~rg~~Fstyatw~iR-----~ai~~~i~~~~r~ir~p~~~--------------~~~l~~~~R~~~~l~~~l~r~~  190 (325)
T PRK05657        130 KFDPERGFRFSTYATWWIR-----QTIERAIMNQTRTIRLPVHV--------------VKELNVYLRAARELEHKLDHEP  190 (325)
T ss_pred             HhCCccCCCHHHHHHHHHH-----HHHHHHHHHcCCccccCHHH--------------HHHHHHHHHHHHHHHHHhCCCC
Confidence            5567889999999999999     88876411112234455443              4555667778888999999999


Q ss_pred             CHHHHHHHcCCCHHHHHHHHh
Q 011992          304 TLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       304 T~eEiA~~lGms~eeL~~~l~  324 (473)
                      +.+|+|..+|++.+++.+.+.
T Consensus       191 t~~eiA~~l~~~~~~v~~~l~  211 (325)
T PRK05657        191 SAEEIAELLDKPVDDVSRMLA  211 (325)
T ss_pred             CHHHHHHHhCcCHHHHHHHHH
Confidence            999999999999999887764

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

Probab=97.57  E-value=0.0003  Score=54.22  Aligned_cols=48  Identities=25%  Similarity=0.376  Sum_probs=42.3

Q ss_pred             CCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRL  456 (473)
Q Consensus       409 LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL  456 (473)
                      |+++|+++|..-|..+.   -++-|+.|||+.||||.+++..++.+|.+||
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            78999999988775432   3788999999999999999999999999987

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

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.42  E-value=0.00027  Score=68.00  Aligned_cols=46  Identities=11%  Similarity=0.237  Sum_probs=43.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|++|+.+.-     +|+|.+|||+.||+|+.||+...++.++||.-
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            49999999999887     79999999999999999999999999999963

>PRK05572 sporulation sigma factor SigF; Validated

Probab=97.40  E-value=0.00012  Score=72.22  Aligned_cols=78  Identities=22%  Similarity=0.189  Sum_probs=63.4

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhh--cccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFL--WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGR  301 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~--~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGR  301 (473)
                      +..+..+..|.+|+.++|+     ++|+|+   +|...  |.|++.              .+...+++++...+..++||
T Consensus        76 ~f~~~~~~~f~twl~~~i~-----~~i~~~---lr~~~~~r~~~~~--------------~~~~~~~~~~~~~l~~~~~r  133 (252)
T PRK05572         76 KFDLSYDVKFSTYAVPMII-----GEIQRF---LRDDGTVKVSRSL--------------KETANKIRKDKDELSKELGR  133 (252)
T ss_pred             HcCCCCCCChHHHHHHHHH-----HHHHHH---HHhCCCCCCCHHH--------------HHHHHHHHHHHHHHHHHHCc
Confidence            4455566789999999999     999984   77654  566655              35667888899999999999


Q ss_pred             CCCHHHHHHHcCCCHHHHHHHH
Q 011992          302 EPTLIEWAKAIGLSCRDLKSEL  323 (473)
Q Consensus       302 ePT~eEiA~~lGms~eeL~~~l  323 (473)
                      +|+..|+|+.+|++.+++....
T Consensus       134 ~p~~~eia~~l~~~~~~v~~~~  155 (252)
T PRK05572        134 EPTIEELAEYLGVTPEEVVLAQ  155 (252)
T ss_pred             CCCHHHHHHHhCcCHHHHHHHH
Confidence            9999999999999998876543

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.36  E-value=0.00036  Score=66.21  Aligned_cols=46  Identities=22%  Similarity=0.291  Sum_probs=43.0

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|++||++|+.+.-     +|+|.+|||+.||+|..||+.+.++.++||-
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            359999999999887     6999999999999999999999999999984

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.35  E-value=0.00038  Score=67.31  Aligned_cols=47  Identities=19%  Similarity=0.320  Sum_probs=43.7

Q ss_pred             HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      +..|++||++|+.+.-     +|+|.+|||+.|+||+.||+....+.++||.
T Consensus       132 ~~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg  178 (207)
T PRK11475        132 SRMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLG  178 (207)
T ss_pred             cCCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            3469999999999887     6999999999999999999999999999985

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.34  E-value=0.00036  Score=68.35  Aligned_cols=48  Identities=19%  Similarity=0.267  Sum_probs=44.3

Q ss_pred             HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ...|+++|++||.+..     +|+|.+|||++||||+.+|+..+.++++||+.
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.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=97.34  E-value=0.00019  Score=70.04  Aligned_cols=80  Identities=28%  Similarity=0.436  Sum_probs=64.3

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe  302 (473)
                      .+..+..|..|.+|+.++++     +.++|   .+|+..|.|+..              .+...++..+...+.+.+|++
T Consensus        54 ~~f~~~~~~~f~tyl~~~ir-----n~~~~---~lR~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~  111 (236)
T PRK06986         54 RRYDGEQGASFETYAGQRIR-----GAMLD---ELRSLDWVPRSV--------------RRNAREVAQAIRQLEQELGRE  111 (236)
T ss_pred             HhcCcccCCChHHHHHHHHH-----HHHHH---HHHHcCCCCHHH--------------HHHHHHHHHHHHHHHHHHCCC
Confidence            34566678899999999999     99998   488876655433              234456777888999999999


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHh
Q 011992          303 PTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       303 PT~eEiA~~lGms~eeL~~~l~  324 (473)
                      |+.+|||+.+|++.+++..++.
T Consensus       112 ~~~~ela~~l~i~~~~v~~~~~  133 (236)
T PRK06986        112 PTDTEVAEKLGLSLEEYREMLL  133 (236)
T ss_pred             CCHHHHHHHcCCCHHHHHHHHH
Confidence            9999999999999998876554

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.33  E-value=0.00039  Score=67.93  Aligned_cols=50  Identities=8%  Similarity=-0.050  Sum_probs=46.6

Q ss_pred             HHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          403 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       403 ~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .+++..|+++|++|+.+.-     +|+|.+|||+.|++|+.||+...++.++||.
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            5667889999999999987     6999999999999999999999999999985

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=97.33  E-value=0.00047  Score=65.44  Aligned_cols=47  Identities=23%  Similarity=0.352  Sum_probs=43.6

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ..|+++|++|+.+.-     +|+|.+|||+.||+|..||+....++++||.-
T Consensus       132 ~~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV  178 (198)
T PRK15201        132 RHFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV  178 (198)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            359999999999887     79999999999999999999999999999864

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.31  E-value=0.00043  Score=68.96  Aligned_cols=48  Identities=21%  Similarity=0.261  Sum_probs=44.3

Q ss_pred             HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      +..|+++|++|+.+..     +|+|.+|||++||||+.||+..+.++++||.-
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            4579999999999865     79999999999999999999999999999864

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.

>PRK13870 transcriptional regulator TraR; Provisional

Probab=97.30  E-value=0.00043  Score=68.14  Aligned_cols=46  Identities=26%  Similarity=0.364  Sum_probs=42.9

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|++||++||.+.=     +|+|..|||.+||||+.||..+++.|++||-.
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            59999999998877     79999999999999999999999999999853

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=97.27  E-value=0.0005  Score=66.87  Aligned_cols=47  Identities=17%  Similarity=0.145  Sum_probs=43.9

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ..|+++|++|+.+.+     .|+|.+|||+.|++|+.||+...+++++||.-
T Consensus       154 ~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v  200 (216)
T PRK10100        154 ALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAV  200 (216)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            459999999999998     59999999999999999999999999999864

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=97.27  E-value=0.00047  Score=66.73  Aligned_cols=47  Identities=30%  Similarity=0.352  Sum_probs=43.6

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ..|++||++|+.+.-     +|+|.+|||+.|++|+.||+.+.++.++||.-
T Consensus       147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v  193 (211)
T COG2197         147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGV  193 (211)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence            469999999999877     79999999999999999999999999999853

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=97.23  E-value=0.0006  Score=67.38  Aligned_cols=46  Identities=15%  Similarity=0.251  Sum_probs=43.2

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|++||.+..     +|+|.+|||++||||+.||+.++.++++||--
T Consensus       179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~  224 (240)
T PRK10188        179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFNA  224 (240)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            59999999999986     79999999999999999999999999999863

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=97.13  E-value=0.00043  Score=68.39  Aligned_cols=81  Identities=19%  Similarity=0.196  Sum_probs=64.4

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHH-HHHHHHHHHHHHHHHHHhCCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQ-IQDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~-iq~l~kle~a~~~L~~~lGRe  302 (473)
                      +..+..+..|.+|+.++|+     ++++|   .+|+..|..+ .|           +. .....++..+...+...+|+.
T Consensus        73 ~~~~~~~~~f~tyl~~~i~-----n~~~~---~lr~~~~~ir-i~-----------~~~~~~~~~~~~~~~~l~~~~~r~  132 (255)
T TIGR02941        73 RYDYSIGNAFEPFAIPTII-----GEIKR---YLRDKTWSVH-VP-----------RRIKELGPKIKKAIDELTDHLQRS  132 (255)
T ss_pred             HcCCcCCCCcHhHHHHHHH-----HHHHH---HHHHcCCCcC-CC-----------HHHHHHHHHHHHHHHHHHHHhCCC
Confidence            4456677899999999999     99998   4888877443 32           11 233457888899999999999


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHh
Q 011992          303 PTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       303 PT~eEiA~~lGms~eeL~~~l~  324 (473)
                      |+.+|+|+.+|++.+++...+.
T Consensus       133 p~~~eia~~l~i~~~~~~~~~~  154 (255)
T TIGR02941       133 PKIIEIADHLGLSEEEVLEIME  154 (255)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHH
Confidence            9999999999999998876554

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

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=97.10  E-value=0.0021  Score=61.73  Aligned_cols=59  Identities=17%  Similarity=0.271  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          396 QLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       396 ~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      ......+...+.+|++|||+|+...-     .|+..++||..||||+.||.-+..+.+.|++..
T Consensus       130 ~~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~  188 (202)
T COG4566         130 ADRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQAR  188 (202)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhc
Confidence            34567888999999999999999887     699999999999999999999999999998764

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.10  E-value=0.00093  Score=57.27  Aligned_cols=49  Identities=22%  Similarity=0.244  Sum_probs=41.9

Q ss_pred             HHHHHHH-hhCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHH
Q 011992          400 QHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQL  448 (473)
Q Consensus       400 e~L~~aL-~~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi  448 (473)
                      +.+...| ..|+|+|+.+|..||+|.+   ..++|++|||+.+|||..+|...
T Consensus        23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~   75 (94)
T TIGR01321        23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG   75 (94)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence            3455566 3499999999999999987   67999999999999999999764

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.

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=97.08  E-value=0.0015  Score=57.26  Aligned_cols=52  Identities=19%  Similarity=0.170  Sum_probs=48.4

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~  463 (473)
                      .|+..|-+.|+|.++    +++|++|.|+.||||+.|+..++..|.+|+-..|-..
T Consensus        41 ~L~~dElEAiRL~D~----egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~G   92 (106)
T PF02001_consen   41 VLTVDELEAIRLVDY----EGLSQEEAAERMGVSRPTFQRILESARKKIADALVEG   92 (106)
T ss_pred             EeeHHHHHHHHHHHH----cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCC
Confidence            488899999999999    9999999999999999999999999999999887654

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=97.06  E-value=0.00076  Score=49.67  Aligned_cols=41  Identities=24%  Similarity=0.339  Sum_probs=24.8

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ..|++.||..|...+-    +|+|..|||+.||++.+||+..++|
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            3589999999988887    8999999999999999999998876

>PRK09483 response regulator; Provisional

Probab=96.99  E-value=0.0014  Score=60.91  Aligned_cols=46  Identities=22%  Similarity=0.300  Sum_probs=42.1

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++|++|+.+..     +|++.+|||+.|++|..||+.+.++.++||-
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     7999999999999999999999999999984

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=96.94  E-value=0.003  Score=48.56  Aligned_cols=48  Identities=33%  Similarity=0.432  Sum_probs=43.0

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      ..|+++|.+++.+.-     .|++.+|||..+|+|..+|+....++..||.-.
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            358999999998877     579999999999999999999999999998643

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.93  E-value=0.002  Score=58.33  Aligned_cols=46  Identities=22%  Similarity=0.382  Sum_probs=42.3

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++|++|+.+ +.    ++++.+|||+.|++|..||+....++++||.
T Consensus       148 ~~lt~~e~~vl~l-~~----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~  193 (211)
T PRK15369        148 PLLTPRERQILKL-IT----EGYTNRDIAEQLSISIKTVETHRLNMMRKLD  193 (211)
T ss_pred             cCCCHHHHHHHHH-HH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            4599999999998 44    8999999999999999999999999999985

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.90  E-value=0.0068  Score=54.25  Aligned_cols=64  Identities=20%  Similarity=0.237  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHH-hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          396 QLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       396 ~el~e~L~~aL-~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      ......+..++ +.|++.+|.||..+|. + .++++..+|+..||+|+.+...+..+|+.++-..+.
T Consensus        66 ~~~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~  130 (132)
T TIGR01637        66 EQEARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG  130 (132)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence            34456777888 9999999999999998 1 128899999999999999999999999999877664

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.

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=96.84  E-value=0.0005  Score=49.01  Aligned_cols=33  Identities=42%  Similarity=0.469  Sum_probs=29.2

Q ss_pred             hhHHhhhcccCccCCCChHHHHHHHHHHHHHHH
Q 011992          255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIR  287 (473)
Q Consensus       255 ~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~k  287 (473)
                      |+++.|+..+++.|+||++||++|+++|+....
T Consensus         2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~   34 (37)
T PF00140_consen    2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE   34 (37)
T ss_dssp             HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence            579999999999999999999999999998654

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 ....

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.79  E-value=0.0032  Score=61.02  Aligned_cols=54  Identities=20%  Similarity=0.265  Sum_probs=47.0

Q ss_pred             hCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          408 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      .|+++|++||..-|-.+.   -+.-+++|||+.||||.+++.+++++|.+||=..+.
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~~  211 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAYF  211 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence            699999999998776432   478899999999999999999999999999866543

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.75  E-value=0.0035  Score=54.24  Aligned_cols=48  Identities=25%  Similarity=0.328  Sum_probs=43.9

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .-|+.+++..+.+||.    .++|+.|||+.++||++.|...++|+-..|-.
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            3489999999999999    99999999999999999999999998877654

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.71  E-value=0.005  Score=55.45  Aligned_cols=54  Identities=13%  Similarity=0.185  Sum_probs=47.4

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ..+...+..|++++++|+.+.+     .+++.++||+.+|+|..+|+....++++||+.
T Consensus       133 ~~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~  186 (202)
T PRK09390        133 ADIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQA  186 (202)
T ss_pred             HHHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence            3456677889999999999744     68999999999999999999999999999864

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=96.69  E-value=0.0011  Score=66.78  Aligned_cols=79  Identities=19%  Similarity=0.192  Sum_probs=60.2

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhh---hcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLF---LWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG  300 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~---~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lG  300 (473)
                      +..+..|..|.||+.|+++     +++.++   ++..   .|.|++.              ++.++.+.+....+...+|
T Consensus        90 ~fd~~~g~~f~tya~w~i~-----~ain~~---i~~~~~~~~~p~~~--------------~~~~~~~~r~~~~l~~~~~  147 (285)
T TIGR02394        90 KFDPERGFRFSTYATWWIR-----QTIERA---IMNQARTIRLPVHV--------------IKELNVYLRAARQLEKKLG  147 (285)
T ss_pred             HhCCCCCCCcHhhhHHHHH-----HHHHHH---HHHcCCceeCcHHH--------------HHHHHHHHHHHHHHHHHhC
Confidence            4567788899999999999     888663   4333   3445544              3455556666677788899


Q ss_pred             CCCCHHHHHHHcCCCHHHHHHHHh
Q 011992          301 REPTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       301 RePT~eEiA~~lGms~eeL~~~l~  324 (473)
                      ++|+..|+|..+|++.+++..++.
T Consensus       148 r~~~~~e~a~~l~~~~~~~~~~~~  171 (285)
T TIGR02394       148 REPSVEEIAELLDKPVEDVSRVLA  171 (285)
T ss_pred             CCCCHHHHHHHhCcCHHHHHHHHH
Confidence            999999999999999988887654

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).

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.64  E-value=0.0037  Score=57.34  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=42.2

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++|++|+.+..     ++++.+|||+.|++|..||+...++.++||.
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            359999999999865     7899999999999999999999999999985

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=96.36  E-value=0.0095  Score=58.91  Aligned_cols=81  Identities=17%  Similarity=0.219  Sum_probs=63.2

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHH-HHHHHHHHHHHHHHHHhCCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQI-QDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~i-q~l~kle~a~~~L~~~lGRe  302 (473)
                      +..+..+..|.+|+.++|+     +.++|   .+|+..|..+ +|           +.+ ....++..+...+...+|+.
T Consensus        73 ~f~~~~~~~f~tyl~~~i~-----n~~~~---~lr~~~~~~~-i~-----------r~~~~~~~~~~~~~~~~~~~~~r~  132 (257)
T PRK08583         73 RYDPSFGRSFEAFAVPTII-----GEIKR---YLRDKTWSVH-VP-----------RRIKELGPKIKKAVDELTTELQRS  132 (257)
T ss_pred             HcCccCCCChHHHHHHHHH-----HHHHH---HHHhcCCCcC-CC-----------HHHHHHHHHHHHHHHHHHHHhCCC
Confidence            4556677789999999999     99998   4888888443 22           222 33457778888899999999


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHh
Q 011992          303 PTLIEWAKAIGLSCRDLKSELH  324 (473)
Q Consensus       303 PT~eEiA~~lGms~eeL~~~l~  324 (473)
                      |+.+|+|+.+|++.+++.....
T Consensus       133 ~~~~e~a~~~~~~~~~~~~~~~  154 (257)
T PRK08583        133 PKISEIADRLGVSEEEVLEAME  154 (257)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHH
Confidence            9999999999999988766543

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=96.21  E-value=0.013  Score=50.26  Aligned_cols=51  Identities=20%  Similarity=0.133  Sum_probs=47.3

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccC
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK  463 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~  463 (473)
                      |+..|-++|+|..+    ++++++|-|..||||+.|+...+..|++|+-..|-+.
T Consensus        34 lt~eElEAlRLvD~----~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG   84 (99)
T COG1342          34 LTIEELEALRLVDY----EGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG   84 (99)
T ss_pred             ecHHHHHHHHHHhH----hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence            77888999999999    9999999999999999999999999999999887654

>PRK01381 Trp operon repressor; Provisional

Probab=96.17  E-value=0.0066  Score=52.54  Aligned_cols=48  Identities=27%  Similarity=0.320  Sum_probs=39.5

Q ss_pred             HHHHHHHhh-CCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHH
Q 011992          400 QHVRNLLTL-LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQ  447 (473)
Q Consensus       400 e~L~~aL~~-LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrq  447 (473)
                      +.+...|.. |+|+|+.+|..||.|..   ..++|++|||+.+|||..+|..
T Consensus        23 ~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR   74 (99)
T PRK01381         23 DLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR   74 (99)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence            445555655 99999999999998876   4579999999999999887754

>PRK10403 transcriptional regulator NarP; Provisional

Probab=96.16  E-value=0.01  Score=54.17  Aligned_cols=46  Identities=15%  Similarity=0.230  Sum_probs=41.8

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++|.+|+.+..     ++.|.+|||+.+|+|+.||+..+.+.++||.
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            359999999998765     6899999999999999999999999999884

>PRK15320 transcriptional activator SprB; Provisional

Probab=96.04  E-value=0.012  Score=56.92  Aligned_cols=67  Identities=19%  Similarity=0.212  Sum_probs=50.6

Q ss_pred             CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          386 VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       386 ~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .+.|++.+..-. .-.....--.|+++|.+|+.+--     .|+|.+|||+.|++|.++|+...++.+.||.-
T Consensus       143 ~~~~~~~~~~~~-~~~~~~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA  209 (251)
T PRK15320        143 GETPEEVLFNIN-QYAWWNLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM  209 (251)
T ss_pred             CCChHHHhhhcc-ceeeecCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence            455665443211 11233344679999999998876     69999999999999999999999999988863

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=95.96  E-value=0.006  Score=54.84  Aligned_cols=47  Identities=26%  Similarity=0.352  Sum_probs=43.7

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      |++++-+|+.||-     .|+|.+|||++||-|+..|+-|+++|+.++.+..
T Consensus         9 lte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar   55 (143)
T COG1356           9 LTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR   55 (143)
T ss_pred             eehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence            8899999999998     6999999999999999999999999999987753

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.84  E-value=0.014  Score=66.69  Aligned_cols=47  Identities=11%  Similarity=0.155  Sum_probs=43.4

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ..|+++|++|+.+..     +|+|.+|||+.|+||.+||+.++++...||.-
T Consensus       837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v  883 (903)
T PRK04841        837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLGI  883 (903)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            349999999999977     79999999999999999999999999999863

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.73  E-value=0.023  Score=52.10  Aligned_cols=45  Identities=24%  Similarity=0.242  Sum_probs=40.1

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .|+++|..|+.+..     ++++.+|||+.|++|..+|+....++++||.
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            38899998887643     6899999999999999999999999999985

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.68  E-value=0.022  Score=63.26  Aligned_cols=55  Identities=13%  Similarity=0.085  Sum_probs=46.3

Q ss_pred             HhhCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          406 LTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       406 L~~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ...|+++|+++|..-|..+.   -++-|..|||+.||||.+++++++++|.+||=..+
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            46799999999999887221   13449999999999999999999999999986654

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=95.65  E-value=0.025  Score=51.93  Aligned_cols=47  Identities=21%  Similarity=0.320  Sum_probs=42.3

Q ss_pred             HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      +..|+++|.+|+.+..     .+.+.+|||+.+++|..+|+...++.++||.
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            3569999999998877     6889999999999999999999999998884

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=95.63  E-value=0.032  Score=42.48  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=43.2

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      +|+..++.++.|.|.   -.+.+++.||..+|||+++|+++.+..+.-|...+
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            588889988887665   38899999999999999999999999988877654

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=95.63  E-value=0.015  Score=57.05  Aligned_cols=73  Identities=10%  Similarity=0.024  Sum_probs=50.7

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe  302 (473)
                      .+.++.+|..|.+|+.++|+     |+++|+   +|+.......+++-...+|        ....+..+..++..++++.
T Consensus        54 ~~yd~~kg~~F~sya~~~Ir-----~~i~dy---lRk~~k~~~~v~~~~~~~e--------~~~~~~~~~~~~~~~~~~~  117 (218)
T TIGR02895        54 ESYDSNKGKSFLSFAKLIIK-----RRLIDY---IRKNQKYQNLLYLDEDYDE--------NPLEFNKSMEEYRNEIENE  117 (218)
T ss_pred             HHCCCCCCCCHHHHHHHHHH-----HHHHHH---HHhcccccCeeeCCchHHH--------HHHHHHHHHHHHHHHHccc
Confidence            45678999999999999999     999994   8876522112221111111        2335556677888899999


Q ss_pred             CCHHHHHHH
Q 011992          303 PTLIEWAKA  311 (473)
Q Consensus       303 PT~eEiA~~  311 (473)
                      |+.+||+..
T Consensus       118 ~~~eEI~~~  126 (218)
T TIGR02895       118 NRRLEILEY  126 (218)
T ss_pred             cHHHHHHHH
Confidence            999999873

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).

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.61  E-value=0.03  Score=51.02  Aligned_cols=46  Identities=20%  Similarity=0.255  Sum_probs=41.8

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++|.+|+.+..     ++++.++||+.|++|..+|+.+.++.++||.
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            359999999999866     5899999999999999999999999998885

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

Probab=95.53  E-value=0.14  Score=53.31  Aligned_cols=125  Identities=16%  Similarity=0.149  Sum_probs=80.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCC-C-------cccc------------------C
Q 011992          331 EKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAG-C-------RFAN------------------T  384 (473)
Q Consensus       331 e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg-~-------~FsT------------------~  384 (473)
                      +..+..-.+.+..-.-+|.++-.-+||.+||+|+...+...+--+... .       +|..                  .
T Consensus         8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el~~   87 (415)
T COG4941           8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRNPAAWLIAVGRNRAIDRVRRRARRDAAPPELLL   87 (415)
T ss_pred             HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCChHHHHHHHHhhhHHHHHHHHHHhccCChhhcc
Confidence            334444555566666677788888999999999865544332211110 0       0000                  0


Q ss_pred             CCCCchHH---------HHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992          385 GVEIPDIS---------VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  455 (473)
Q Consensus       385 ~~~~pee~---------le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K  455 (473)
                      ..++.+..         +.++.++-.+.-|=-.||+.+|-.+.|+..    .|+|..|||..+=|++.++-|.+.||..+
T Consensus        88 ~~e~~e~~~a~~~~d~~i~Dd~LRLiFvccHPal~~~~riALtLR~v----~GLs~~eIArAFLv~e~am~QRivRAK~r  163 (415)
T COG4941          88 SDEDEEMEEAEALDDEHIRDDRLRLIFVCCHPALPPEQRIALTLRLV----GGLSTAEIARAFLVPEAAMAQRIVRAKAR  163 (415)
T ss_pred             cccchhhhccccccccccchhhHHhhhhhcCCCCChhhHHHHHHHHH----cCCcHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            00111111         111112222222225699999999999999    89999999999999999999999999999


Q ss_pred             HHHH
Q 011992          456 LKQS  459 (473)
Q Consensus       456 LR~~  459 (473)
                      ++..
T Consensus       164 i~~a  167 (415)
T COG4941         164 IREA  167 (415)
T ss_pred             HHhc
Confidence            9974

>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=95.47  E-value=0.024  Score=45.34  Aligned_cols=46  Identities=17%  Similarity=0.403  Sum_probs=30.3

Q ss_pred             HhhCCHHHHHHHHH--HhhccCCCCCCHHHHHHHHCCC-HHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLS-KERVRQLESR  451 (473)
Q Consensus       406 L~~LperER~VL~L--rY~L~~ge~lTlkEIAe~LGIS-~~rVrqi~~R  451 (473)
                      +..|+++|++||..  .|.-..|..+|+.|||+.+|++ .++|.+.+..
T Consensus         1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~   49 (65)
T PF01726_consen    1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA   49 (65)
T ss_dssp             -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            35799999999865  3333457899999999999996 9999886543

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.

>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=95.26  E-value=0.057  Score=39.76  Aligned_cols=42  Identities=17%  Similarity=0.226  Sum_probs=30.6

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      |++.++.||..-+.   +.+.|..|||+.+|+|.++|++++++-.
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            56778888866554   3569999999999999999999776543

...

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=95.24  E-value=0.026  Score=58.22  Aligned_cols=36  Identities=22%  Similarity=0.344  Sum_probs=33.2

Q ss_pred             HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      .|-.|||.    +++|..|||+.||||+.+|++++.+|++
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            46678998    9999999999999999999999999985

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=95.17  E-value=0.019  Score=42.56  Aligned_cols=32  Identities=28%  Similarity=0.361  Sum_probs=22.9

Q ss_pred             HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          416 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       416 VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      +|.++.     +|.|..+||+.+|||+.+|+.+.++-
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            455555     59999999999999999999998764

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=94.56  E-value=0.082  Score=44.86  Aligned_cols=39  Identities=15%  Similarity=0.244  Sum_probs=31.3

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ..|++| ..|+.+.-     .|+|..|||+.+|||+.||..+ .++
T Consensus        35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi-~R~   73 (88)
T TIGR02531        35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRV-KRC   73 (88)
T ss_pred             HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHH-HHh
Confidence            458888 77766644     6899999999999999999984 444

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.

>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=94.51  E-value=0.092  Score=34.10  Aligned_cols=36  Identities=19%  Similarity=0.335  Sum_probs=28.7

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL  448 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi  448 (473)
                      +++.++..+...|.    .+.+..+||+.+|++..+|+.+
T Consensus         6 ~~~~~~~~i~~~~~----~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLLA----AGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHh
Confidence            55666666666665    6789999999999999999875

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=94.32  E-value=0.26  Score=44.21  Aligned_cols=54  Identities=19%  Similarity=0.121  Sum_probs=48.3

Q ss_pred             HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      .|..-.+.+-.+|.+||.    .+.|...||..+++|...|++.+.+|-.-+..+|.-
T Consensus        59 ~L~~~~~~~~~ll~~~Yv----~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~  112 (125)
T PF06530_consen   59 RLKKRDPEEYDLLILYYV----YGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSM  112 (125)
T ss_pred             HHHccCHHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHH
Confidence            345578889999999999    999999999999999999999999999998887643

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

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=93.48  E-value=0.31  Score=44.32  Aligned_cols=56  Identities=16%  Similarity=0.337  Sum_probs=46.4

Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 011992          399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRL  456 (473)
Q Consensus       399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KL  456 (473)
                      ...|...++.|.+.++.||.|+|.  ...++|-.+||..|++++.+++.+...-...+
T Consensus        72 k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i  127 (130)
T PF05263_consen   72 KEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKNDI  127 (130)
T ss_pred             HHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence            456778889999999999999998  22459999999999999999998776654433

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>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=93.30  E-value=0.15  Score=40.37  Aligned_cols=38  Identities=16%  Similarity=0.279  Sum_probs=29.0

Q ss_pred             HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +--..+.+|..  .+..+++++||+.||||.++|+...++
T Consensus         8 ~rdkA~e~y~~--~~g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen    8 NRDKAFEIYKE--SNGKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             CHHHHHHHHHH--hCCCccHHHHHHHHCCCHHHHHHHhhh
Confidence            33445555543  346899999999999999999987654

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 [].

>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=92.98  E-value=0.3  Score=35.68  Aligned_cols=40  Identities=33%  Similarity=0.422  Sum_probs=27.6

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++-.+.||...-.   +...++.+||+.+|+|+.+|...+.+
T Consensus         1 lD~~D~~Il~~Lq~---d~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    1 LDELDRKILRLLQE---DGRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence            34556677665443   25789999999999999999987764

...

>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=92.97  E-value=0.13  Score=37.90  Aligned_cols=33  Identities=24%  Similarity=0.296  Sum_probs=24.2

Q ss_pred             HHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          413 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       413 ER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      ..+|+.|+-     +|+|..+||+.+|||+.||..++.
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            455666665     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 ....

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=92.96  E-value=1.3  Score=47.67  Aligned_cols=24  Identities=29%  Similarity=0.483  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      .++|+++||+.+|++++||+...+
T Consensus       317 kPLtlkdiA~~lglheSTVSRav~  340 (429)
T TIGR02395       317 KPLTLREVAEELGLHESTISRAIN  340 (429)
T ss_pred             cCCcHHHHHHHhCCCccchhhhhc
Confidence            789999999999999999998765

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations

>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=92.80  E-value=0.23  Score=38.90  Aligned_cols=33  Identities=18%  Similarity=0.249  Sum_probs=27.4

Q ss_pred             HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .+..||.     .|++.+|||+.||++..+|.....+-
T Consensus         5 ~A~~LY~-----~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen    5 QARSLYL-----QGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             HHHHHHH-----cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            3445554     79999999999999999999988763

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=92.77  E-value=0.15  Score=52.90  Aligned_cols=36  Identities=22%  Similarity=0.262  Sum_probs=32.3

Q ss_pred             HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      .+-.|||.    +++|..|||+.||||+.+|+..+.+|++
T Consensus        17 ~~A~lYY~----~gltQ~eIA~~LgiSR~~v~rlL~~Ar~   52 (321)
T COG2390          17 RAAWLYYV----EGLTQSEIAERLGISRATVSRLLAKARE   52 (321)
T ss_pred             HHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            34578998    9999999999999999999999999875

>PHA00675 hypothetical protein

Probab=92.73  E-value=0.22  Score=41.22  Aligned_cols=41  Identities=17%  Similarity=0.072  Sum_probs=33.2

Q ss_pred             hhCCHHHHHHHHHHh-hccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRF-GIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       407 ~~LperER~VL~LrY-~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ..|++.+-+.|+..+ .    .+.|+.+||+.||||+++|.+|...
T Consensus        21 AKLt~~qV~~IR~l~~r----~G~s~~~IA~~fGVsrstV~~I~~g   62 (78)
T PHA00675         21 AKLTDAEVERIRELHEV----EGMSYAVLAEKFEQSKGAIAKICRY   62 (78)
T ss_pred             cccCHHHHHHHHHHHHh----cCccHHHHHHHhCCCHHHHHHHHcc
Confidence            357777777666555 5    7889999999999999999998754

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=92.70  E-value=0.33  Score=43.13  Aligned_cols=50  Identities=20%  Similarity=0.299  Sum_probs=43.3

Q ss_pred             HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .+..|++.+..-|.....    ..=+++|+++.||||..|||..+.+.+.+|.-
T Consensus        30 ~~~~L~~E~~~Fi~~Fi~----~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   30 WFARLSPEQLEFIKLFIK----NRGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hhhcCCHHHHHHHHHHHH----hcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            456799888887776665    56699999999999999999999999999976

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=92.63  E-value=0.25  Score=47.69  Aligned_cols=48  Identities=15%  Similarity=0.070  Sum_probs=36.8

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  455 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K  455 (473)
                      .|++++.+++.....=..++|+|.+|||+.||+|+.||+....++...
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            488888777654431112389999999999999999999999887543

>PF13518 HTH_28: Helix-turn-helix domain

Probab=92.62  E-value=0.23  Score=36.62  Aligned_cols=28  Identities=25%  Similarity=0.336  Sum_probs=24.1

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      ++.|+.+||+.+|||..+|+.++.+-..
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~~y~~   38 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIKRYRE   38 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence            5669999999999999999998876543

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=92.20  E-value=0.17  Score=58.15  Aligned_cols=47  Identities=17%  Similarity=0.093  Sum_probs=43.6

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      .|+.||++|+.+.|     .|+|.+|||+.|.||..||+.++...-.||.-.
T Consensus       831 ~Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~  877 (894)
T COG2909         831 PLSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVA  877 (894)
T ss_pred             CccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence            49999999999999     699999999999999999999999999998643

>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=92.19  E-value=0.19  Score=38.45  Aligned_cols=40  Identities=20%  Similarity=0.305  Sum_probs=28.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|+-.++.=+.-+|.    .|.+..+||..+||+.+||+.|+..
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            466667665555566    7889999999999999999999875

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.

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=92.17  E-value=0.18  Score=35.07  Aligned_cols=24  Identities=21%  Similarity=0.573  Sum_probs=17.7

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          428 PKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       428 ~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ++|.+|||+.+|+++++|+.++++
T Consensus         2 ~mtr~diA~~lG~t~ETVSR~l~~   25 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVSRILKK   25 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHHHHHHH
Confidence            478999999999999999875543

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 ....

>smart00351 PAX Paired Box domain

Probab=91.91  E-value=0.44  Score=42.57  Aligned_cols=42  Identities=14%  Similarity=0.051  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      ++..+|.-|.+.|.    ++.+..+||+.+|||..+|..++.+...
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            56666665556666    7899999999999999999999998653

>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=91.86  E-value=0.39  Score=36.64  Aligned_cols=45  Identities=22%  Similarity=0.262  Sum_probs=32.8

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .|++.+..||...+. .++.++|..|||+.+|++.++|+.++.+-.
T Consensus         2 glt~~q~~vL~~l~~-~~~~~~t~~~la~~l~~~~~~vs~~v~~L~   46 (62)
T PF12802_consen    2 GLTPSQFRVLMALAR-HPGEELTQSELAERLGISKSTVSRIVKRLE   46 (62)
T ss_dssp             TSTHHHHHHHHHHHH-STTSGEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH-CCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477788888776555 122338999999999999999998766543

...

>PRK05932 RNA polymerase factor sigma-54; Reviewed

Probab=91.25  E-value=2.6  Score=45.89  Aligned_cols=45  Identities=13%  Similarity=0.373  Sum_probs=32.0

Q ss_pred             HhhCCHHHHHHHHH---------HhhccCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       406 L~~LperER~VL~L---------rY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      +..|.-|.+.++..         -|+..|.   .++|+++||+.+|+.++||+...+
T Consensus       309 i~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~  365 (455)
T PRK05932        309 IKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATT  365 (455)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhc
Confidence            34566666655433         3433332   789999999999999999998764

>PF13730 HTH_36: Helix-turn-helix domain

Probab=91.16  E-value=0.82  Score=34.34  Aligned_cols=43  Identities=16%  Similarity=0.200  Sum_probs=31.0

Q ss_pred             hCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      .|++.++.|+..-....+   +--+|.+.||+.+|+|+.+|...+.
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~   47 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIK   47 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            588888888754333322   2334999999999999999987443

>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=90.49  E-value=0.98  Score=36.15  Aligned_cols=56  Identities=18%  Similarity=0.287  Sum_probs=43.9

Q ss_pred             HHHHHhhcchHHHHHHHHHHHHHHHHHHHhh----c--CCcchhhHhhhhHHHHHHHhhhhC
Q 011992          319 LKSELHSGNSSREKLINANLRLVVHVAKQYQ----G--RGISLHDLLQEGSMGLMKSVEKFK  374 (473)
Q Consensus       319 L~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~----~--~~~saEDLiQEg~lgL~kAiekFD  374 (473)
                      +.++..|+..|.++++..|.+++.+++.+-.    +  ++.-=+|+-|+--..|+.++-+|+
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            4455556669999999999999999997732    2  123347999999999999999885

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

>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=90.19  E-value=0.78  Score=33.81  Aligned_cols=37  Identities=27%  Similarity=0.390  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |.-..|+.+-..    .+++..||++.+|+|+++|++.+..
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            344455555544    7899999999999999999997654

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 ....

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=89.84  E-value=0.49  Score=43.78  Aligned_cols=50  Identities=14%  Similarity=0.050  Sum_probs=42.9

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLS-----KERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS-----~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|.+|+.+... +.|+.+|.+||++.++.+     ..+|+.++++.++||..
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            499999999987764 445679999999999986     78999999999999974

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=89.45  E-value=0.81  Score=38.66  Aligned_cols=45  Identities=29%  Similarity=0.339  Sum_probs=34.7

Q ss_pred             HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH--CCCHHHHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF--GLSKERVRQLESRAL  453 (473)
Q Consensus       406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~L--GIS~~rVrqi~~RAL  453 (473)
                      ++.||+..+++..+|..   ..+.|+.|+|+.|  .||.+.|..++.+..
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            47899999999988875   4789999999999  999999998876643

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>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=89.17  E-value=0.66  Score=36.38  Aligned_cols=43  Identities=19%  Similarity=0.396  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHhhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~-~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++....-|...|.|. +++..+..+||+.||+|..+|...+++
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~   45 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKR   45 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHH
Confidence            4555555555555554 468899999999999999999985443

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 ....

>cd00131 PAX Paired Box domain

Probab=89.15  E-value=1.1  Score=40.37  Aligned_cols=42  Identities=12%  Similarity=-0.005  Sum_probs=33.1

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      |+...|.-|.+.|.    +|++..+||+.+|||.++|..++++-..
T Consensus        18 lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~e   59 (128)
T cd00131          18 LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYYE   59 (128)
T ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            55555554445566    8999999999999999999999887553

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=89.14  E-value=0.75  Score=42.26  Aligned_cols=35  Identities=26%  Similarity=0.232  Sum_probs=29.2

Q ss_pred             HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .++..+++    +|+|.+|||+++|||.++|..++.+-.
T Consensus        12 ~~~~~~~~----~G~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415          12 RVVDAVVG----EGLSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             HHHHHHHH----cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence            34455555    899999999999999999999988754

>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=88.90  E-value=1.1  Score=37.43  Aligned_cols=43  Identities=23%  Similarity=0.409  Sum_probs=35.2

Q ss_pred             hCCHHHHHHHHH--HhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          408 LLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       408 ~LperER~VL~L--rY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      .|++++++||..  .-++..|++-.-++||+.+|+|..+||+.+.
T Consensus         1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~   45 (78)
T PF03444_consen    1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA   45 (78)
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence            388999999864  2234567999999999999999999999654

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

>PHA02591 hypothetical protein; Provisional

Probab=88.68  E-value=0.9  Score=37.84  Aligned_cols=24  Identities=21%  Similarity=0.436  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      .|+|.++||+.||++.++|++.+.
T Consensus        58 qGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         58 KGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHh
Confidence            799999999999999999999865

>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=88.50  E-value=1.6  Score=33.76  Aligned_cols=36  Identities=28%  Similarity=0.374  Sum_probs=27.4

Q ss_pred             HHHHHHHHHH-hhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          411 PKERCIVRLR-FGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       411 erER~VL~Lr-Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      |.-+.|+.+- -.    +++|..|||+.+|++.++|+..+.
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            5555565554 33    899999999999999999988654

...

>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=88.21  E-value=0.95  Score=33.97  Aligned_cols=39  Identities=21%  Similarity=0.417  Sum_probs=26.9

Q ss_pred             HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      |++.|+.+-+  ..++..|.+|||+.||||+.+|+..+...
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            3455555432  23355999999999999999999865543

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 ....

>PRK12469 RNA polymerase factor sigma-54; Provisional

Probab=87.97  E-value=8.7  Score=42.21  Aligned_cols=45  Identities=20%  Similarity=0.261  Sum_probs=32.6

Q ss_pred             HhhCCHHHHHHHHH---------HhhccCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRL---------RFGIEDG---KPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       406 L~~LperER~VL~L---------rY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      +..|..|.+.++..         -|+..|.   .++++++||+.+|+.++||+...+
T Consensus       335 i~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~  391 (481)
T PRK12469        335 IRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG  391 (481)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence            35566666666543         3333332   789999999999999999998765

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=87.92  E-value=1.5  Score=35.11  Aligned_cols=24  Identities=17%  Similarity=0.284  Sum_probs=21.1

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          428 PKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       428 ~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +.+..|||+.+||+..+|++++.+
T Consensus        22 ~~ta~eLa~~lgl~~~~v~r~L~~   45 (68)
T smart00550       22 TSTALQLAKNLGLPKKEVNRVLYS   45 (68)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHH
Confidence            599999999999999999886553

Helix-turn-helix-containing domain. Also known as Zab.

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=87.65  E-value=1.4  Score=32.68  Aligned_cols=26  Identities=27%  Similarity=0.429  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      +..|+++||+.+|||..+|..++.+.
T Consensus        26 ~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   26 ESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            34799999999999999999998764

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=87.64  E-value=1.1  Score=36.91  Aligned_cols=37  Identities=27%  Similarity=0.352  Sum_probs=26.6

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH-----HHHHHHHHHhccC
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLES-----RALYRLKQSLGGK  463 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~-----RAL~KLR~~L~~~  463 (473)
                      .++|..|+|+.||++.++|+.+++     -.+.+|...+..-
T Consensus        30 ~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aL   71 (80)
T PF13744_consen   30 RGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEAL   71 (80)
T ss_dssp             CT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHc
Confidence            899999999999999999999985     2466666665543

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=87.54  E-value=0.91  Score=41.83  Aligned_cols=49  Identities=16%  Similarity=0.180  Sum_probs=41.6

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK  457 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR  457 (473)
                      .|+++|.+|+.+... +.|..+|.+||++.+.     ++..+|+..+++.++||.
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            499999999986663 3345699999999996     999999999999888885

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=87.40  E-value=0.61  Score=44.68  Aligned_cols=40  Identities=15%  Similarity=0.174  Sum_probs=29.4

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|+++  +|+.+.-.  +..|+|.+|||+.||||+.||+.....
T Consensus       161 ~Lt~r--~Vl~~~~~--g~~g~s~~eIa~~l~iS~~Tv~~~~~~  200 (225)
T PRK10046        161 PLTLN--AVRKLFKE--PGVQHTAETVAQALTISRTTARRYLEY  200 (225)
T ss_pred             HHHHH--HHHHHHHc--CCCCcCHHHHHHHhCccHHHHHHHHHH
Confidence            35554  56655432  223799999999999999999998753

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=87.29  E-value=1.5  Score=37.28  Aligned_cols=42  Identities=26%  Similarity=0.224  Sum_probs=32.5

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      |++.++.|+.....   +...|..|||+.+|+|+.+|+..+.+-.
T Consensus         1 ld~~D~~il~~L~~---~~~~~~~~la~~l~~s~~tv~~~l~~L~   42 (108)
T smart00344        1 LDEIDRKILEELQK---DARISLAELAKKVGLSPSTVHNRVKRLE   42 (108)
T ss_pred             CCHHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            46677888765543   2468999999999999999998766543

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=86.76  E-value=1  Score=42.13  Aligned_cols=50  Identities=18%  Similarity=0.120  Sum_probs=44.0

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|++|+.+... +.|++.+.++|++.+.     ++..+|...+++.++||..
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            499999999987765 4457899999999998     9999999999999999963

>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=86.75  E-value=1.5  Score=35.15  Aligned_cols=25  Identities=28%  Similarity=0.417  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +..|..|||+.||||...|+.++..
T Consensus        19 r~Pt~eEiA~~lgis~~~v~~~l~~   43 (78)
T PF04539_consen   19 REPTDEEIAEELGISVEEVRELLQA   43 (78)
T ss_dssp             S--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCCCHHHHHHHHcccHHHHHHHHHh
Confidence            8999999999999999999987764

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 ....

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=86.73  E-value=0.68  Score=34.58  Aligned_cols=22  Identities=18%  Similarity=0.356  Sum_probs=20.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q 011992          430 SLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       430 TlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++|||+..|||..+|+..++.
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            6899999999999999998764

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 ....

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=86.59  E-value=1.3  Score=34.31  Aligned_cols=43  Identities=19%  Similarity=0.286  Sum_probs=27.3

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      |+..+..||....  ..+++++..+||+.+|++..+|+.++++..
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~   43 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKLE   43 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4556666655444  234899999999999999999997655544

>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=86.48  E-value=1  Score=33.81  Aligned_cols=34  Identities=35%  Similarity=0.461  Sum_probs=25.6

Q ss_pred             HHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          418 RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       418 ~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|.++-..+.++++.|||+.+|+++++|..++..
T Consensus         8 iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~t   41 (52)
T PF09339_consen    8 ILEALAESGGPLTLSEIARALGLPKSTVHRLLQT   41 (52)
T ss_dssp             HHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4444445557789999999999999999887653

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.

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=86.08  E-value=1.3  Score=40.73  Aligned_cols=49  Identities=18%  Similarity=0.233  Sum_probs=41.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLK  457 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR  457 (473)
                      .|+++|.+|+.+... +.|...+.++|++.+.     +|..+|...+++.++||.
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            499999999977653 3346679999999986     999999999999999885

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=85.99  E-value=2.9  Score=34.04  Aligned_cols=54  Identities=19%  Similarity=0.272  Sum_probs=36.4

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHhh-ccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          398 MRQHVRNLLTLLNPKERCIVRLRFG-IEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       398 l~e~L~~aL~~LperER~VL~LrY~-L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +...|......|++.|+.|.....- .+.-..+|..|||+..|||.++|....++
T Consensus         3 l~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kk   57 (77)
T PF01418_consen    3 LLEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKK   57 (77)
T ss_dssp             HHHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHH
Confidence            3456777888999999998754221 00116899999999999999999876554

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.

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=85.95  E-value=0.61  Score=42.98  Aligned_cols=49  Identities=16%  Similarity=0.117  Sum_probs=41.6

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEV-----GNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEI-----Ae~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .|+++|.+|+.+... +.|+++|.++|     |+.++++..+|+..+++.++||.
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~  207 (226)
T TIGR02154       154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALN  207 (226)
T ss_pred             EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhc
Confidence            499999999887764 33467888888     77899999999999999999986

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.

>PRK12423 LexA repressor; Provisional

Probab=85.90  E-value=1.5  Score=42.09  Aligned_cols=48  Identities=29%  Similarity=0.468  Sum_probs=35.7

Q ss_pred             hhCCHHHHHHHHHHh--hccCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRF--GIEDGKPKSLSEVGNIFG-LSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       407 ~~LperER~VL~LrY--~L~~ge~lTlkEIAe~LG-IS~~rVrqi~~RAL~KLR~  458 (473)
                      ..|++++++|+..--  ....|-.+|..|||+.+| +|+++|+.    +++.|++
T Consensus         2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~   52 (202)
T PRK12423          2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE   52 (202)
T ss_pred             CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence            348999999986422  223345789999999999 59999995    6666665

>PF12728 HTH_17: Helix-turn-helix domain

Probab=85.74  E-value=0.88  Score=33.72  Aligned_cols=24  Identities=17%  Similarity=0.376  Sum_probs=21.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          429 KSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       429 lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      +|.+|+|+.||||..+|.++..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g   25 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQG   25 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            689999999999999999998654

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=85.53  E-value=3.1  Score=38.39  Aligned_cols=64  Identities=19%  Similarity=0.326  Sum_probs=37.0

Q ss_pred             HHHHHhhCCHHHHHHHHHH----hhccCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHhccCch
Q 011992          402 VRNLLTLLNPKERCIVRLR----FGIEDGKPKSLSEVGNIFGLSKERVRQLES--RALYRLKQSLGGKAS  465 (473)
Q Consensus       402 L~~aL~~LperER~VL~Lr----Y~L~~ge~lTlkEIAe~LGIS~~rVrqi~~--RAL~KLR~~L~~~~l  465 (473)
                      +.+.=..|++.++....+-    |..++|+.+|+.|||+.+||++.++..+.+  ++.....+.+....+
T Consensus         4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~   73 (142)
T PF13022_consen    4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFL   73 (142)
T ss_dssp             HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence            3344467898888854432    222345789999999999999999999985  344444444444433

>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=85.49  E-value=1  Score=38.23  Aligned_cols=45  Identities=24%  Similarity=0.323  Sum_probs=31.9

Q ss_pred             CCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       409 LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      +++.|+.-+..|+.+-.   .+++|+.||++.+|+|..+|.. .+|+|+
T Consensus        27 ~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk   74 (87)
T PF01371_consen   27 CTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLK   74 (87)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHH
Confidence            67777766655544322   2689999999999999999875 344443

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 ....

>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=85.16  E-value=1.7  Score=32.95  Aligned_cols=42  Identities=24%  Similarity=0.384  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      |+..|-.+|...+.   ..+.+..|||+.+|++.++|..+..+-.
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            45556666655443   2679999999999999999998766543

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 ....

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=84.44  E-value=2.3  Score=39.06  Aligned_cols=41  Identities=15%  Similarity=0.261  Sum_probs=33.1

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.++.||.+--.   +...++.|||+.+|+|+++|+.++.+
T Consensus         6 ~lD~~D~~Il~~Lq~---d~R~s~~eiA~~lglS~~tV~~Ri~r   46 (153)
T PRK11179          6 QIDNLDRGILEALME---NARTPYAELAKQFGVSPGTIHVRVEK   46 (153)
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            378888888875543   25789999999999999999987655

>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=84.21  E-value=1.1  Score=35.29  Aligned_cols=41  Identities=17%  Similarity=0.213  Sum_probs=31.0

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.|..|+..-..   ..+.|..|||+.+|+++.+|+..+.+
T Consensus         5 gLs~~E~~vy~~Ll~---~~~~t~~eIa~~l~i~~~~v~~~L~~   45 (68)
T PF01978_consen    5 GLSENEAKVYLALLK---NGPATAEEIAEELGISRSTVYRALKS   45 (68)
T ss_dssp             CHHHHHHHHHHHHHH---HCHEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            467778887643321   16899999999999999999885543

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.

>CHL00148 orf27 Ycf27; Reviewed

Probab=83.98  E-value=1.5  Score=41.09  Aligned_cols=50  Identities=18%  Similarity=0.115  Sum_probs=42.4

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHH-------CCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-------GLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~L-------GIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|.+|+.+... +.|+++|.+||++.+       +++..+|..++++.++||..
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            399999999986653 345789999999999       48999999999999999974

>TIGR00498 lexA SOS regulatory protein LexA

Probab=83.57  E-value=2  Score=40.87  Aligned_cols=45  Identities=18%  Similarity=0.268  Sum_probs=34.6

Q ss_pred             hhCCHHHHHHHHHHhh--ccCCCCCCHHHHHHHHCCC-HHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFG--IEDGKPKSLSEVGNIFGLS-KERVRQLESR  451 (473)
Q Consensus       407 ~~LperER~VL~LrY~--L~~ge~lTlkEIAe~LGIS-~~rVrqi~~R  451 (473)
                      ..|+++|+.||.....  ..+|.+.|..|||+.+|++ .++|..++.+
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~   49 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKA   49 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHH
Confidence            3589999999876442  2345679999999999998 9999875443

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.

>TIGR01764 excise DNA binding domain, excisionase family

Probab=83.12  E-value=1.4  Score=31.41  Aligned_cols=24  Identities=25%  Similarity=0.407  Sum_probs=21.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          429 KSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       429 lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      +|.+|+|+.||||+.+|.++.+..
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            689999999999999999998765

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=82.95  E-value=2.5  Score=40.40  Aligned_cols=45  Identities=24%  Similarity=0.263  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHh--hccCCCCCCHHHHHHHHCC-CHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRF--GIEDGKPKSLSEVGNIFGL-SKERVRQLESRAL  453 (473)
Q Consensus       409 LperER~VL~LrY--~L~~ge~lTlkEIAe~LGI-S~~rVrqi~~RAL  453 (473)
                      |+++|+.||.+..  ....+.++|+.|||+.+|+ +.++|..++.+-.
T Consensus         2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~   49 (205)
T PRK00215          2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE   49 (205)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence            7888999886543  2344578899999999999 9999998765533

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=82.13  E-value=2.6  Score=40.14  Aligned_cols=35  Identities=29%  Similarity=0.358  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          412 KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       412 rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++.|..++ .    +|+|+.+||+.||||.++|..+.+.
T Consensus       161 ~~~~i~~~~-~----~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        161 KEEKIKKLL-D----KGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             hHHHHHHHH-H----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            345566554 3    6899999999999999999998863

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=82.07  E-value=2.4  Score=39.56  Aligned_cols=50  Identities=14%  Similarity=0.087  Sum_probs=41.2

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHH--HHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEV--GNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEI--Ae~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|.+||.+... +.|.-+|.++|  |..++++..+|+.+.++.++||..
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            399999999887663 12344699999  888999999999999999999863

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.

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=82.05  E-value=3.3  Score=35.96  Aligned_cols=45  Identities=29%  Similarity=0.369  Sum_probs=33.1

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHH
Q 011992          400 QHVRNLLTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVR  446 (473)
Q Consensus       400 e~L~~aL~~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVr  446 (473)
                      +.|..++  |++.||+.+-.|+.|-.   ..+++.+||+..||+|..+|-
T Consensus        31 ~~lL~ll--LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT   78 (103)
T COG2973          31 QPLLTLL--LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT   78 (103)
T ss_pred             HHHHHHH--cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc
Confidence            3444444  78888887766665432   268999999999999999874

>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=81.58  E-value=4.8  Score=32.15  Aligned_cols=34  Identities=24%  Similarity=0.292  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHcCCC-HHHHHH
Q 011992          288 LEKEKSKLQSQFGREPTLIEWAKAIGLS-CRDLKS  321 (473)
Q Consensus       288 le~a~~~L~~~lGRePT~eEiA~~lGms-~eeL~~  321 (473)
                      +-....+.....|.+||..|||+.+|+. ...+..
T Consensus        11 vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~   45 (65)
T PF01726_consen   11 VLEFIREYIEENGYPPTVREIAEALGLKSTSTVQR   45 (65)
T ss_dssp             HHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH
Confidence            3344556677899999999999999996 544443

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.

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=81.53  E-value=1.8  Score=30.61  Aligned_cols=25  Identities=16%  Similarity=0.300  Sum_probs=22.6

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          429 KSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       429 lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      +|..|+|+.+|||..+|+.+.....
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~   25 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGK   25 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence            5789999999999999999988764

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=81.50  E-value=2.6  Score=31.25  Aligned_cols=29  Identities=38%  Similarity=0.533  Sum_probs=23.2

Q ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          426 GKPK-SLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       426 ge~l-TlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      |+.+ |..|||+.+|+|+.+|++    ++++|.+
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~~----~l~~L~~   46 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVRE----ALSRLEA   46 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence            4556 899999999999999988    5555554

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=81.38  E-value=3.3  Score=37.19  Aligned_cols=43  Identities=30%  Similarity=0.269  Sum_probs=33.8

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ..|++.++.||.+--.  | -..++.|||+.+|+|..+|+.++.+-
T Consensus         4 ~~lD~~D~~IL~~L~~--d-~r~~~~eia~~lglS~~~v~~Ri~~L   46 (154)
T COG1522           4 MKLDDIDRRILRLLQE--D-ARISNAELAERVGLSPSTVLRRIKRL   46 (154)
T ss_pred             ccccHHHHHHHHHHHH--h-CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3578888888875443  2 45999999999999999999876653

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=81.31  E-value=2.6  Score=39.12  Aligned_cols=41  Identities=22%  Similarity=0.098  Sum_probs=32.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.++.||.+--.   +...|+.|||+.+|+|+++|+.++.+
T Consensus        11 ~lD~~D~~IL~~Lq~---d~R~s~~eiA~~lglS~~tv~~Ri~r   51 (164)
T PRK11169         11 DLDRIDRNILNELQK---DGRISNVELSKRVGLSPTPCLERVRR   51 (164)
T ss_pred             hHHHHHHHHHHHhcc---CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            367778888764332   36789999999999999999987665

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=81.07  E-value=6.2  Score=35.80  Aligned_cols=53  Identities=17%  Similarity=0.217  Sum_probs=41.0

Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ...+..++-.|++.+-+|+..-..  .+.++|..|||+.||+++++|..    |+++|-
T Consensus        15 ~~dvl~c~~GLs~~Dv~v~~~LL~--~~~~~tvdelae~lnr~rStv~r----sl~~L~   67 (126)
T COG3355          15 CEDVLKCVYGLSELDVEVYKALLE--ENGPLTVDELAEILNRSRSTVYR----SLQNLL   67 (126)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHh--hcCCcCHHHHHHHHCccHHHHHH----HHHHHH
Confidence            345677778899999998765541  23799999999999999999976    555553

>PF13551 HTH_29: Winged helix-turn helix

Probab=80.94  E-value=2.5  Score=35.56  Aligned_cols=26  Identities=19%  Similarity=0.349  Sum_probs=23.5

Q ss_pred             CCC-CHHHHHHHHCCCHHHHHHHHHHH
Q 011992          427 KPK-SLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       427 e~l-TlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ++. |..+||+.+|+|+.+|..++++-
T Consensus        10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~   36 (112)
T PF13551_consen   10 EGVSTIAEIARRLGISRRTVYRWLKRY   36 (112)
T ss_pred             cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            677 59999999999999999998873

>PHA01976 helix-turn-helix protein

Probab=80.82  E-value=3.1  Score=32.30  Aligned_cols=25  Identities=16%  Similarity=0.238  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|..|+|+.+|+|.++|+++++.
T Consensus        14 ~glt~~~lA~~~gvs~~~v~~~e~g   38 (67)
T PHA01976         14 RAWSAPELSRRAGVRHSLIYDFEAD   38 (67)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            7899999999999999999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	473
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		4e-14
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		1e-07
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		5e-13
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		1e-12
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		1e-07
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		2e-12
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		2e-12
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		9e-12
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		9e-08
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		9e-12
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		9e-08
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		1e-11
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		1e-07
1tty_A	87	Solution Structure Of Sigma A Region 4 From Thermot		1e-11
4g6d_A	73	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		5e-11
4g94_A	62	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		7e-11
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		2e-10
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		6e-08
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		2e-10
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		5e-08
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		2e-10
1rio_H	73	Structure Of Bacteriophage Lambda Ci-Ntd In Complex		8e-07
1ku3_A	73	Crystal Structure Of Thermus Aquaticus Rna Polymera		1e-06
1tlh_B	81	T4 Asia Bound To Sigma70 Region 4 Length = 81		1e-06
3t72_q	99	Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna		2e-06
3n97_A	72	Rna Polymerase Alpha C-Terminal Domain (E. Coli) An		2e-06
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		7e-06
2p7v_B	68	Crystal Structure Of The Escherichia Coli Regulator		1e-05

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score = 75.9 bits (185), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 52/148 (35%), Positives = 84/148 (56%), Gaps = 21/148 (14%)
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 HDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
            DL+QEG+ GL+++VEKF+ +   +F+ 
Sbjct: 119 LDLIQEGNQGLIRAVEKFEYKRRFKFST 146

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
           P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+
Sbjct: 250 PVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQI 309
Query: 449 ESRALYRLK 457
           E++AL +LK
Sbjct: 310 ENKALRKLK 318

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 72.4 bits (176), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 35/70 (50%), Positives = 51/70 (72%), Gaps = 3/70 (4%)
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 KPQAGCRFAN 383
           + + G  F+ 
Sbjct: 151 EYKRGFAFST 160

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score = 70.9 bits (172), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/163 (31%), Positives = 84/163 (51%), Gaps = 36/163 (22%)
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 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
           VV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F+ 
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST 252

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
           P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+
Sbjct: 356 PVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQI 415
Query: 449 ESRALYRLK 457
           E++AL +LK
Sbjct: 416 ENKALRKLK 424

>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 = 70.5 bits (171), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/70 (48%), Positives = 51/70 (72%), Gaps = 3/70 (4%)
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 KPQAGCRFAN 383
           + +   +F+ 
Sbjct: 152 EYKRRFKFST 161

>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 = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 34/70 (48%), Positives = 51/70 (72%), Gaps = 3/70 (4%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKF 373
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF
Sbjct: 96  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 155
Query: 374 KPQAGCRFAN 383
           + +   +F+ 
Sbjct: 156 EYKRRFKFST 165

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 30/58 (51%), Positives = 45/58 (77%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F+ 
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST 237

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
           P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+
Sbjct: 341 PVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQI 400
Query: 449 ESRALYRLK 457
           E++AL +LK
Sbjct: 401 ENKALRKLK 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 = 68.2 bits (165), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 30/58 (51%), Positives = 45/58 (77%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F+ 
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST 237

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
           P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+
Sbjct: 341 PVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQI 400
Query: 449 ESRALYRLK 457
           E++AL +LK
Sbjct: 401 ENKALRKLK 409

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/58 (51%), Positives = 45/58 (77%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F+ 
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST 257

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 47/69 (68%)
Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
           P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++ER+RQ+
Sbjct: 361 PVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQI 420
Query: 449 ESRALYRLK 457
           E++AL +LK
Sbjct: 421 ENKALRKLK 429

>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga Maritima Length = 87

Iteration: 1
 Score = 67.8 bits (164), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 48/64 (75%)
Query: 395 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY 454
           + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +AL 
Sbjct: 5   RMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALR 64
Query: 455 RLKQ 458
           +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 = 5e-11,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 51/73 (69%)
Query: 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           M++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 458 QSLGGKASYGYAD 470
                K    + D
Sbjct: 61  HPSRSKRLKDFMD 73

>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 62

Iteration: 1
 Score = 65.5 bits (158), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 48/61 (78%)
Query: 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           M++ + ++L  L  +E  ++RLRFG++DG+ ++L EVG +FG+++ER+RQ+E++AL +L+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 458 Q 458
Sbjct: 61  H 61

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

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 50/72 (69%), Gaps = 4/72 (5%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFAN 383
           KF+ + G +F+ 
Sbjct: 418 KFEYRRGYKFST 429

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 49/80 (61%)
Query: 378 GCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 437
           G    +T +E+P  S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  
Sbjct: 520 GDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQ 579
Query: 438 FGLSKERVRQLESRALYRLK 457
           F +++ER+RQ+E++AL +L+
Sbjct: 580 FDVTRERIRQIEAKALRKLR 599

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 50/72 (69%), Gaps = 4/72 (5%)
Query: 316 CRDLKSELHSGNS----SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVE 371
            +D+   +  G +    ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+
Sbjct: 358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 417
Query: 372 KFKPQAGCRFAN 383
           KF+ + G +F+ 
Sbjct: 418 KFEYRRGYKFST 429

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 49/80 (61%)
Query: 378 GCRFANTGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNI 437
           G    +T +E+P  S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  
Sbjct: 520 GDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQ 579
Query: 438 FGLSKERVRQLESRALYRLK 457
           F +++ER+RQ+E++AL +L+
Sbjct: 580 FDVTRERIRQIEAKALRKLR 599

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 63.5 bits (153), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 25/55 (45%), Positives = 44/55 (80%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN 383
           ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F+ 
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 320

>pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With Sigma-Region4 Of Thermus Aquaticus Bound To Dna Length = 73

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 40/52 (76%)
Query: 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           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: 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           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 = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 2   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 61
Query: 452 ALYRLKQ 458
           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 = 50.8 bits (120), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 42/67 (62%)
Query: 392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 3   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62
Query: 452 ALYRLKQ 458
           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 = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 40/53 (75%)
Query: 406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458
           L+ L+ +E  ++++R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +L+ 
Sbjct: 8   LSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRH 60

>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 = 48.9 bits (115), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGV 386
           +R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF      +F+   V
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAV 86

>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of Sigma 70, Rsd, In Complex With Sigma 70 Domain 4 Length = 68

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 38/55 (69%)
Query: 404 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458
           ++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	473
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	3e-19
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	6e-12
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	1e-18
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	2e-18
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	2e-15
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	2e-17
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	1e-15
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	3e-17
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	1e-16
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	4e-15
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	1e-16
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	4e-15
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	3e-13
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	9e-15
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	2e-14
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	2e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-08

>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 = 86.1 bits (214), Expect = 3e-19
 Identities = 40/174 (22%), Positives = 73/174 (41%), Gaps = 38/174 (21%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
           R+++   KL+ + GREPT  E AK +G+S  +L   L   N S                 
Sbjct: 100 RIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI--------------- 144

Query: 347 QYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLL 406
                 +SL ++ ++ +    + +                   +  V K+ + + V+  +
Sbjct: 145 ------LSLEEVFRDFARDYSELIPS-------------STNVEEEVIKRELTEKVKEAV 185

Query: 407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL 460
           + L  +E+ +++L F  E        EV  I   S  RV QL+++AL RL++ L
Sbjct: 186 SKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLREML 235

>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 = 64.5 bits (158), Expect = 6e-12
 Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 3/61 (4%)

Query: 324 HSGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 8   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 67

Query: 381 F 381
            
Sbjct: 68  A 68

>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 = 84.2 bits (208), Expect = 1e-18
 Identities = 45/160 (28%), Positives = 76/160 (47%), Gaps = 34/160 (21%)

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 VHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
           V +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F
Sbjct: 124 VSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 163

>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 = 83.4 bits (207), Expect = 2e-18
 Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 317 RDLKSELHSGNSS-REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP 375
           ++L      G+   R+++I  N+RLV  V +++  RG    DL Q G +GL+KSV+KF  
Sbjct: 16  KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDL 75

Query: 376 QAGCRF 381
               +F
Sbjct: 76  SYDVKF 81

>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 = 74.9 bits (185), Expect = 2e-15
 Identities = 35/177 (19%), Positives = 72/177 (40%), Gaps = 43/177 (24%)

Query: 282 IQDLI-RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRL 340
           ++++  ++ K K +L    GR PT+ E A  +G+S               E ++ A    
Sbjct: 109 LKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGIS--------------PEDVVLA---- 150

Query: 341 VVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQ 400
                +       S+H+ + E     +  +++               I D        + 
Sbjct: 151 -QEAVRLP----TSIHETVYENDGDPITLLDQ---------------IADADEASWFDKI 190

Query: 401 HVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
            ++  +  L+ +ER IV LR+     K ++ SEV +  G+S+ ++ +LE + L  +K
Sbjct: 191 ALKKAIEELDERERLIVYLRYY----KDQTQSEVASRLGISQVQMSRLEKKILQHIK 243

>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 = 83.0 bits (205), Expect = 2e-17
 Identities = 47/164 (28%), Positives = 76/164 (46%), Gaps = 30/164 (18%)

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 LRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
           LRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F
Sbjct: 192 LRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 235

>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 = 77.6 bits (191), Expect = 1e-15
 Identities = 25/75 (33%), Positives = 48/75 (64%)

Query: 384 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 443
             +  P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++E
Sbjct: 336 EHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRE 395

Query: 444 RVRQLESRALYRLKQ 458
           R+RQ+E++AL +LK 
Sbjct: 396 RIRQIENKALRKLKY 410

>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 = 3e-17
 Identities = 28/66 (42%), Positives = 48/66 (72%)

Query: 392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451
              + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +
Sbjct: 2   EAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVK 61

Query: 452 ALYRLK 457
           AL +L+
Sbjct: 62  ALRKLR 67

>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 = 80.8 bits (199), Expect = 1e-16
 Identities = 38/119 (31%), Positives = 59/119 (49%), Gaps = 4/119 (3%)

Query: 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322
           G +   +        L       I   KEK   ++    +  L    K +    +     
Sbjct: 136 GLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKEL----KRYLHI 191

Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
              G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F
Sbjct: 192 AREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 250

>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 = 76.1 bits (187), Expect = 4e-15
 Identities = 25/75 (33%), Positives = 48/75 (64%)

Query: 384 TGVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKE 443
             +  P  +  + L+ + +   L+ L+ +E  +++LR G+ DG+  +L EVG  FG+++E
Sbjct: 351 ENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRE 410

Query: 444 RVRQLESRALYRLKQ 458
           R+RQ+E++AL +LK 
Sbjct: 411 RIRQIENKALRKLKY 425

>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 = 1e-16
 Identities = 23/66 (34%), Positives = 42/66 (63%)

Query: 392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR 451
           S   + +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++
Sbjct: 3   SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK 62

Query: 452 ALYRLK 457
           AL +L+
Sbjct: 63  ALRKLR 68

>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 = 77.0 bits (189), Expect = 4e-15
 Identities = 47/180 (26%), Positives = 86/180 (47%), Gaps = 36/180 (20%)

Query: 278 LIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINAN 337
           +I  I  L R+ ++   +  + GREPT  E A+ + +                +K+    
Sbjct: 456 MIETINKLNRISRQ---MLQEMGREPTPEELAERMLMPE--------------DKI---- 494

Query: 338 LRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQL 397
            R V+ +AK+     IS+     E  +G     +      G    +T +E+P  S   + 
Sbjct: 495 -RKVLKIAKE----PISM-----ETPIG-----DDEDSHLGDFIEDTTLELPLDSATTES 539

Query: 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           +R    ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +L+
Sbjct: 540 LRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599

>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 = 71.2 bits (174), Expect = 3e-13
 Identities = 58/333 (17%), Positives = 121/333 (36%), Gaps = 37/333 (11%)

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 GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
            RG+   DL+QEG++GLMK+V+KF+ + G +F+
Sbjct: 396 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 428

>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 = 68.1 bits (167), Expect = 9e-15
 Identities = 21/54 (38%), Positives = 38/54 (70%)

Query: 404 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           ++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 = 2e-14
 Identities = 22/59 (37%), Positives = 42/59 (71%)

Query: 400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458
           + +   L+ L+ +E  ++++R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 60

>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 = 73.4 bits (180), Expect = 2e-14
 Identities = 31/102 (30%), Positives = 54/102 (52%), Gaps = 10/102 (9%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK-------LINANLR 339
           +L     ++     +   L +  +  GL+   +K      +    K       ++ ANLR
Sbjct: 220 KLHDVSEEVHRALQK---LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLR 276

Query: 340 LVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRF 381
           LV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F
Sbjct: 277 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 318

>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 = 63.3 bits (153), Expect = 1e-10
 Identities = 64/487 (13%), Positives = 138/487 (28%), Gaps = 117/487 (24%)

Query: 58  HFPTSVLLQEQRDEYRPLLHMFK------------EDKTSQATSD--------SRNIETE 97
           H        E + +Y+ +L +F+            +D      S         S++  + 
Sbjct: 6   HMDFET--GEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG 63

Query: 98  AFFV----EEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTM-----QSL 148
              +      K    + + V+++      +  L   SP       PS+   M       L
Sbjct: 64  TLRLFWTLLSKQEEMVQKFVEEVLRINYKF--LM--SPIKTEQRQPSMMTRMYIEQRDRL 119

Query: 149 SNDTEESVD-----AEPFDAVALARKALSASKEAASLAENPKLNG-AEFTDISLTSSLGY 202
            ND +          +P+  +   R+AL   + A ++     ++G        +   +  
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKL---RQALLELRPAKNVL----IDGVLGSGKTWVALDVCL 172

Query: 203 PLEEVKQFSQPRF---LERRSKKRKVSKPQVT-------NHETYNSRKASVKKKLSEGFD 252
             +   +     F   L+  +    V +           N  + +   +++K ++     
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 253 RNDPLRLFLWGPETRKLLTAD--------EEFE-----LI----AQIQDLIRLEKEK--- 292
                RL    P    LL             F      L+     Q+ D +         
Sbjct: 233 E--LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHIS 290

Query: 293 -SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGR 351
                     +       K +    +DL  E+ + N  R  +I  ++R  +     ++  
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK-- 348

Query: 352 GISLHDLLQEGSMGLMKSVEKFKPQAGCR-----FA--NTGVEIP-----------DISV 393
               H    + +  +  S+   +P A  R      +       IP             S 
Sbjct: 349 ----HVNCDKLTTIIESSLNVLEP-AEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403

Query: 394 QKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL 453
              ++ +  +  L    PKE         I     +   ++ N + L +  V        
Sbjct: 404 VMVVVNKLHKYSLVEKQPKES-----TISIPSIYLELKVKLENEYALHRSIVDH------ 452

Query: 454 YRLKQSL 460
           Y + ++ 
Sbjct: 453 YNIPKTF 459

>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 = 56.4 bits (135), Expect = 1e-08
 Identities = 82/525 (15%), Positives = 159/525 (30%), Gaps = 168/525 (32%)

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--PQV---------------T 231
            ISL   S+    +EVK      ++L+ R +   R+V    P+                 
Sbjct: 288 HISLDHHSMTLTPDEVKSLLL--KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345

Query: 232 NHETYNSRKASVKKKLSEGFDRNDP---------LRLF-------------LWG------ 263
           N +  N  K  +   +    +  +P         L +F             +W       
Sbjct: 346 NWKHVNCDK--LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403

Query: 264 PET------RKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIE---------- 307
                    +  L   +  E    I  +    K K + +    R  ++++          
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR--SIVDHYNIPKTFDS 461

Query: 308 -----------WAKAIGLSCRDLKSELHSGNSSREKLINANLRL----VVHVAKQYQGRG 352
                      +   IG     LK+  H    +  +++  + R     + H +  +   G
Sbjct: 462 DDLIPPYLDQYFYSHIG---HHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASG 518

Query: 353 ISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTGVEIPDISVQKQLMRQHVRNLLT----- 407
             L+ L Q         ++ +KP               I        + V  +L      
Sbjct: 519 SILNTLQQ---------LKFYKPY--------------ICDNDPKYERLVNAILDFLPKI 555

Query: 408 ---LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE 449
              L+  K   ++R+    ED              + +E  +Q++
Sbjct: 556 EENLICSKYTDLLRIALMAEDE------------AIFEEAHKQVQ 588

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	473
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	99.97
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	99.97
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	99.91
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	99.84
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.83
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.82
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.8
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.74
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.64
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.6
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.5
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.46
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.32
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.32
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.28
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.23
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	99.06
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.93
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.77
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.77
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	98.71
3c57_A	95	Two component transcriptional regulatory protein;	98.56
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.56
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.56
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.44
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.36
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.27
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	98.06
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	98.03
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	98.0
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.97
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	97.89
2q0o_A	236	Probable transcriptional activator protein TRAR; h	97.6
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	97.59
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	97.59
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	97.43
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	97.42
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	97.42
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	97.31
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	97.12
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.95
1yio_A	208	Response regulatory protein; transcription regulat	96.66
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.64
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	96.64
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.35
3c3w_A	225	Two component transcriptional regulatory protein;	96.06
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	95.58
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	95.46
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	95.4
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	93.97
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	93.94
2oqr_A	230	Sensory transduction protein REGX3; response regul	93.74
2gwr_A	238	DNA-binding response regulator MTRA; two-component	93.66
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	93.24
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	92.52
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	92.51
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	92.48
1ys7_A	233	Transcriptional regulatory protein PRRA; response	92.27
1u78_A	141	TC3 transposase, transposable element TC3 transpos	92.12
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	92.03
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	91.65
3q9s_A	249	DNA-binding response regulator; DNA binding protei	91.37
3r0j_A	250	Possible two component system response transcript	91.35
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	90.5
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	90.46
2hqr_A	223	Putative transcriptional regulator; phosporylation	90.33
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	89.96
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	89.19
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	89.09
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	88.88
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	88.59
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	88.55
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	88.42
3nqo_A	189	MARR-family transcriptional regulator; structural	88.36
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	88.14
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	88.1
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	87.97
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	87.83
1y0u_A	96	Arsenical resistance operon repressor, putative; s	87.71
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	87.67
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	87.56
3r0a_A	123	Putative transcriptional regulator; structural gen	87.47
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	87.21
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	87.03
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	86.83
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	86.7
2w25_A	150	Probable transcriptional regulatory protein; trans	86.59
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	86.56
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	86.53
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	86.28
1sfx_A	109	Conserved hypothetical protein AF2008; structural	86.22
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	86.08
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	86.02
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	85.98
2gxg_A	146	146AA long hypothetical transcriptional regulator;	85.88
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	85.81
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	85.79
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	85.79
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	85.63
2k27_A	159	Paired box protein PAX-8; paired domain, solution	85.57
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	85.56
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	85.54
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	84.99
2nnn_A	140	Probable transcriptional regulator; structural gen	84.87
3jth_A	98	Transcription activator HLYU; transcription factor	84.68
3iwf_A	107	Transcription regulator RPIR family; transcription	84.44
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	84.43
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	84.24
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	84.06
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	83.91
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	83.81
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	83.81
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	83.68
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	83.67
1ku9_A	152	Hypothetical protein MJ223; putative transcription	83.5
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	83.49
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	83.45
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	82.92
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	82.92
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	82.88
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	82.87
3frw_A	107	Putative Trp repressor protein; structural genomic	82.76
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	82.75
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	82.62
3f3x_A	144	Transcriptional regulator, MARR family, putative;	82.54
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	82.38
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	82.33
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	82.19
2kko_A	108	Possible transcriptional regulatory protein (possi	82.17
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	81.95
3qbm_A	199	TETR transcriptional regulator; DNA/RNA-binding th	81.83
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	81.69
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	81.6
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	81.48
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	81.34
3ppb_A	195	Putative TETR family transcription regulator; DNA-	81.27
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	81.1
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	81.07
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	80.99
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	80.94
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	80.92
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	80.87
3dcf_A	218	Transcriptional regulator of the TETR/ACRR family;	80.85
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	80.82
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	80.81
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	80.76
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	80.74
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	80.69
3s2w_A	159	Transcriptional regulator, MARR family; structural	80.64
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	80.4
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	80.33

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

Probab=99.97  E-value=2e-31  Score=280.09  Aligned_cols=217  Identities=32%  Similarity=0.548  Sum_probs=181.1

Q ss_pred             ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHH------------------HHHHHHHhCCCCCHHHHHH-----
Q 011992          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKE------------------KSKLQSQFGREPTLIEWAK-----  310 (473)
Q Consensus       254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a------------------~~~L~~~lGRePT~eEiA~-----  310 (473)
                      .++++.|++.++++|+||+|||++|+++++....+...                  +......+|+.|+..||+.     
T Consensus        93 ~d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  172 (438)
T 1l9z_H           93 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE  172 (438)
T ss_pred             CChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchhhh
Confidence            35799999999999999999999999999986433221                  1122234567888777632     


Q ss_pred             -------HcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992          311 -------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN  383 (473)
Q Consensus       311 -------~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT  383 (473)
                             .++++..+|...+.+|..|++.||..|+++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+|
T Consensus       173 ~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rFsT  252 (438)
T 1l9z_H          173 EVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST  252 (438)
T ss_pred             hhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHH
Confidence                   2456778888888888899999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC-----------------------------------------------------------------------------
Q 011992          384 TGV-----------------------------------------------------------------------------  386 (473)
Q Consensus       384 ~~~-----------------------------------------------------------------------------  386 (473)
                      +..                                                                             
T Consensus       253 YA~~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~~~~~SL  332 (438)
T 1l9z_H          253 YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL  332 (438)
T ss_pred             HHHHHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccccccc
Confidence            100                                                                             


Q ss_pred             ---------------------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHH
Q 011992          387 ---------------------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERV  445 (473)
Q Consensus       387 ---------------------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rV  445 (473)
                                           ..|+..+...+....|..+|..||+++|.||.+||+|+||+++|++|||+.||||++||
T Consensus       333 d~~~~~d~d~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~ereR~VI~LRygL~~~e~~TleEIAe~LgIS~erV  412 (438)
T 1l9z_H          333 ETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERI  412 (438)
T ss_pred             ccccccccchhhhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCCCCHHHHHHHHCcCHHHH
Confidence                                 01122233445667899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH-HHhccCchhhhhh
Q 011992          446 RQLESRALYRLK-QSLGGKASYGYAD  470 (473)
Q Consensus       446 rqi~~RAL~KLR-~~L~~~~l~~yld  470 (473)
                      +|++++|++||| ..+....+++|++
T Consensus       413 Rqi~~RAlkKLR~~~~~~~~l~~yl~  438 (438)
T 1l9z_H          413 RQIENKALRKLKYHESRTRKLRDFLE  438 (438)
T ss_pred             HHHHHHHHHHHHHhHhhHHHHHHhhC
Confidence            999999999999 7788777888874

>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=99.97  E-value=3.3e-31  Score=277.58  Aligned_cols=217  Identities=33%  Similarity=0.549  Sum_probs=175.4

Q ss_pred             ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHH------------------HHHHHHhCCCCCHHH--------
Q 011992          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK------------------SKLQSQFGREPTLIE--------  307 (473)
Q Consensus       254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~------------------~~L~~~lGRePT~eE--------  307 (473)
                      .++++.|++.+++.|+||+|||++|+++++....+....                  ......+|+.|+..|        
T Consensus        78 ~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (423)
T 2a6h_F           78 SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE  157 (423)
T ss_dssp             HHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHHH
T ss_pred             CcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhhh
Confidence            458999999999999999999999999999864322211                  111122345665333        


Q ss_pred             -HH---HHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992          308 -WA---KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN  383 (473)
Q Consensus       308 -iA---~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT  383 (473)
                       |+   .+++++..+|...+.+|..|++.||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|
T Consensus       158 ~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~Fst  237 (423)
T 2a6h_F          158 EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST  237 (423)
T ss_dssp             HHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCHHH
T ss_pred             hhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHH
Confidence             32   23567788888888888899999999999999999999999999999999999999999999999999999987


Q ss_pred             CC------------------------------------------------------------------------------
Q 011992          384 TG------------------------------------------------------------------------------  385 (473)
Q Consensus       384 ~~------------------------------------------------------------------------------  385 (473)
                      +.                                                                              
T Consensus       238 Ya~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~~~Sl  317 (423)
T 2a6h_F          238 YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL  317 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSCCEES
T ss_pred             HHHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccCCccc
Confidence            00                                                                              


Q ss_pred             --------------------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHH
Q 011992          386 --------------------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERV  445 (473)
Q Consensus       386 --------------------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rV  445 (473)
                                          ...|+..+...++...|..+|..||+++|.||.+||+|+||+++|++|||+.||||++||
T Consensus       318 d~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~L~~aL~~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS~erV  397 (423)
T 2a6h_F          318 ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERI  397 (423)
T ss_dssp             SCBCSSSSSCBGGGSSCCSSSCCHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTCC-----CHHHHSSSSCHHHH
T ss_pred             ccccCCCCccchhhhhccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHH
Confidence                                012344455666778899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH-HHhccCchhhhhh
Q 011992          446 RQLESRALYRLK-QSLGGKASYGYAD  470 (473)
Q Consensus       446 rqi~~RAL~KLR-~~L~~~~l~~yld  470 (473)
                      +|++++|++||| ..+....+++|++
T Consensus       398 rqi~~rAl~kLR~~~~~~~~l~~~l~  423 (423)
T 2a6h_F          398 RQIENKALRKLKYHESRTRKLRDFLD  423 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSSSSCCC
T ss_pred             HHHHHHHHHHHHhhhhhhHHHHHhhC
Confidence            999999999999 7888888888874

>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=99.91  E-value=8.3e-25  Score=213.81  Aligned_cols=199  Identities=28%  Similarity=0.430  Sum_probs=114.5

Q ss_pred             ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHH-HHHHHHH------HHHH-------------------hCCCCCHHH
Q 011992          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR-LEKEKSK------LQSQ-------------------FGREPTLIE  307 (473)
Q Consensus       254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~k-le~a~~~------L~~~-------------------lGRePT~eE  307 (473)
                      .|++|.|+..+.++|+||++||++|+++|+.+.. .+.+...      +...                   .+++|+..+
T Consensus         6 ~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~~   85 (245)
T 3ugo_A            6 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE   85 (245)
T ss_dssp             CHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHHH
T ss_pred             CCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhHH
Confidence            5789999999999999999999999999998654 3333211      1000                   146889999


Q ss_pred             HHHHcCCCH----HHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992          308 WAKAIGLSC----RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN  383 (473)
Q Consensus       308 iA~~lGms~----eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT  383 (473)
                      ||.+.|++.    .++...+.+|..|++.||..|.++|+++|++|.+++.+++|++||||+|+|+++++||+.+|++|+|
T Consensus        86 ~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~t  165 (245)
T 3ugo_A           86 EVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST  165 (245)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHH
T ss_pred             HHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHHH
Confidence            999988753    4566777888899999999999999999999999999999999999999999999999999999988


Q ss_pred             CCCCCchHHHHHH--------HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC--CCHHHHHHHHHHHH
Q 011992          384 TGVEIPDISVQKQ--------LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG--LSKERVRQLESRAL  453 (473)
Q Consensus       384 ~~~~~pee~le~~--------el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LG--IS~~rVrqi~~RAL  453 (473)
                      +..+.....+...        ..-..+.+.+..|++..+.+ ...|+    +++|++|||+.||  ||.++|+.++.+|+
T Consensus       166 ya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L-~~~~~----~~ps~~EIAe~Lg~~is~~tVk~~l~~ar  240 (245)
T 3ugo_A          166 YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQL-QQELG----REPSYEEIAEAMGPGWDAKRVEETLKIAQ  240 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHTC-------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHH-HHHhC----CCCCHHHHHHHHCCCCCHHHHHHHHHHHh
Confidence            4433332222110        11224666778888888774 44555    8999999999999  99999999999998


Q ss_pred             HHHH
Q 011992          454 YRLK  457 (473)
Q Consensus       454 ~KLR  457 (473)
                      +.|.
T Consensus       241 ~~ls  244 (245)
T 3ugo_A          241 EPVS  244 (245)
T ss_dssp             ----
T ss_pred             hccC
Confidence            7763

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=99.84  E-value=2.9e-22  Score=218.54  Aligned_cols=155  Identities=34%  Similarity=0.672  Sum_probs=135.3

Q ss_pred             HHHHHHHHhhcc-hH---HHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccC-------
Q 011992          316 CRDLKSELHSGN-SS---REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANT-------  384 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A---~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~-------  384 (473)
                      ..+|...+..|+ .|   |+.||..|+++|+++|++|.+++.+++||+||||+|||+++++|++.+|++|+|+       
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            445566566665 55   9999999999999999999999999999999999999999999999999999870       


Q ss_pred             ---------C----------------------------------------------------------------------
Q 011992          385 ---------G----------------------------------------------------------------------  385 (473)
Q Consensus       385 ---------~----------------------------------------------------------------------  385 (473)
                               .                                                                      
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                     0                                                                      


Q ss_pred             ----------CCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992          386 ----------VEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYR  455 (473)
Q Consensus       386 ----------~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~K  455 (473)
                                ...|+..+...++...|..+|..||+++|.||.|+|++++++++|++|||+.||||++||++++++|+++
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                      0134455555666678999999999999999999999988899999999999999999999999999999


Q ss_pred             HHHHhccCchhhhhh
Q 011992          456 LKQSLGGKASYGYAD  470 (473)
Q Consensus       456 LR~~L~~~~l~~yld  470 (473)
                      ||+.+....++.|++
T Consensus       598 LR~~~~~~~l~~~l~  612 (613)
T 3iyd_F          598 LRHPSRSEVLRSFLD  612 (613)
T ss_dssp             TTSCSSSCSSTTCC-
T ss_pred             hhCcchhhHHHHHhc
Confidence            999999988988886

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=99.82  E-value=1e-19  Score=171.30  Aligned_cols=131  Identities=27%  Similarity=0.395  Sum_probs=115.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhh---cCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc---------------CC----
Q 011992          328 SSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN---------------TG----  385 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~---~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT---------------~~----  385 (473)
                      .+++.||..|.++|+++|+++.   ++..+++|++||+++++|+++++|++.+|..|.+               ..    
T Consensus        12 ~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~~~~   91 (239)
T 1rp3_A           12 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLDFGS   91 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSSTTC
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCccc
Confidence            5899999999999999999998   7889999999999999999999999988878877               10    


Q ss_pred             -------------------------------------------------------------------------CCCchHH
Q 011992          386 -------------------------------------------------------------------------VEIPDIS  392 (473)
Q Consensus       386 -------------------------------------------------------------------------~~~pee~  392 (473)
                                                                                               ...|+..
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~  171 (239)
T 1rp3_A           92 RQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTNVEEE  171 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTGGGSCHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccccCCCcccccccCCCCCHHHH
Confidence                                                                                     1122333


Q ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          393 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       393 le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      +...+....|..+|..||+++|.||.++|+    +++|++|||+.||||.++|++++++|+++||+.+..
T Consensus       172 ~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l~~  237 (239)
T 1rp3_A          172 VIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQLKAKALERLREMLSN  237 (239)
T ss_dssp             HHHHHHHHHHHHHHTTSCHHHHHHHHHHHT----SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHh----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            444556678999999999999999999998    999999999999999999999999999999998864

>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=99.80  E-value=1.6e-19  Score=165.55  Aligned_cols=140  Identities=18%  Similarity=0.190  Sum_probs=116.6

Q ss_pred             HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------
Q 011992          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------  383 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------  383 (473)
                      ..+|...+..|+ .+++.|+..|.+.|+++|+++.+ ..+++|++||+|+++|+++++|++..  .|.+           
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            445666665665 89999999999999999999999 99999999999999999999998764  3555           


Q ss_pred             --------CC------------C---------CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHH
Q 011992          384 --------TG------------V---------EIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEV  434 (473)
Q Consensus       384 --------~~------------~---------~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEI  434 (473)
                              ..            .         ..|+..+...+....|..+|..||+++|.||.|+|+    +|+|++||
T Consensus        87 d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EI  162 (194)
T 1or7_A           87 NYLVAQGRRPPSSDVDAIEAENFESGGALKEISNPENLMLSEELRQIVFRTIESLPEDLRMAITLREL----DGLSYEEI  162 (194)
T ss_dssp             HHHHHHTTCCTHHHHHHHHHHSCCSSCC--------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHT----TCCCHHHH
T ss_pred             HHHHHHhccCccccccccccccccccccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHH----cCCCHHHH
Confidence                    00            0         112222233456678899999999999999999998    99999999


Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          435 GNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       435 Ae~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      |+.||+|+++|+++++||+++||+.+..
T Consensus       163 A~~lgis~~tV~~~l~ra~~~Lr~~l~~  190 (194)
T 1or7_A          163 AAIMDCPVGTVRSRIFRAREAIDNKVQP  190 (194)
T ss_dssp             HHHTTSCHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999998864

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

Probab=99.74  E-value=1.6e-19  Score=169.64  Aligned_cols=138  Identities=30%  Similarity=0.520  Sum_probs=0.3

Q ss_pred             HHHHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCccccCC---------
Q 011992          316 CRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG---------  385 (473)
Q Consensus       316 ~eeL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~---------  385 (473)
                      ..+|...+..|+ .+++.||..|.++|+++|+++.++..+++|++||+++++|+++++|++.+|..|.+..         
T Consensus        15 ~~~l~~~~~~gd~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~~   94 (243)
T 1l0o_C           15 MKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQ   94 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHH
Confidence            344555555554 9999999999999999999999999999999999999999999999998777787611         


Q ss_pred             ------C---------------------------CCc-------------------------------------------
Q 011992          386 ------V---------------------------EIP-------------------------------------------  389 (473)
Q Consensus       386 ------~---------------------------~~p-------------------------------------------  389 (473)
                            .                           ..+                                           
T Consensus        95 d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~  174 (243)
T 1l0o_C           95 RFLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITL  174 (243)
T ss_dssp             -----CCCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC------------------
T ss_pred             HHHHhcCCccCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCcccch
Confidence                  0                           000                                           


Q ss_pred             -----hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          390 -----DISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       390 -----ee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                           +..+...+....|..+|..||+++|.||.|+|+    +|+|++|||+.||||.++|++++++|+++||
T Consensus       175 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr  243 (243)
T 1l0o_C          175 LDQIADADEASWFDKIALKKAIEELDERERLIVYLRYY----KDQTQSEVASRLGISQVQMSRLEKKILQHIK  243 (243)
T ss_dssp             -------------------------------------------------------------------------
T ss_pred             hhccCcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHh----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence                 111222344567889999999999999999998    9999999999999999999999999999997

>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=99.64  E-value=9.2e-16  Score=135.77  Aligned_cols=107  Identities=15%  Similarity=0.230  Sum_probs=88.3

Q ss_pred             CcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------------------CC-----------------
Q 011992          352 GISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------------------TG-----------------  385 (473)
Q Consensus       352 ~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------------------~~-----------------  385 (473)
                      |.+++|++||+++++|+++.+|++.+ ..|.+                             ..                 
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   79 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLNEALKTNAILEDSAYFDDEGHNI   79 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhHHHhhhhhhhccCCCCCcccchh
Confidence            46889999999999999999999876 67777                             00                 


Q ss_pred             ------CCCchHHHHHHHHHHHHHHHHh-hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          386 ------VEIPDISVQKQLMRQHVRNLLT-LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       386 ------~~~pee~le~~el~e~L~~aL~-~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                            ...|+..+...+....|..+|. .||+++|.||. +|+    +|+|++|||+.||||.++|+++++||+++||+
T Consensus        80 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~~L~~~~r~v~~-~~~----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~  154 (164)
T 3mzy_A           80 NNYKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLT-YLI----RGYSYREIATILSKNLKSIDNTIQRIRKKSEE  154 (164)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHSCHHHHHHHH-HHT----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             hhhcccCCCHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHH-HHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence                  1145566677777888999999 99999999999 677    89999999999999999999999999999999


Q ss_pred             HhccCc
Q 011992          459 SLGGKA  464 (473)
Q Consensus       459 ~L~~~~  464 (473)
                      .+...+
T Consensus       155 ~l~~~~  160 (164)
T 3mzy_A          155 WIKEEE  160 (164)
T ss_dssp             HHHHHT
T ss_pred             HHHHcC
Confidence            987543

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

Probab=99.60  E-value=1e-17  Score=151.26  Aligned_cols=125  Identities=11%  Similarity=0.110  Sum_probs=105.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------------C-CCCCchH
Q 011992          330 REKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------------T-GVEIPDI  391 (473)
Q Consensus       330 ~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------------~-~~~~pee  391 (473)
                      |+.||..|.+.|+++|+++.++..+++|++||+|+++|+++++|++..  .|.+                 . ....++ 
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~~~~~~e-   79 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGEAQTSQSD-   79 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTSCCCCCCS-
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccCcccCCcc-
Confidence            567889999999999999999999999999999999999999998653  3444                 1 011111 


Q ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992          392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       392 ~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                         ..+....|..+|..||+++|+||.|+|+    +|+|++|||+.||||+++|++++.||+++||+.+....
T Consensus        80 ---~~~~~~~l~~~l~~Lp~~~r~vl~L~~~----~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~  145 (157)
T 2lfw_A           80 ---AEGTEAVARARLARMTPLSRQALLLTAM----EGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRALE  145 (157)
T ss_dssp             ---CSSSSSTTTTTTTTSCTTHHHHHTTTSS----SCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSCCC
T ss_pred             ---hHHHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence               1233456788999999999999999999    99999999999999999999999999999999887653

>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=99.50  E-value=7.5e-14  Score=118.75  Aligned_cols=79  Identities=29%  Similarity=0.514  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992          392 SVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  470 (473)
Q Consensus       392 ~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yld  470 (473)
                      .+...++...|..+|+.||+++|.||.|+|+++|++++|++|||+.||||.++|++++.+|+++||..+....+..|+.
T Consensus         3 ~~~~~el~~~l~~aL~~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l~~~~~   81 (99)
T 3t72_q            3 SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSGSS   81 (99)
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566778899999999999999999999999888899999999999999999999999999999999999988888875

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

Probab=99.46  E-value=2.8e-14  Score=141.23  Aligned_cols=126  Identities=11%  Similarity=0.032  Sum_probs=106.0

Q ss_pred             hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc-----------C------CCC
Q 011992          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN-----------T------GVE  387 (473)
Q Consensus       325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT-----------~------~~~  387 (473)
                      ++..+|+.||..|.+.++++|++++++..+++|++||.|+.+|++.++|++..  .|.+           +      ...
T Consensus        18 g~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~~--~~~~wL~~ia~n~~~d~~r~~~~~~   95 (286)
T 3n0r_A           18 GSEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANL--SPRVALYRVFHAIWLSSGAQLEVGH   95 (286)
T ss_dssp             --CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSSS--CHHHHHHHHHHHHHSCTTC----CC
T ss_pred             CCcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCCc--ChHHHHHHHHHHHHHhhccccccCC
Confidence            44589999999999999999999999999999999999999999999997643  4554           0      000


Q ss_pred             CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          388 IPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       388 ~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      .+.     .+....|..+|+.||+++|.||.|+|+    +++|++|||+.+|++.++|+..+.+|+.+|+..+.
T Consensus        96 ~~~-----~~~~~~l~~al~~Lp~~~R~v~~L~~~----eg~s~~EIA~~lgis~~tVks~l~rA~~~Lr~~l~  160 (286)
T 3n0r_A           96 DQG-----LHAGDDAAQRLMRIAPRSRQAFLLTAL----EGFTPTEAAQILDCDFGEVERLIGDAQAEIDAELA  160 (286)
T ss_dssp             CCC-----CCTTSHHHHHHHHHSCHHHHHHHHHHT----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCC
T ss_pred             Ccc-----cchHHHHHHHHHhCCHHHeeEEEEEee----CCCCHHHHHHHhCcCHHHHHHHHHHHHhhhhccCC
Confidence            110     112346899999999999999999999    99999999999999999999999999999997654

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

Probab=99.32  E-value=2e-12  Score=106.38  Aligned_cols=73  Identities=38%  Similarity=0.725  Sum_probs=66.9

Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhhh
Q 011992          399 RQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADL  471 (473)
Q Consensus       399 ~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yldl  471 (473)
                      ...|..+|+.||+++|.||.++|+|++++++|++|||+.||||.++|++++.+|+++||..+....+..|+..
T Consensus         9 ~~~l~~~l~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l~~~~~~~~~~~   81 (87)
T 1tty_A            9 REELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLSL   81 (87)
T ss_dssp             CSHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            3568889999999999999999998888999999999999999999999999999999999888777777653

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

Probab=99.32  E-value=7.5e-12  Score=103.60  Aligned_cols=76  Identities=16%  Similarity=0.201  Sum_probs=70.5

Q ss_pred             CCCCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992          385 GVEIPDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       385 ~~~~pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      ....|++.+...+....|..+|..||+++|.||.|+|+    +|+|++|||+.||||.++|++++++|+++||+.+...+
T Consensus        14 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~   89 (92)
T 3hug_A           14 PEQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYY----RGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELG   89 (92)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHT----SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCchHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            34578888999999999999999999999999999998    99999999999999999999999999999999987543

>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=99.28  E-value=1.4e-12  Score=103.51  Aligned_cols=68  Identities=32%  Similarity=0.627  Sum_probs=55.6

Q ss_pred             HHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-HHhccCchhhhh
Q 011992          402 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK-QSLGGKASYGYA  469 (473)
Q Consensus       402 L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR-~~L~~~~l~~yl  469 (473)
                      |..+|+.||++++.||.++|+|++++++|++|||+.||+|.++|++++.+|+++|| ..+....+..|+
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            45678899999999999999988889999999999999999999999999999999 888777777775

>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=99.23  E-value=3.9e-12  Score=99.61  Aligned_cols=66  Identities=33%  Similarity=0.614  Sum_probs=60.0

Q ss_pred             HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992          405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  470 (473)
Q Consensus       405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yld  470 (473)
                      +|+.||+++++||.++|++++.+++|++|||+.||+|+++|++++.+|+++||..+....+..|++
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            467899999999999997766699999999999999999999999999999999988887777764

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

Probab=99.06  E-value=2.7e-10  Score=88.33  Aligned_cols=65  Identities=15%  Similarity=0.052  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992          397 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       397 el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      +....+..+|+.||++++.||.++|+    +++|++|||+.||+|.++|++++++|+++||..+....+
T Consensus         4 e~~~~l~~~l~~L~~~~r~il~l~~~----~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l~~~~~   68 (70)
T 2o8x_A            4 EDLVEVTTMIADLTTDQREALLLTQL----LGLSYADAAAVCGCPVGTIRSRVARARDALLADAEPDDL   68 (70)
T ss_dssp             HHHHHHHTTTTSSCHHHHHHHHHHHT----SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcccC
Confidence            45667889999999999999999998    999999999999999999999999999999998876543

>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=98.93  E-value=2.8e-09  Score=92.16  Aligned_cols=69  Identities=22%  Similarity=0.202  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHHHHH-hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992          393 VQKQLMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       393 le~~el~e~L~~aL-~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      ++..+....+..+| ..||+++|.||.++|+    +|+|++|||+.||+|+++|+.+++||+++||..+....+
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            45556677899999 9999999999999998    999999999999999999999999999999999876544

>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=98.77  E-value=1e-08  Score=88.84  Aligned_cols=65  Identities=20%  Similarity=0.181  Sum_probs=59.0

Q ss_pred             HHHHHHHHHH-hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCch
Q 011992          397 LMRQHVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKAS  465 (473)
Q Consensus       397 el~e~L~~aL-~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l  465 (473)
                      .....+.+++ ..||++++.||.++|+    +|+|++|||+.||+|+++|+.++++|+.+||..+...++
T Consensus        10 ~~~~~l~~~l~~~L~~~~r~vl~l~y~----~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   75 (113)
T 1s7o_A           10 NRMNALFEFYAALLTDKQMNYIELYYA----DDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   75 (113)
T ss_dssp             HHHHHHHHHHGGGSCHHHHHHHHHHHH----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            3456788888 8999999999999998    999999999999999999999999999999999876544

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

Probab=98.77  E-value=6.3e-10  Score=108.14  Aligned_cols=135  Identities=10%  Similarity=-0.000  Sum_probs=99.9

Q ss_pred             HHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHh----hhhHHHHHHHhhhhCccCCCcccc---------
Q 011992          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLL----QEGSMGLMKSVEKFKPQAGCRFAN---------  383 (473)
Q Consensus       318 eL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLi----QEg~lgL~kAiekFDp~kg~~FsT---------  383 (473)
                      .+...++.++ .+++.+...|.++++.+..........+.|+.    ||.++.+|+.+..|++..  .|.+         
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            3444445454 67899999999999999888877778888886    999999999999887543  2333         


Q ss_pred             --CC--C----CCchHHHHHH-HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          384 --TG--V----EIPDISVQKQ-LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       384 --~~--~----~~pee~le~~-el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                        +.  .    .......... .....+..++..||+++|+||.|+ +    +|+|.+|||+.||+|.++|+.+++||++
T Consensus       164 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~erevl~L~-~----~G~s~~EIA~~L~iS~~TVk~~l~ra~~  238 (258)
T 3clo_A          164 SADQRPEQGIYATITQMERGEVETLSLSEEHRNILSEREKEILRCI-R----KGLSSKEIAATLYISVNTVNRHRQNILE  238 (258)
T ss_dssp             CSCCCCCSSCCCEEEETTTTEEEECCCHHHHTTSSCHHHHHHHHHH-H----TTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HcchhhhhHHHHHHHhhcccccccchhhHHHHccCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence              00  0    0000000000 000135677899999999999998 5    8999999999999999999999999999


Q ss_pred             HHHHH
Q 011992          455 RLKQS  459 (473)
Q Consensus       455 KLR~~  459 (473)
                      |||..
T Consensus       239 kL~~~  243 (258)
T 3clo_A          239 KLSVG  243 (258)
T ss_dssp             HTTCS
T ss_pred             HHcCC
Confidence            99864

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=98.71  E-value=1.5e-08  Score=102.42  Aligned_cols=77  Identities=38%  Similarity=0.755  Sum_probs=62.9

Q ss_pred             HHHHcCCCHH---HHHHHHhhc-c---hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCc
Q 011992          308 WAKAIGLSCR---DLKSELHSG-N---SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR  380 (473)
Q Consensus       308 iA~~lGms~e---eL~~~l~~g-~---~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~  380 (473)
                      +....|++..   .|...+..| .   .|++.||..|+++|+++|++|.+++.+++|++||||+|||+++++|++.+|.+
T Consensus       238 ie~~~~l~~~~~~~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~  317 (339)
T 1sig_A          238 IEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK  317 (339)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCC
T ss_pred             HHHHcCCChHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCC
Confidence            3444455443   344444444 4   79999999999999999999999999999999999999999999999988888


Q ss_pred             cccC
Q 011992          381 FANT  384 (473)
Q Consensus       381 FsT~  384 (473)
                      |+|+
T Consensus       318 f~tw  321 (339)
T 1sig_A          318 FSTY  321 (339)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8763

>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=98.56  E-value=8.5e-08  Score=79.95  Aligned_cols=60  Identities=20%  Similarity=0.241  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          397 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       397 el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      +....|..+|..|+++|++||.++ .    +|+|++|||+.||||..+|+.++.++++||+..-.
T Consensus        16 ~~~~~l~~~l~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   75 (95)
T 3c57_A           16 PRGSHMQDPLSGLTDQERTLLGLL-S----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERR   75 (95)
T ss_dssp             -----------CCCHHHHHHHHHH-H----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence            445678889999999999999997 5    89999999999999999999999999999986543

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

Probab=98.56  E-value=2.6e-08  Score=82.07  Aligned_cols=62  Identities=21%  Similarity=0.196  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          393 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       393 le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      .........+..++..|+++|++||.++ .    +|+|++|||+.||||.++|+.++.++++||+..
T Consensus        14 ~~~~~~~~~l~~~l~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   75 (91)
T 2rnj_A           14 VPRGSHMKKRAELYEMLTEREMEILLLI-A----KGYSNQEIASASHITIKTVKTHVSNILSKLEVQ   75 (91)
T ss_dssp             -----------CTGGGCCSHHHHHHHHH-H----TTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCC
T ss_pred             CCcHHHHHHHHHHHhcCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            3344556778889999999999999995 5    899999999999999999999999999999753

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

Probab=98.56  E-value=9.7e-08  Score=75.71  Aligned_cols=54  Identities=15%  Similarity=0.190  Sum_probs=50.0

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ..+..++..|+++|+.||.++ +    +|+|++|||+.||+|..+|++++.++++||+.
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            467888999999999999995 5    89999999999999999999999999999985

>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=98.44  E-value=1.4e-07  Score=76.46  Aligned_cols=56  Identities=16%  Similarity=0.226  Sum_probs=47.9

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          400 QHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       400 e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ..+..++..|+++|++||.++ .    +|+|++|||+.||||.++|+.++.++++||+...
T Consensus        13 ~~~~~~~~~Lt~~e~~vl~l~-~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~   68 (82)
T 1je8_A           13 ATTERDVNQLTPRERDILKLI-A----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKS   68 (82)
T ss_dssp             ----CCGGGSCHHHHHHHHHH-T----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSS
T ss_pred             hHHHHHHccCCHHHHHHHHHH-H----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCC
Confidence            346678889999999999995 5    7999999999999999999999999999997643

>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=98.36  E-value=3.3e-07  Score=78.16  Aligned_cols=63  Identities=24%  Similarity=0.209  Sum_probs=53.8

Q ss_pred             HHHHHHHH-hhCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          399 RQHVRNLL-TLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       399 ~e~L~~aL-~~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      .+.+...+ ..|+++|+.+|.+||+|.+   +.++|++|||+.+|+|.++|+.+ +|++++|...++.
T Consensus        25 ~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k~   91 (101)
T 1jhg_A           25 NDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELRQ   91 (101)
T ss_dssp             TTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHHH
Confidence            34566666 5699999999999999975   45699999999999999999999 9999998876553

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

Probab=98.27  E-value=8.3e-07  Score=69.14  Aligned_cols=52  Identities=25%  Similarity=0.242  Sum_probs=45.5

Q ss_pred             HHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          402 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       402 L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ....+..|+++|+.|+.++ .    +|+|.+|||+.||+|..+|++++.+++.+|+.
T Consensus         5 ~~~~~~~L~~~e~~il~~~-~----~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   56 (74)
T 1fse_A            5 EFQSKPLLTKREREVFELL-V----QDKTTKEIASELFISEKTVRNHISNAMQKLGV   56 (74)
T ss_dssp             ---CCCCCCHHHHHHHHHH-T----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             cCCCCCCCCHHHHHHHHHH-H----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            4456788999999999995 5    79999999999999999999999999999975

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=98.06  E-value=5.9e-06  Score=68.41  Aligned_cols=49  Identities=20%  Similarity=0.225  Sum_probs=42.8

Q ss_pred             HHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          404 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       404 ~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .....|+++|++||.+.+     +|+|.+|||+.||||..+|+..+.++++||.
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            456789999999999987     6999999999999999999999999999885

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

Probab=98.03  E-value=4e-06  Score=63.21  Aligned_cols=43  Identities=14%  Similarity=0.227  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ++|++|+.+ +.    +|+|.+|||+.||+|..+|+..+.++++||+.
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            478999999 66    89999999999999999999999999999875

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

Probab=98.00  E-value=9.1e-06  Score=68.30  Aligned_cols=57  Identities=23%  Similarity=0.214  Sum_probs=50.0

Q ss_pred             HHHHHHhhcc-hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCc
Q 011992          318 DLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP  375 (473)
Q Consensus       318 eL~~~l~~g~-~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp  375 (473)
                      ++...+..|+ .+++.|+..|.+.++++|.++ ++..+++|++||+|+.+|+++.+|++
T Consensus        13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~   70 (112)
T 2o7g_A           13 ALALSAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSA   70 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            3444555555 899999999999999999999 99999999999999999999999875

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

Probab=97.97  E-value=9.8e-06  Score=68.39  Aligned_cols=47  Identities=21%  Similarity=0.275  Sum_probs=43.3

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      ..|+++|++||.+.+     +|+|.+|||+.||||..+|+..+.++++||.-
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     69999999999999999999999999999853

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

Probab=97.89  E-value=7.1e-06  Score=65.87  Aligned_cols=51  Identities=18%  Similarity=0.117  Sum_probs=47.6

Q ss_pred             hcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCc
Q 011992          325 SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKP  375 (473)
Q Consensus       325 ~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp  375 (473)
                      ++..+++.|+..|.+.++++|.++.++..+++|++||+|+.+|+.++.|++
T Consensus         9 g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~   59 (87)
T 1h3l_A            9 ERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFRE   59 (87)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCS
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            445899999999999999999999999999999999999999999999875

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=97.60  E-value=9e-05  Score=70.51  Aligned_cols=46  Identities=24%  Similarity=0.327  Sum_probs=42.7

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|++|+.+.+     +|+|.+|||++||||+.||+.++.++++||.-
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     79999999999999999999999999999863

>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=97.59  E-value=2e-06  Score=83.65  Aligned_cols=82  Identities=20%  Similarity=0.252  Sum_probs=24.9

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF  299 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l  299 (473)
                      .+..+.+|.+|++|+.|+|+     +++.++   ++...+   .|...              .+.+.+|..+...|...+
T Consensus       153 ~~fd~~~g~~F~tya~~~ir-----~~i~~~---ir~~~r~~r~p~~l--------------~e~i~~l~~~~~~L~~~~  210 (245)
T 3ugo_A          153 EKFEYKRRFKFSTYATWWIR-----QAINRA---IADQARTIRIPVHM--------------VETINKLSRTARQLQQEL  210 (245)
T ss_dssp             HHCCGGGCCCHHHHHHHHHH-----HHHHHH---HHHHTC----------------------------------------
T ss_pred             HHcCcccCCcHHHHHHHHHH-----HHHHHH---HHHhcccccccHHH--------------HHHHHHHHHHHHHHHHHh
Confidence            45677889999999999999     998874   554433   33322              344567888888999999


Q ss_pred             CCCCCHHHHHHHcC--CCHHHHHHHHhhc
Q 011992          300 GREPTLIEWAKAIG--LSCRDLKSELHSG  326 (473)
Q Consensus       300 GRePT~eEiA~~lG--ms~eeL~~~l~~g  326 (473)
                      |+.||.+|||+.||  ++.+.+...+...
T Consensus       211 ~~~ps~~EIAe~Lg~~is~~tVk~~l~~a  239 (245)
T 3ugo_A          211 GREPSYEEIAEAMGPGWDAKRVEETLKIA  239 (245)
T ss_dssp             -----------------------------
T ss_pred             CCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            99999999999999  9999988776543

>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=97.59  E-value=9e-05  Score=70.43  Aligned_cols=45  Identities=27%  Similarity=0.383  Sum_probs=42.1

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .|+++|++|+.+.+     +|+|.+|||++||||+.||+..+.++++||.
T Consensus       173 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~  217 (234)
T 1l3l_A          173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD  217 (234)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence            59999999999964     7999999999999999999999999999985

>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=97.43  E-value=3.2e-05  Score=80.83  Aligned_cols=82  Identities=20%  Similarity=0.250  Sum_probs=62.2

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGRE  302 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGRe  302 (473)
                      .|..+.+|.+|+||+.|||+     ++|.++   ++...+..+ .|       ..+   ...+.++.+++..+.+.+||+
T Consensus       225 ~kFd~~~g~~FstYa~~wIr-----~~i~~~---i~~~~r~ir-~p-------~~~---~~~~~~lrr~~~~l~~~~~r~  285 (423)
T 2a6h_F          225 EKFEYKRRFKFSTYATWWIR-----QAINRA---IADQARTIR-IP-------VHM---VETINKLSRTARQLQQELGRE  285 (423)
T ss_dssp             HHCCTTSCCCHHHHHHHHHH-----HHHHHH---HHHHSSSSC-CC-------HHH---HHHHHHHHHHHHHHHHHHSSC
T ss_pred             HhcCcccCCCHHHHHHHHHH-----HHHHHH---HHHccceee-cc-------HHH---HHHHHHHHHHHHHHHHHhCCC
Confidence            35678889999999999999     887763   554443332 32       111   345566777888899999999


Q ss_pred             CCHHHHHHHcC--CCHHHHHHHH
Q 011992          303 PTLIEWAKAIG--LSCRDLKSEL  323 (473)
Q Consensus       303 PT~eEiA~~lG--ms~eeL~~~l  323 (473)
                      |+.+|+|..+|  ++.+++...+
T Consensus       286 p~~~eiA~~l~~~~~~~~v~~~~  308 (423)
T 2a6h_F          286 PTYEEIAEAMGPGWDAKRVEETL  308 (423)
T ss_dssp             CCHHHHHHHHCTTCCHHHHHHHH
T ss_pred             CCHHHHHHHhCCCCCHHHHHHHH
Confidence            99999999999  9998887654

>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=97.42  E-value=0.00017  Score=69.01  Aligned_cols=46  Identities=20%  Similarity=0.307  Sum_probs=42.8

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++|++|+.+..     +|+|.+|||+.||||+.||+..+.++++||.
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     7999999999999999999999999999885

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

Probab=97.42  E-value=5.2e-05  Score=79.74  Aligned_cols=80  Identities=20%  Similarity=0.264  Sum_probs=61.9

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF  299 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l  299 (473)
                      .+..+.+|.+|.||++|||+     ++|.++   ++...+   .|.+.              ...+.++.+++..+.+.+
T Consensus       240 ekFDp~kG~rFsTYA~~wIR-----~~I~~~---i~~~~R~irlp~~~--------------~~~l~~lrr~~r~l~~~l  297 (438)
T 1l9z_H          240 EKFEYKRRFKFSTYATWWIR-----QAINRA---IADQARTIRIPVHM--------------VETINKLSRTARQLQQEL  297 (438)
T ss_pred             HhcCcccCCChHHHHHHHHH-----HHHHHH---HHHhcchhccchHH--------------HHHHHHHHHHHHHHHHHh
Confidence            35678889999999999999     888774   544333   33333              355667778888899999


Q ss_pred             CCCCCHHHHHHHcC--CCHHHHHHHHh
Q 011992          300 GREPTLIEWAKAIG--LSCRDLKSELH  324 (473)
Q Consensus       300 GRePT~eEiA~~lG--ms~eeL~~~l~  324 (473)
                      ||+|+.+|||..+|  ++.+++...+.
T Consensus       298 gr~pt~eeiA~~l~~~v~~e~V~~~~~  324 (438)
T 1l9z_H          298 GREPSYEEIAEAMGPGWDAKRVEETLK  324 (438)
T ss_pred             CCCCCHHHHHHHhCCCCCHHHHHHHHH
Confidence            99999999999999  99888876543

>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=97.31  E-value=0.00026  Score=69.12  Aligned_cols=46  Identities=20%  Similarity=0.239  Sum_probs=43.1

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|++|+.+..     +|+|.+|||++||||+.||+..+.++++||..
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     79999999999999999999999999999863

>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=97.12  E-value=0.0007  Score=47.45  Aligned_cols=40  Identities=20%  Similarity=0.124  Sum_probs=33.5

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.++..+...|.    +++|..|||+.||||..+|+.++.+
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            478888866666666    7899999999999999999998754

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.95  E-value=0.0018  Score=55.07  Aligned_cols=46  Identities=17%  Similarity=0.147  Sum_probs=42.8

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .+++.-..|..+||.    +|+|..|||+.||||+.+|++++.+|...+.
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            588888899999999    9999999999999999999999999998764

>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=96.66  E-value=0.0057  Score=55.32  Aligned_cols=50  Identities=14%  Similarity=0.310  Sum_probs=44.2

Q ss_pred             HHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          403 RNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       403 ~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ...+..|+++|++|+.+..     ++++.+|||+.||+|..+|+.+.+++++||.
T Consensus       137 ~~~~~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~  186 (208)
T 1yio_A          137 EQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLN  186 (208)
T ss_dssp             HHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhcCHHHHHHHHHHH-----cCCcHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence            4455679999999998764     6899999999999999999999999999885

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

Probab=96.64  E-value=0.0012  Score=48.58  Aligned_cols=39  Identities=15%  Similarity=0.204  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      +++..+.|+.+ |.    +++|..|||+.||||+.+|+.++.+|
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            34555666666 55    78999999999999999999987654

>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=96.64  E-value=2.7e-05  Score=84.90  Aligned_cols=81  Identities=17%  Similarity=0.159  Sum_probs=63.8

Q ss_pred             hccCCCCCCcccccccccccccccccccCCCChhHHhhhc---ccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011992          223 RKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW---GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQF  299 (473)
Q Consensus       223 ~~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~---~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~l  299 (473)
                      .+..+.+|.+|.||+.|||+     ++++++   +|+..+   .|.+.              +..+.+++++...+.+.+
T Consensus       417 ~~fd~~~g~~Fstyl~~~ir-----n~i~~~---lr~~~r~~rip~~~--------------~~~~~k~~r~~~~l~~~~  474 (613)
T 3iyd_F          417 DKFEYRRGYKFSTYATWWIR-----QAITRS---IADQARTIRIPVHM--------------IETINKLNRISRQMLQEM  474 (613)
T ss_dssp             TSCCTTSSSCSTTTHHHHHH-----HHHHHH---TTTSCSSSCCCSHH--------------HHTTTTTTTTTTTTTTTT
T ss_pred             HHcCccccCcHHHHHHHHHH-----HHHHHH---HHhcCcceeCcHHH--------------HHHHHHHHHHHHHHHHHh
Confidence            44577788999999999999     888873   655443   33333              344567788888999999


Q ss_pred             CCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992          300 GREPTLIEWAKAIGLSCRDLKSELHS  325 (473)
Q Consensus       300 GRePT~eEiA~~lGms~eeL~~~l~~  325 (473)
                      ||+||.+|+|+.||++.+.+...+..
T Consensus       475 gr~pt~eela~~l~~~~~~v~~~~~~  500 (613)
T 3iyd_F          475 GREPTPEELAERMLMPEDKIRKVLKI  500 (613)
T ss_dssp             CSCCCTTTTTTTSSCCSSHHHHHHHH
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            99999999999999999888877643

>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=96.35  E-value=0.0065  Score=55.33  Aligned_cols=46  Identities=20%  Similarity=0.294  Sum_probs=42.0

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++|++|+.+..     +++|.+|||+.+++|..||+.+.++.++||.
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            359999999998776     6899999999999999999999999999985

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=96.06  E-value=0.009  Score=55.33  Aligned_cols=46  Identities=22%  Similarity=0.260  Sum_probs=41.6

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++|++|+.+..     +++|.+|||+.|++|..||+..+++.++||.
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            459999999998765     6899999999999999999999999888874

>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=95.58  E-value=0.0046  Score=57.19  Aligned_cols=80  Identities=28%  Similarity=0.371  Sum_probs=64.3

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP  303 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP  303 (473)
                      +..+.+|..|.+|+.++++     +.++|   .+|+..+.++..              .+...++..+...+...+|+.|
T Consensus        59 ~~~~~~~~~f~~~l~~~~~-----~~~~d---~~r~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~~  116 (239)
T 1rp3_A           59 NLSTENPKRAEAYIKLRIK-----GAIYD---YLRSLDFGSRQV--------------REKERRIKEVVEKLKEKLGREP  116 (239)
T ss_dssp             TCCCCCTHHHHHHHHHHHH-----HHHHH---HHHTSSTTCHHH--------------HHHHHHHHHHHHHHHHHHSSCC
T ss_pred             HcCcccCCCHHHHHHHHHH-----HHHHH---HHHhcCccchHH--------------HHHHHHHHHHHHHHHHHhCCCC
Confidence            4456667899999999999     88888   477665544433              3556788899999999999999


Q ss_pred             CHHHHHHHcCCCHHHHHHHHhh
Q 011992          304 TLIEWAKAIGLSCRDLKSELHS  325 (473)
Q Consensus       304 T~eEiA~~lGms~eeL~~~l~~  325 (473)
                      +.+|+|+.+|++.+++..++..
T Consensus       117 ~~~~~a~~~~~~~~~~~~~~~~  138 (239)
T 1rp3_A          117 TDEEVAKELGISTEELFKTLDK  138 (239)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CHHHHHHHhCcCHHHHHHHHHH
Confidence            9999999999999888776543

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=95.46  E-value=0.041  Score=51.18  Aligned_cols=56  Identities=21%  Similarity=0.293  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          397 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       397 el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .......+.+..|+++++.++.+..     .+++.++||..||+|..+|+..+.++++||.
T Consensus       187 ~~~~~~~~~l~~L~~r~~~i~~~~~-----~g~~~~eia~~l~~s~~tv~~~l~~i~~kl~  242 (258)
T 3p7n_A          187 ARRERAAEMLKTLSPRQLEVTTLVA-----SGLRNKEVAARLGLSEKTVKMHRGLVMEKLN  242 (258)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            3456678889999999999999876     5899999999999999999999999988874

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=95.40  E-value=0.014  Score=53.70  Aligned_cols=46  Identities=17%  Similarity=0.201  Sum_probs=41.2

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..|+++|++|+.+..     +++|.+|||+.|++|..+|+..+++.++||.
T Consensus       158 ~~Lt~rE~~vL~~l~-----~g~s~~~Ia~~l~~s~~Tv~~~i~~l~~KL~  203 (225)
T 3klo_A          158 AKLTKREQQIIKLLG-----SGASNIEIADKLFVSENTVKTHLHNVFKKIN  203 (225)
T ss_dssp             HTSCHHHHHHHHHHT-----TTCCHHHHHHHTTCCHHHHHHHHHHHTTTSC
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            469999999998854     6899999999999999999999999888874

>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=93.97  E-value=0.027  Score=39.68  Aligned_cols=33  Identities=21%  Similarity=0.296  Sum_probs=26.4

Q ss_pred             HHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          414 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       414 R~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +.|+.+ +.    ++.|..|||+.+|||..+|..++.+
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            445555 44    6799999999999999999987654

>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=93.94  E-value=0.071  Score=48.48  Aligned_cols=50  Identities=20%  Similarity=0.121  Sum_probs=42.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG---LSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG---IS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|++|+.+... +.|+.+|.+|||+.++   +|..+|+..+++.++||..
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            499999999876653 2235599999999999   9999999999999988863

>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=93.74  E-value=0.074  Score=48.61  Aligned_cols=50  Identities=10%  Similarity=0.034  Sum_probs=42.6

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~L-----GIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|.+|+.+... +.|+.+|.+|||+.+     ++|..+|+.++++.++||..
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            499999999987664 234569999999999     99999999999999988853

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=93.66  E-value=0.11  Score=48.23  Aligned_cols=50  Identities=10%  Similarity=-0.049  Sum_probs=41.5

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~L-----GIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|.+|+.+... +.|+.+|.+|||+.+     ++|..+|+..+++.++||..
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            499999999987664 223559999999999     99999999999999999853

>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=93.24  E-value=0.11  Score=41.40  Aligned_cols=41  Identities=15%  Similarity=0.325  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +.++.||.+-.....|++.|..|||+.||||..+|++++.+
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~   54 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYS   54 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            44566765555433346899999999999999999886543

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=92.52  E-value=0.12  Score=45.09  Aligned_cols=40  Identities=13%  Similarity=0.180  Sum_probs=30.8

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      ..|..| .+|+.+-.     +|+|+.|||+.+|+|..||.. .+++|
T Consensus        60 ~aLs~R-~eV~klL~-----~G~syreIA~~~g~S~aTIsR-v~r~L   99 (119)
T 3kor_A           60 QSLSQR-LQVAKMIK-----QGYTYATIEQESGASTATISR-VKRSL   99 (119)
T ss_dssp             HHHHHH-HHHHHHHH-----HTCCHHHHHHHHCCCHHHHHH-HHHHH
T ss_pred             HHHHHH-HHHHHHHH-----cCCCHHHHHHHHCCCHHHHHH-HHHHH
Confidence            456666 67777755     579999999999999999987 44444

>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=92.51  E-value=0.21  Score=40.40  Aligned_cols=44  Identities=20%  Similarity=0.466  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      +.++.||.+......|...|..|||+.||||+.+|++.    |.+|.+
T Consensus        10 ~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~----L~~Le~   53 (81)
T 1qbj_A           10 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRV----LYSLAK   53 (81)
T ss_dssp             HHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHH----HHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            34566665554433356899999999999999998774    555543

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=92.48  E-value=0.099  Score=47.48  Aligned_cols=50  Identities=12%  Similarity=0.056  Sum_probs=42.4

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|.+|+.+... +.|..+|.+|||+.++     +|..+|+..+++.++||..
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            499999999977653 2234599999999998     9999999999999999964

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=92.27  E-value=0.09  Score=48.02  Aligned_cols=50  Identities=10%  Similarity=-0.023  Sum_probs=41.5

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|.+|+.+... +.|..+|.+|||+.++     +|..+|+.++++.++||..
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            499999999987664 2234499999999998     9999999999999999974

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=92.12  E-value=0.19  Score=42.74  Aligned_cols=40  Identities=20%  Similarity=0.124  Sum_probs=33.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.++..|...+.    .|.|..+||+.||+|..+|+.++.+
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            467777776666666    7899999999999999999998865

>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=92.03  E-value=0.26  Score=40.70  Aligned_cols=42  Identities=12%  Similarity=-0.018  Sum_probs=32.8

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .++..++.-+...|.    ++.+..+||+.||||..+|+.++.+..
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            366666655544455    789999999999999999999988753

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=91.65  E-value=0.17  Score=47.58  Aligned_cols=36  Identities=19%  Similarity=0.183  Sum_probs=29.9

Q ss_pred             HHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          413 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       413 ER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      -..+..+ |.    .|+|..|||+.||||+.+|++++..|.
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            3444555 66    889999999999999999999988765

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=91.37  E-value=0.17  Score=47.61  Aligned_cols=50  Identities=24%  Similarity=0.246  Sum_probs=42.2

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGN-----IFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe-----~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|++||.+... +.|+.+|.+|||+     .++++..+|+..+++.++||..
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            499999999988774 3346699999999     5888999999999998888863

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=91.35  E-value=0.32  Score=45.31  Aligned_cols=50  Identities=18%  Similarity=0.130  Sum_probs=43.2

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-----GLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~L-----GIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|.+|+.+... +.|+..|.+||++.+     +++..+|+.++++.++||..
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            499999999887664 446889999999999     78999999999998888864

>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=90.50  E-value=0.43  Score=41.45  Aligned_cols=42  Identities=12%  Similarity=-0.002  Sum_probs=33.5

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .++..+|.-+...+.    .|.+..+||+.+|||..+|+.++.+..
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            466666665555555    789999999999999999999988754

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

Probab=90.46  E-value=0.26  Score=45.06  Aligned_cols=80  Identities=23%  Similarity=0.117  Sum_probs=36.9

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP  303 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~~~lGReP  303 (473)
                      +..+.+|..|.+|+.+.++     +.++|.   +|+..+  .+.|    .      .......+++.+...+....|+.|
T Consensus        72 ~~~~~~~~~f~~~l~~i~~-----~~~~d~---~r~~~~--~~~~----~------~~~~~~~~~~~~~~~~~~~~~~~~  131 (243)
T 1l0o_C           72 KFDLSYDVKFSTYAVPMII-----GEIQRF---LRDDGT--VKVS----R------SLKEMGNKIRKAKDELSKTRGRAP  131 (243)
T ss_dssp             ------------------------------------CCC--CTTH----H------HHHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             HcCcccCCCHHHHHHHHHH-----HHHHHH---HHhcCC--ccCc----H------HHHHHHHHHHHHHHHHHHHcCCCC
Confidence            3455567899999999999     999884   665331  1121    0      113445678888899999999999


Q ss_pred             CHHHHHHHcCCCHHHHHHHH
Q 011992          304 TLIEWAKAIGLSCRDLKSEL  323 (473)
Q Consensus       304 T~eEiA~~lGms~eeL~~~l  323 (473)
                      +.++++..+|++.+++...+
T Consensus       132 ~~~~~~~~~~~~~~~~~~~~  151 (243)
T 1l0o_C          132 TVTEIADHLGISPEDVVLAQ  151 (243)
T ss_dssp             BHHHHHHHHTSCHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHH
Confidence            99999999999988776543

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=90.33  E-value=0.086  Score=48.03  Aligned_cols=50  Identities=4%  Similarity=-0.050  Sum_probs=42.1

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFG-----LSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LG-----IS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+++|++|+.+... +.|+.+|.+|||+.++     +|..+|+..+++.++||..
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            499999999987663 1123399999999999     9999999999999999974

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=89.96  E-value=0.64  Score=37.23  Aligned_cols=44  Identities=20%  Similarity=0.228  Sum_probs=33.3

Q ss_pred             HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ...|++.+..+|...+.  .+.+.|..|||+.+|+|.++|+.++.+
T Consensus        16 ~~~l~~~~~~~l~~l~~--~~~~~t~~ela~~l~is~~tv~~~l~~   59 (109)
T 2d1h_A           16 CYKITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVENSLKK   59 (109)
T ss_dssp             HHTCCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45788888877654431  126899999999999999999885543

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=89.19  E-value=0.7  Score=37.04  Aligned_cols=27  Identities=15%  Similarity=0.139  Sum_probs=23.8

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .+.+..+||+.+|||..+|+.++.+..
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            568999999999999999999986544

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=89.09  E-value=0.4  Score=47.38  Aligned_cols=37  Identities=14%  Similarity=0.258  Sum_probs=31.6

Q ss_pred             HHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          414 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       414 R~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      ..|..|||.    ++++..|||+.||||+.+||..+..+.+
T Consensus        11 ~~ia~l~~~----~~~~~~ela~~l~vS~~tIrRdL~~l~~   47 (315)
T 2w48_A           11 VKIAQLYYE----QDMTQAQIARELGIYRTTISRLLKRGRE   47 (315)
T ss_dssp             HHHHHHHHT----SCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            346678887    8999999999999999999998877644

>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=88.88  E-value=0.47  Score=43.59  Aligned_cols=42  Identities=17%  Similarity=0.235  Sum_probs=32.7

Q ss_pred             hCCHHHHHHHHHHhhc--cCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGI--EDGKPKSLSEVGNIFGLSKERVRQLE  449 (473)
Q Consensus       408 ~LperER~VL~LrY~L--~~ge~lTlkEIAe~LGIS~~rVrqi~  449 (473)
                      .|+++|++|+......  ..|.++|.+|||+.||++..+|+.++
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            5899999998764321  23478999999999999988876644

>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=88.59  E-value=1.2  Score=37.56  Aligned_cols=51  Identities=16%  Similarity=0.222  Sum_probs=40.5

Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccCC---CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          399 RQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       399 ~e~L~~aL~~LperER~VL~LrY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ...|......|++.|+.|......  +.   ..+|..|||+..|+|..+|....++
T Consensus         9 ~~~i~~~~~~ls~~e~~ia~yil~--~~~~~~~~si~elA~~~~vS~aTv~Rf~kk   62 (111)
T 2o3f_A            9 LAIIQSMXHXLPPSERKLADYILA--HPHXAIESTVNEISALANSSDAAVIRLCXS   62 (111)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHHH--CHHHHHTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhccCCHHHHHHHHHHHH--ChHHHHhcCHHHHHHHHCCCHHHHHHHHHH
Confidence            455777788999999999765442  11   3799999999999999999887654

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=88.55  E-value=0.54  Score=36.14  Aligned_cols=40  Identities=18%  Similarity=0.201  Sum_probs=27.6

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      +++..+.||.+--.  ++..++..|||+.+|+|+++|.+++.
T Consensus         8 m~~~~~~IL~~L~~--~~~~~s~~eLA~~lglsr~tv~~~l~   47 (67)
T 2heo_A            8 GDNLEQKILQVLSD--DGGPVAIFQLVKKCQVPKKTLNQVLY   47 (67)
T ss_dssp             -CHHHHHHHHHHHH--HCSCEEHHHHHHHHCSCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHH--cCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            44455556554322  23579999999999999999987543

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=88.42  E-value=0.35  Score=39.39  Aligned_cols=25  Identities=8%  Similarity=0.133  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .+.|..|||+.||||+++|++++.+
T Consensus        29 ~g~sa~eLAk~LgiSk~aVr~~L~~   53 (82)
T 1oyi_A           29 EGATAAQLTRQLNMEKREVNKALYD   53 (82)
T ss_dssp             STEEHHHHHHHSSSCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4499999999999999999997665

>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=88.36  E-value=1.2  Score=40.34  Aligned_cols=54  Identities=11%  Similarity=0.244  Sum_probs=41.4

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       398 l~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      +...+...+..|++.+-.||...+... +++.|..+||+.+|++.++|+.++.+-
T Consensus        28 ~~~~~~~~~~~lt~~q~~vL~~L~~~~-~~~~t~~eLa~~l~is~~tvs~~l~~L   81 (189)
T 3nqo_A           28 IQIEGDKYFGILTSRQYMTILSILHLP-EEETTLNNIARKMGTSKQNINRLVANL   81 (189)
T ss_dssp             HHHHHHHHHCSSCHHHHHHHHHHHHSC-GGGCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHhcc-CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            344556666779999999987666311 268999999999999999999865543

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=88.14  E-value=0.98  Score=39.33  Aligned_cols=42  Identities=12%  Similarity=0.245  Sum_probs=32.9

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ..|++.++.||.+-..   +...|..|||+.+|+|+.+|+.++.+
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            3588999988865433   25799999999999999999876544

>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=88.10  E-value=1.8  Score=35.57  Aligned_cols=48  Identities=17%  Similarity=0.192  Sum_probs=33.4

Q ss_pred             HHHHHHHhhCCH-HHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          400 QHVRNLLTLLNP-KERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       400 e~L~~aL~~Lpe-rER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ..+...+..|.. ....||.+-..    .+.+..|||+.+|+|.++|+++++.
T Consensus        14 ~~~~~~~~~l~~~~r~~IL~~L~~----~~~~~~ela~~l~is~stvs~~L~~   62 (106)
T 1r1u_A           14 ERVTEIFKALGDYNRIRIMELLSV----SEASVGHISHQLNLSQSNVSHQLKL   62 (106)
T ss_dssp             HHHHHHHHHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            345555555654 44455554333    5789999999999999999986543

>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=87.97  E-value=0.89  Score=39.46  Aligned_cols=40  Identities=20%  Similarity=0.167  Sum_probs=32.0

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++.++.||.+-..   +...|..|||+.+|+|+++|+.++.+
T Consensus         3 ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   42 (144)
T 2cfx_A            3 LDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVRQ   42 (144)
T ss_dssp             CCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            78888888875443   25799999999999999999876544

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=87.83  E-value=1  Score=33.38  Aligned_cols=46  Identities=9%  Similarity=0.179  Sum_probs=31.8

Q ss_pred             CHHHHHHHHHHhhccCCCCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Q 011992          410 NPKERCIVRLRFGIEDGKPKS----LSEVGNIFGLSKERVRQLESRALYRLKQSL  460 (473)
Q Consensus       410 perER~VL~LrY~L~~ge~lT----lkEIAe~LGIS~~rVrqi~~RAL~KLR~~L  460 (473)
                      ++..+.-+..++.    .+.+    ..+||..+||+.++|+.+..+ ...++..+
T Consensus         7 s~efK~~~~~~~~----~g~s~~~~~~~vA~~~gIs~~tl~~W~~~-~~~~~~~~   56 (59)
T 2glo_A            7 TPHFKLQVLESYR----NDNDCKGNQRATARKYNIHRRQIQKWLQC-ESNLRSSV   56 (59)
T ss_dssp             CHHHHHHHHHHHH----HCTTTTTCHHHHHHHTTSCHHHHHHHHTT-HHHHHHHH
T ss_pred             CHHHHHHHHHHHH----cCCCcchHHHHHHHHHCcCHHHHHHHHHH-HHHHHHHH
Confidence            4444443334443    4668    999999999999999999764 45555544

>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=87.71  E-value=2.6  Score=33.83  Aligned_cols=37  Identities=30%  Similarity=0.345  Sum_probs=28.5

Q ss_pred             CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          410 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       410 perER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ++....||.+. .    .+++..|||+.+|+|..+|++++..
T Consensus        30 ~~~r~~Il~~L-~----~~~~~~eLa~~l~is~~tv~~~L~~   66 (96)
T 1y0u_A           30 NPVRRKILRML-D----KGRSEEEIMQTLSLSKKQLDYHLKV   66 (96)
T ss_dssp             CHHHHHHHHHH-H----TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHH-c----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45555666554 4    6799999999999999999986543

>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=87.67  E-value=2.3  Score=35.55  Aligned_cols=51  Identities=12%  Similarity=0.086  Sum_probs=37.4

Q ss_pred             HHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          401 HVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       401 ~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .+...+.  .|++.+..||...+. .++.+.+..|||+.+|++.++|+.++.+-
T Consensus        22 ~~~~~~~~~~lt~~~~~iL~~l~~-~~~~~~~~~ela~~l~~~~~tvs~~l~~L   74 (141)
T 3bro_A           22 RFDIFAKKYDLTGTQMTIIDYLSR-NKNKEVLQRDLESEFSIKSSTATVLLQRM   74 (141)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHH-TTTSCCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHH-CCCCCcCHHHHHHHHCCCcchHHHHHHHH
Confidence            3444443  589999888876665 22237999999999999999998865543

>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=87.56  E-value=1.4  Score=37.30  Aligned_cols=52  Identities=15%  Similarity=0.211  Sum_probs=36.7

Q ss_pred             HHHHHHHHhh----CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          399 RQHVRNLLTL----LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       399 ~e~L~~aL~~----LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      ...+...+..    |++.+-.||..-+.   ..+.|..|||+.+|++.++|+.++.+-.
T Consensus        21 ~~~~~~~l~~~~~~lt~~~~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L~   76 (142)
T 3ech_A           21 RTRIQSELDCQRLDLTPPDVHVLKLIDE---QRGLNLQDLGRQMCRDKALITRKIRELE   76 (142)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHH---TTTCCHHHHHHHHC---CHHHHHHHHHH
T ss_pred             HHHHHHHHhhccCCCCHHHHHHHHHHHh---CCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3445555554    89999988876654   2589999999999999999998766543

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=87.47  E-value=1.3  Score=37.75  Aligned_cols=46  Identities=7%  Similarity=0.067  Sum_probs=35.2

Q ss_pred             HHHhhCCHHHHHHHHHHhhccCCCC-CCHHHHHHHHCCCHHHHHHHHHH
Q 011992          404 NLLTLLNPKERCIVRLRFGIEDGKP-KSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       404 ~aL~~LperER~VL~LrY~L~~ge~-lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ...-.|++.+..|+..-..  .+.+ +|..|||+.+|++.++|...+.+
T Consensus        19 ~~~~gLt~~e~~il~~L~~--~~~~~~t~~eLa~~l~~s~sTV~r~L~~   65 (123)
T 3r0a_A           19 KCALNLTKADLNVMKSFLN--EPDRWIDTDALSKSLKLDVSTVQRSVKK   65 (123)
T ss_dssp             HHHHTCCHHHHHHHHHHHH--STTCCEEHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHH--CCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4456799999998876553  2233 89999999999999999875443

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=87.21  E-value=1.1  Score=37.91  Aligned_cols=41  Identities=17%  Similarity=0.135  Sum_probs=33.2

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .|++.+..||..-+.    .+.|..|||+.+|++.++|+.++.+-
T Consensus        35 ~lt~~~~~iL~~l~~----~~~t~~eLa~~l~~s~~tvs~~l~~L   75 (146)
T 3tgn_A           35 ALTNTQEHILMLLSE----ESLTNSELARRLNVSQAAVTKAIKSL   75 (146)
T ss_dssp             CCCHHHHHHHHHHTT----CCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            478888888876654    33999999999999999999865543

>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=87.03  E-value=1.4  Score=38.52  Aligned_cols=41  Identities=17%  Similarity=0.326  Sum_probs=32.5

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.++.||.+-..   +...|+.|||+.+|+|.++|+.++.+
T Consensus         4 ~ld~~~~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   44 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN---DGKAPLREISKITGLAESTIHERIRK   44 (151)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHCSCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888875432   25799999999999999999886554

>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=86.83  E-value=1.4  Score=38.46  Aligned_cols=41  Identities=22%  Similarity=0.408  Sum_probs=32.7

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.++.||.+-..   +...|+.|||+.+|+|+++|+.++.+
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            378888888875432   25799999999999999999886554

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=86.70  E-value=0.7  Score=37.36  Aligned_cols=40  Identities=15%  Similarity=0.186  Sum_probs=29.8

Q ss_pred             CCHHHHH-HHHHHhhccCCC-CCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          409 LNPKERC-IVRLRFGIEDGK-PKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       409 LperER~-VL~LrY~L~~ge-~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .++..+. |+.++..    . +.|..+||+.+|||.++|+.+..+.
T Consensus         6 ys~e~k~~~v~~~~~----~~g~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            6 YSEEFKRDAVALYEN----SDGASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCHHHHHHHHHHHTT----GGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH----cCCChHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555554 4444443    3 7999999999999999999998653

>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=86.59  E-value=1.2  Score=38.88  Aligned_cols=41  Identities=29%  Similarity=0.293  Sum_probs=32.6

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.++.||.+-..   +...|+.|||+.+|+|.++|+.++.+
T Consensus         4 ~ld~~~~~iL~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   44 (150)
T 2w25_A            4 ALDDIDRILVRELAA---DGRATLSELATRAGLSVSAVQSRVRR   44 (150)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            488888888875432   25799999999999999999886544

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=86.56  E-value=1.1  Score=39.51  Aligned_cols=41  Identities=12%  Similarity=0.042  Sum_probs=32.9

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.++.||.+-..   +...|..|||+.+|+|.++|+.++.+
T Consensus         7 ~ld~~~~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   47 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE---NGRLTNVELSERVALSPSPCLRRLKQ   47 (162)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            488888888875443   24689999999999999999886554

>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=86.53  E-value=2.4  Score=35.55  Aligned_cols=53  Identities=8%  Similarity=0.113  Sum_probs=39.4

Q ss_pred             HHHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          399 RQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       399 ~e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ...+...+.  .|++.+-.|+..-+. .++++.|..|||+.+|++.++|+.++.+-
T Consensus        17 ~~~~~~~~~~~~lt~~~~~vL~~l~~-~~~~~~t~~ela~~l~~~~~tvs~~l~~L   71 (139)
T 3eco_A           17 KQKADQKLEQFDITNEQGHTLGYLYA-HQQDGLTQNDIAKALQRTGPTVSNLLRNL   71 (139)
T ss_dssp             HHHHHHHHGGGTCCHHHHHHHHHHHH-STTTCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHh-cCCCCcCHHHHHHHhCCCcccHHHHHHHH
Confidence            344444443  589999998877665 22258999999999999999999866553

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=86.28  E-value=1.2  Score=36.31  Aligned_cols=38  Identities=24%  Similarity=0.260  Sum_probs=29.0

Q ss_pred             CHHHHHHH-HHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          410 NPKERCIV-RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       410 perER~VL-~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ++....|+ .+.-.    ++.+..|||+.+|+|.++|+++++.
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            45556676 33333    5799999999999999999997664

>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=86.22  E-value=1.1  Score=35.68  Aligned_cols=41  Identities=22%  Similarity=0.191  Sum_probs=32.2

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.+..|+.....   +.+.|..|||+.+|++.++|+.++.+
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            478888888765432   25799999999999999999886554

>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=86.08  E-value=1.3  Score=37.80  Aligned_cols=40  Identities=15%  Similarity=0.344  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++.++.||.....   +...+..|||+.+|+|+.+|+..+.+
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            66777788764432   25689999999999999999885544

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=86.02  E-value=2.4  Score=35.31  Aligned_cols=50  Identities=12%  Similarity=0.062  Sum_probs=37.5

Q ss_pred             HHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          400 QHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       400 e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ..+...+.  .|++.+..|+...+.   +.+.+..|||+.+|++.++|+.++.+-
T Consensus        16 ~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~~~~ela~~l~~s~~tvs~~l~~L   67 (138)
T 3bpv_A           16 VFIGRELGHLNLTDAQVACLLRIHR---EPGIKQDELATFFHVDKGTIARTLRRL   67 (138)
T ss_dssp             HHHHHHSGGGTCCHHHHHHHHHHHH---STTCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34444443  589998888876554   367999999999999999998865543

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=85.98  E-value=1.2  Score=37.72  Aligned_cols=46  Identities=11%  Similarity=0.094  Sum_probs=34.4

Q ss_pred             hhCCHHHHHHHHHHhhc-cCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       407 ~~LperER~VL~LrY~L-~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      -.|++.+..+|...+.+ ..+.+.|..|||+.+|++.++|+.++.+-
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            46888888877655433 33478999999999999999999866553

>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=85.88  E-value=2.5  Score=35.58  Aligned_cols=42  Identities=12%  Similarity=0.149  Sum_probs=34.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .|++.+..||...+.    .+.|..|||+.+|++.++|+.++.+-.
T Consensus        34 ~l~~~~~~iL~~l~~----~~~~~~ela~~l~~s~~tvs~~l~~Le   75 (146)
T 2gxg_A           34 NLSYLDFLVLRATSD----GPKTMAYLANRYFVTQSAITASVDKLE   75 (146)
T ss_dssp             TCCHHHHHHHHHHTT----SCBCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHhc----CCcCHHHHHHHhCCCchhHHHHHHHHH
Confidence            589998888876553    789999999999999999988665443

>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=85.81  E-value=1.3  Score=38.37  Aligned_cols=40  Identities=13%  Similarity=0.135  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++.++.||.+-..   +...+..|||+.+|+|+++|+.++.+
T Consensus         1 ld~~~~~il~~L~~---~~~~~~~ela~~lg~s~~tv~~~l~~   40 (150)
T 2pn6_A            1 MDEIDLRILKILQY---NAKYSLDEIAREIRIPKATLSYRIKK   40 (150)
T ss_dssp             CCHHHHHHHHHHTT---CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45667777764332   25799999999999999999886544

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=85.79  E-value=1.4  Score=35.00  Aligned_cols=47  Identities=28%  Similarity=0.289  Sum_probs=31.8

Q ss_pred             HHHHHhhCC-HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          402 VRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       402 L~~aL~~Lp-erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +...+..|. +.+..|+.+..   .+.+.|..|||+.+|+|.++|++++.+
T Consensus        14 ~~~~~~~l~~~~~~~il~~l~---~~~~~s~~ela~~l~is~~tvs~~l~~   61 (99)
T 3cuo_A           14 AAALLKAMSHPKRLLILCMLS---GSPGTSAGELTRITGLSASATSQHLAR   61 (99)
T ss_dssp             HHHHHHHHCSHHHHHHHHHHT---TCCSEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHHH---hCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            334444443 45555654433   345899999999999999999886543

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=85.79  E-value=2.3  Score=35.48  Aligned_cols=42  Identities=7%  Similarity=0.036  Sum_probs=34.1

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .|++.+..||...+.   +.+.|..|||+.+|++.++|+.++.+-
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            799999888876543   257999999999999999998865543

>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=85.63  E-value=2.4  Score=34.24  Aligned_cols=47  Identities=23%  Similarity=0.240  Sum_probs=31.8

Q ss_pred             HHHHHHHhhCCHHHHH-HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          400 QHVRNLLTLLNPKERC-IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       400 e~L~~aL~~LperER~-VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      ..+...+..|...-|. ||.+-..    .+.+..|||+.+|+|.++|++++.
T Consensus        11 ~~~~~~~~~l~~~~r~~Il~~L~~----~~~~~~ela~~l~is~~tvs~~L~   58 (102)
T 3pqk_A           11 NEVANLLKTLSHPVRLMLVCTLVE----GEFSVGELEQQIGIGQPTLSQQLG   58 (102)
T ss_dssp             HHHHHHHHHHCSHHHHHHHHHHHT----CCBCHHHHHHHHTCCTTHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3455555555544444 4443322    469999999999999999988544

>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=85.57  E-value=0.48  Score=41.72  Aligned_cols=40  Identities=13%  Similarity=0.007  Sum_probs=31.1

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++..++..|...+.    ++.+..+||+.||||..+|+.++.+
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            355665654444444    6899999999999999999998865

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=85.56  E-value=1.3  Score=39.27  Aligned_cols=40  Identities=15%  Similarity=0.253  Sum_probs=31.1

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++.++.||.+--.   +...|+.|||+.+|+|+.+|+.++.+
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            46677888765432   25789999999999999999986554

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=85.54  E-value=3.2  Score=35.71  Aligned_cols=45  Identities=20%  Similarity=0.053  Sum_probs=36.3

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      -.|++.+..||...+.   +.+.+..|||+.+|++.++|+.++.+-.+
T Consensus        45 ~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~Le~   89 (162)
T 2fa5_A           45 YGMAIPEWRVITILAL---YPGSSASEVSDRTAMDKVAVSRAVARLLE   89 (162)
T ss_dssp             HCCCHHHHHHHHHHHH---STTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3699999988876654   26899999999999999999987665443

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=84.99  E-value=1.7  Score=36.19  Aligned_cols=47  Identities=15%  Similarity=0.232  Sum_probs=33.7

Q ss_pred             HHHHHHhh-CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          401 HVRNLLTL-LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       401 ~L~~aL~~-LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .+...+.. .++.+..||.+-..    .+.++.|||+.+|+|.++|++++++
T Consensus        21 ~~~~~~~~l~~~~~~~il~~L~~----~~~s~~ela~~l~is~stvsr~l~~   68 (119)
T 2lkp_A           21 QVASTLQALATPSRLMILTQLRN----GPLPVTDLAEAIGMEQSAVSHQLRV   68 (119)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHHH----CCCCHHHHHHHHSSCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34444444 34566667665553    5799999999999999999986654

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=84.87  E-value=1.8  Score=36.06  Aligned_cols=42  Identities=12%  Similarity=0.176  Sum_probs=34.0

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .|++.+..||...+.   +.+.|..|||+.+|++.++|+.++.+-
T Consensus        35 ~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~L   76 (140)
T 2nnn_A           35 GLTPTQWAALVRLGE---TGPCPQNQLGRLTAMDAATIKGVVERL   76 (140)
T ss_dssp             CCCHHHHHHHHHHHH---HSSBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            799999888876543   158999999999999999998865543

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=84.68  E-value=2.7  Score=33.62  Aligned_cols=46  Identities=20%  Similarity=0.208  Sum_probs=31.0

Q ss_pred             HHHHHHhhCCHHHH-HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          401 HVRNLLTLLNPKER-CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       401 ~L~~aL~~LperER-~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      .+...+..|...-| .|+.+-.   + .+.+..|||+.+|+|.++|++.+.
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L~---~-~~~~~~ela~~l~is~~tvs~~L~   58 (98)
T 3jth_A           12 KAVVLLKAMANERRLQILCMLH---N-QELSVGELCAKLQLSQSALSQHLA   58 (98)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHTT---T-SCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHh---c-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45555555554444 4443322   2 578999999999999999987543

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=84.44  E-value=3  Score=35.05  Aligned_cols=63  Identities=16%  Similarity=0.220  Sum_probs=48.1

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHhhccCC---CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHhcc
Q 011992          398 MRQHVRNLLTLLNPKERCIVRLRFGIEDG---KPKSLSEVGNIFGLSKERVRQLESR----ALYRLKQSLGG  462 (473)
Q Consensus       398 l~e~L~~aL~~LperER~VL~LrY~L~~g---e~lTlkEIAe~LGIS~~rVrqi~~R----AL~KLR~~L~~  462 (473)
                      +...|...+..|++.|+.|......  +.   ..+|..|||+..|+|..+|....++    +..-+|..+..
T Consensus         4 i~~~I~~~~~~lt~~e~~ia~yil~--~~~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~gf~efk~~l~~   73 (107)
T 3iwf_A            4 ILYKIDNQYPYFTKNEKKIAQFILN--YPHKVVNMTSQEIANQLETSSTSIIRLSKKVTPGGFNELKTRLSK   73 (107)
T ss_dssp             HHHHHHHHGGGSCHHHHHHHHHHHH--CHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHh--CHHHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            3456788889999999999764332  21   5799999999999999999887765    56666665554

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=84.43  E-value=3.1  Score=35.59  Aligned_cols=44  Identities=14%  Similarity=0.219  Sum_probs=35.6

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      ..|++.+-.||...+.   +.+.|..|||+.+|++.++|+.++.+-.
T Consensus        37 ~~lt~~q~~iL~~l~~---~~~~~~~eLa~~l~~~~~~vs~~l~~L~   80 (149)
T 4hbl_A           37 FGITYSQYLVMLTLWE---ENPQTLNSIGRHLDLSSNTLTPMLKRLE   80 (149)
T ss_dssp             TTCCHHHHHHHHHHHH---SSSEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3589999888876653   2689999999999999999998666543

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=84.06  E-value=3.2  Score=35.49  Aligned_cols=43  Identities=7%  Similarity=0.083  Sum_probs=34.5

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .|++.+..||...+.   +.+.+..|||+.+|++.++|+.++.+-.
T Consensus        40 ~lt~~~~~iL~~l~~---~~~~t~~ela~~l~i~~~tvs~~l~~Le   82 (155)
T 3cdh_A           40 GLRVPEWRVLACLVD---NDAMMITRLAKLSLMEQSRMTRIVDQMD   82 (155)
T ss_dssp             TCCHHHHHHHHHHSS---CSCBCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            589998888876543   3579999999999999999998665543

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=83.91  E-value=2.4  Score=34.55  Aligned_cols=46  Identities=11%  Similarity=0.089  Sum_probs=32.0

Q ss_pred             HHHHHhhCC-HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          402 VRNLLTLLN-PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       402 L~~aL~~Lp-erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +...+..|. +....||.+...    .+.+..|||+.+|+|.++|+.++.+
T Consensus        11 ~~~~~~~l~~~~r~~IL~~L~~----~~~~~~ela~~l~is~~tv~~~l~~   57 (114)
T 2oqg_A           11 LASVFAALSDETRWEILTELGR----ADQSASSLATRLPVSRQAIAKHLNA   57 (114)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHH----SCBCHHHHHHHSSSCHHHHHHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            444455554 445556554332    5799999999999999999886554

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=83.81  E-value=3.1  Score=35.46  Aligned_cols=43  Identities=5%  Similarity=0.060  Sum_probs=34.8

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .|++.+..||...+.   ..+.|..|||+.+|++.++|+.++.+-.
T Consensus        38 ~lt~~~~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~Le   80 (154)
T 2qww_A           38 GLTIQQLAMINVIYS---TPGISVADLTKRLIITGSSAAANVDGLI   80 (154)
T ss_dssp             TCCHHHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            599999888876654   2569999999999999999988665543

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=83.81  E-value=1.1  Score=37.07  Aligned_cols=38  Identities=18%  Similarity=0.209  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      +|...|+.+...    .+.|..+||+.+|||..||+..+..-
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            345555555444    45899999999999999999988753

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=83.68  E-value=0.9  Score=34.95  Aligned_cols=23  Identities=17%  Similarity=0.312  Sum_probs=21.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q 011992          429 KSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       429 lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +|++|||+.+|||..+|+.+++.
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng   23 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVING   23 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            47899999999999999999874

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=83.67  E-value=3.1  Score=35.24  Aligned_cols=50  Identities=18%  Similarity=0.205  Sum_probs=37.3

Q ss_pred             HHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          401 HVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       401 ~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .+...+.  .|++.+..||...+.   ..+.+..|||+.+|++.++|+.++.+-.
T Consensus        30 ~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~Le   81 (150)
T 2rdp_A           30 RGREILTNYPITPPQFVALQWLLE---EGDLTVGELSNKMYLACSTTTDLVDRME   81 (150)
T ss_dssp             HHHHHHTTSSSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCchhHHHHHHHHH
Confidence            3444443  589988888866553   2579999999999999999998665543

>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=83.50  E-value=3.2  Score=34.78  Aligned_cols=42  Identities=21%  Similarity=0.260  Sum_probs=33.7

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.+..|+.+.+. .+ .+.|..|||+.+|++.++|+.++.+
T Consensus        23 gl~~~~~~il~~L~~-~~-~~~t~~ela~~l~~~~stvs~~l~~   64 (152)
T 1ku9_A           23 GLNKSVGAVYAILYL-SD-KPLTISDIMEELKISKGNVSMSLKK   64 (152)
T ss_dssp             TCCHHHHHHHHHHHH-CS-SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCChhHHHHHHHHHH-cC-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            589999888876642 22 5799999999999999999886544

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=83.49  E-value=1.9  Score=38.91  Aligned_cols=42  Identities=17%  Similarity=0.175  Sum_probs=32.8

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ..|++.++.||.+-..   +...|..|||+.+|+|+++|+.++.+
T Consensus        13 ~~ld~~d~~IL~~L~~---~~~~s~~eLA~~lglS~~tv~~~l~~   54 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKK---DARLTISELSEQLKKPESTIHFRIKK   54 (171)
T ss_dssp             -CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4588888888775443   24689999999999999999886554

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=83.45  E-value=3.5  Score=34.33  Aligned_cols=53  Identities=6%  Similarity=0.038  Sum_probs=39.2

Q ss_pred             HHHHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          398 MRQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       398 l~e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      +...+...+.  .|++.+..|+...+.   +.+.+..+||+.+|++.++|+.++.+-.
T Consensus        19 ~~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~~~~~la~~l~~~~~tvs~~l~~L~   73 (138)
T 1jgs_A           19 KDRLLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDRLV   73 (138)
T ss_dssp             HHHHHHHHHTTTTSCHHHHHHHHHHHH---HSSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhcCCCHHHHHHHHHHHh---cCCCCHHHHHHHHCCChHHHHHHHHHHH
Confidence            3444555553  589998888876553   2578999999999999999998665543

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=82.92  E-value=3.3  Score=35.17  Aligned_cols=46  Identities=13%  Similarity=0.282  Sum_probs=31.3

Q ss_pred             HHHHHhhC-CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          402 VRNLLTLL-NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       402 L~~aL~~L-perER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +...+..| .+....||.+-..    .+.+..|||+.+|+|.++|++++++
T Consensus        36 ~~~~~kaL~~~~rl~IL~~L~~----~~~s~~ela~~lgis~stvs~~L~~   82 (122)
T 1r1t_A           36 LAEFFAVLADPNRLRLLSLLAR----SELCVGDLAQAIGVSESAVSHQLRS   82 (122)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHTT----CCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            33334334 4445556654432    5789999999999999999986544

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=82.92  E-value=2.3  Score=36.64  Aligned_cols=43  Identities=5%  Similarity=-0.031  Sum_probs=35.0

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .|++.+..||...+.   +.+.+..|||+.+|++.++|+.++.+-.
T Consensus        49 ~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~Le   91 (162)
T 3cjn_A           49 GLSTAKMRALAILSA---KDGLPIGTLGIFAVVEQSTLSRALDGLQ   91 (162)
T ss_dssp             TCCHHHHHHHHHHHH---SCSEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence            589999988876654   2578999999999999999988665543

>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=82.88  E-value=2  Score=34.45  Aligned_cols=42  Identities=14%  Similarity=0.148  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          397 LMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       397 el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      +..+.+.++|..|++              |+..|..+||+.||+++..|.+.+.+-
T Consensus        12 ~~~~~v~~~i~~L~~--------------~~~~Ta~~IAkkLg~sK~~vNr~LY~L   53 (75)
T 1sfu_A           12 EIFSLVKKEVLSLNT--------------NDYTTAISLSNRLKINKKKINQQLYKL   53 (75)
T ss_dssp             HHHHHHHHHHHTSCT--------------TCEECHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCC--------------CcchHHHHHHHHHCCCHHHHHHHHHHH
Confidence            345556666666664              356899999999999998887766543

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=82.87  E-value=2.4  Score=35.81  Aligned_cols=51  Identities=12%  Similarity=0.061  Sum_probs=37.8

Q ss_pred             HHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          400 QHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       400 e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      ..+...+.  .|++.+-.||..-+.   +.+.|..|||+.+|++.++|+.++.+-.
T Consensus        23 ~~~~~~~~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L~   75 (140)
T 3hsr_A           23 KKYTNYLKEYDLTYTGYIVLMAIEN---DEKLNIKKLGERVFLDSGTLTPLLKKLE   75 (140)
T ss_dssp             HHHHHHHGGGTCCHHHHHHHHHSCT---TCEEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCChhhHHHHHHHHH
Confidence            33444443  589988888765543   3689999999999999999998665543

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=82.76  E-value=2.2  Score=36.41  Aligned_cols=40  Identities=13%  Similarity=0.228  Sum_probs=29.2

Q ss_pred             CCHHHHHHHHHHhhccC--CCCCCHHHHHHHHCCCHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIED--GKPKSLSEVGNIFGLSKERVRQL  448 (473)
Q Consensus       409 LperER~VL~LrY~L~~--ge~lTlkEIAe~LGIS~~rVrqi  448 (473)
                      +++.|+.-|..|+.+-.  .+|+|+.||++.+|+|..+|...
T Consensus        37 ~T~~E~~alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsRv   78 (107)
T 3frw_A           37 CTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRV   78 (107)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHHH
Confidence            67777666554443321  16799999999999999999763

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=82.75  E-value=4.3  Score=34.51  Aligned_cols=52  Identities=15%  Similarity=0.153  Sum_probs=38.1

Q ss_pred             HHHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          399 RQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       399 ~e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ...+...+.  .|++.+-.||...+.  .+++.|..|||+.+|++.++|+.++.+-
T Consensus        25 ~~~~~~~l~~~glt~~q~~vL~~l~~--~~~~~t~~eLa~~l~i~~~tvs~~l~~L   78 (150)
T 3fm5_A           25 LGAVNKALVPTGLRVRSYSVLVLACE--QAEGVNQRGVAATMGLDPSQIVGLVDEL   78 (150)
T ss_dssp             HHHHHHHHGGGTCCHHHHHHHHHHHH--STTCCCSHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHh--CCCCcCHHHHHHHHCCCHhHHHHHHHHH
Confidence            334444443  589999888876543  2356899999999999999999876553

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=82.62  E-value=2.4  Score=36.17  Aligned_cols=44  Identities=11%  Similarity=0.095  Sum_probs=35.0

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      ..|++.+..||...+.   +.+.|..|||+.+|++.++|+.++.+-.
T Consensus        33 ~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~s~~tvs~~l~~Le   76 (155)
T 1s3j_A           33 QGVTPAQLFVLASLKK---HGSLKVSEIAERMEVKPSAVTLMADRLE   76 (155)
T ss_dssp             TTCCHHHHHHHHHHHH---HSEEEHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3699999888876553   2578999999999999999988665433

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=82.54  E-value=3.4  Score=34.87  Aligned_cols=43  Identities=9%  Similarity=0.029  Sum_probs=34.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      .|++.+-.||...+.   +.+ |..|||+.+|++.++|+.++.+-.+
T Consensus        34 ~lt~~~~~iL~~l~~---~~~-~~~~la~~l~~~~~tvs~~l~~Le~   76 (144)
T 3f3x_A           34 NLSYLDFSILKATSE---EPR-SMVYLANRYFVTQSAITAAVDKLEA   76 (144)
T ss_dssp             SCCHHHHHHHHHHHH---SCE-EHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCC-CHHHHHHHHCCChhHHHHHHHHHHH
Confidence            689999988876664   133 9999999999999999986665443

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=82.38  E-value=3.8  Score=34.73  Aligned_cols=42  Identities=7%  Similarity=0.097  Sum_probs=34.1

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .|++.+..|+...+.   +.+.+..|||+.+|++.++|+.++.+-
T Consensus        37 ~lt~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~~vs~~l~~L   78 (152)
T 3bj6_A           37 GVTVGQRAILEGLSL---TPGATAPQLGAALQMKRQYISRILQEV   78 (152)
T ss_dssp             TCCHHHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            589998888876554   257999999999999999998865543

>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=82.33  E-value=1.5  Score=35.27  Aligned_cols=45  Identities=11%  Similarity=0.060  Sum_probs=33.6

Q ss_pred             hCCHHHHHHHHHHhhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIE-DGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       408 ~LperER~VL~LrY~L~-~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .|+.++..||...+.-. +|...+..|||+.+|++.++|..++.+-
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            47888888876554321 2234899999999999999999876543

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=82.19  E-value=2.6  Score=36.93  Aligned_cols=42  Identities=10%  Similarity=0.163  Sum_probs=34.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .|+..+..||...+.   ..+.|..|||+.+|++.++|+.++.+-
T Consensus        42 ~lt~~~~~iL~~L~~---~~~~t~~eLa~~l~is~~tvs~~l~~L   83 (168)
T 2nyx_A           42 NITIPQFRTLVILSN---HGPINLATLATLLGVQPSATGRMVDRL   83 (168)
T ss_dssp             SCCHHHHHHHHHHHH---HCSEEHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            699999888876543   157999999999999999999866543

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=82.17  E-value=1.6  Score=36.08  Aligned_cols=46  Identities=11%  Similarity=0.057  Sum_probs=30.6

Q ss_pred             HHHHHhhCCHH-HHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          402 VRNLLTLLNPK-ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       402 L~~aL~~Lper-ER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +...+..|... ...||.+...    .+.+..|||+.+|+|.++|++.+++
T Consensus        15 ~~~~~~al~~~~r~~IL~~L~~----~~~s~~eLa~~lgis~stvs~~L~~   61 (108)
T 2kko_A           15 VARVGKALANGRRLQILDLLAQ----GERAVEAIATATGMNLTTASANLQA   61 (108)
T ss_dssp             HHHHHHHHTTSTTHHHHHHHTT----CCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHc----CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            44444444433 3445544332    5789999999999999999885543

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=81.95  E-value=2.7  Score=35.48  Aligned_cols=50  Identities=10%  Similarity=0.072  Sum_probs=37.5

Q ss_pred             HHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          400 QHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       400 e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ..+...+.  .|++.+..||...+.   ..+.|..|||+.+|++.++|..++.+-
T Consensus        24 ~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~eLa~~l~~~~~~vs~~l~~L   75 (143)
T 3oop_A           24 LFLMRSIASYDVTPEQWSVLEGIEA---NEPISQKEIALWTKKDTPTVNRIVDVL   75 (143)
T ss_dssp             HHHHHHTTTSSSCHHHHHHHHHHHH---HSSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHhhhCCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCHhhHHHHHHHH
Confidence            34444443  489999888876553   168999999999999999999866553

>3qbm_A TETR transcriptional regulator; DNA/RNA-binding three-helical bundle, structural genomics, J center for structural genomics, JCSG; HET: MSE PGE; 1.80A {Chloroflexus aurantiacus}

Probab=81.83  E-value=21  Score=30.49  Aligned_cols=78  Identities=12%  Similarity=-0.029  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHHhC-CCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHH
Q 011992          287 RLEKEKSKLQSQFG-REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSM  364 (473)
Q Consensus       287 kle~a~~~L~~~lG-RePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~l  364 (473)
                      +|-.+-.++..+.| ...|..+||+..|++...+.......+..+..++..+...+............+..+.+...+.
T Consensus        11 ~Il~aa~~l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~   89 (199)
T 3qbm_A           11 RVVAQAAALFNVSGYAGTAISDIMAATGLEKGGIYRHFESKEQLALAAFDYAAEKVRERFAVGLAGHKHTVDTIIAFLD   89 (199)
T ss_dssp             HHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHTTCSSHHHHHHHHHHHHHHHHHHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcCcCCHHHHHHHhCCCccHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHccCccHHHHHHHHHH
Confidence            56666667777788 5589999999999999999988877667777777777666665555544444455555544433

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=81.69  E-value=2.6  Score=35.72  Aligned_cols=44  Identities=18%  Similarity=0.198  Sum_probs=35.5

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      .|++.+..||...+.   ..+.|..|||+.+|++.++|+.++.+-.+
T Consensus        37 ~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~Le~   80 (148)
T 3nrv_A           37 GIGMTEWRIISVLSS---ASDCSVQKISDILGLDKAAVSRTVKKLEE   80 (148)
T ss_dssp             TCCHHHHHHHHHHHH---SSSBCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc---CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            589998888876554   25899999999999999999987665443

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=81.60  E-value=1.8  Score=31.90  Aligned_cols=25  Identities=12%  Similarity=0.272  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|..++|+.+|||.++|+.+++.
T Consensus        15 ~glsq~~lA~~~gis~~~i~~~e~g   39 (71)
T 1zug_A           15 LKMTQTELATKAGVKQQSIQLIEAG   39 (71)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            6899999999999999999998864

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=81.48  E-value=1.9  Score=31.64  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|..++|+.+|||.++|+++++.
T Consensus        13 ~glsq~~lA~~~gis~~~i~~~e~g   37 (69)
T 1r69_A           13 LGLNQAELAQKVGTTQQSIEQLENG   37 (69)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            6899999999999999999998764

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=81.34  E-value=3.5  Score=34.53  Aligned_cols=50  Identities=10%  Similarity=0.078  Sum_probs=36.4

Q ss_pred             HHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          401 HVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       401 ~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .+...+.  .|++.+..||...+.  .+.+.|..|||+.+|++.++|+.++.+-
T Consensus        25 ~~~~~~~~~~l~~~~~~iL~~l~~--~~~~~t~~~la~~l~~s~~~vs~~l~~L   76 (146)
T 2fbh_A           25 ELDRRLSHLGLSQARWLVLLHLAR--HRDSPTQRELAQSVGVEGPTLARLLDGL   76 (146)
T ss_dssp             HHHHHTGGGCCTTTHHHHHHHHHH--CSSCCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHH--cCCCCCHHHHHHHhCCChhhHHHHHHHH
Confidence            3444443  488888888766522  2368999999999999999998865543

>3ppb_A Putative TETR family transcription regulator; DNA-binding, helix-turn-helix motif, HTH motif, DNA/RNA-BIND helical bundle fold; HET: MSE PG4; 2.10A {Shewanella loihica}

Probab=81.27  E-value=13  Score=31.57  Aligned_cols=82  Identities=11%  Similarity=0.036  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHHhC-CCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHH
Q 011992          287 RLEKEKSKLQSQFG-REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMG  365 (473)
Q Consensus       287 kle~a~~~L~~~lG-RePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lg  365 (473)
                      +|-.+-.++..+.| ...|..+||+.+|++...+......-+..+..++..+...+............+..+.+...+..
T Consensus        13 ~Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~sK~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~   92 (195)
T 3ppb_A           13 AILETALQLFVSQGFHGTSTATIAREAGVATGTLFHHFPSKEQLLEQLFLGVKQEFADAIQASVSSRGDLKQDAEQLWFA   92 (195)
T ss_dssp             HHHHHHHHHHHHTCSTTSCHHHHHHHHTCCHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHTCCCCSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCcccCCHHHHHHHhCCChhHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhcccCHHHHHHHHHHH
Confidence            45566667777788 67899999999999999999988877777777777777666666555555555666555554444


Q ss_pred             HHH
Q 011992          366 LMK  368 (473)
Q Consensus       366 L~k  368 (473)
                      ++.
T Consensus        93 ~~~   95 (195)
T 3ppb_A           93 ALT   95 (195)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=81.10  E-value=1.8  Score=31.45  Aligned_cols=25  Identities=24%  Similarity=0.405  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|..++|+.+|+|.++|+.+++.
T Consensus        13 ~g~s~~~lA~~~gis~~~i~~~e~g   37 (66)
T 2xi8_A           13 KKISQSELAALLEVSRQTINGIEKN   37 (66)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            6899999999999999999999874

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=81.07  E-value=11  Score=28.75  Aligned_cols=56  Identities=16%  Similarity=0.173  Sum_probs=35.6

Q ss_pred             HHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHh
Q 011992          292 KSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLL  359 (473)
Q Consensus       292 ~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLi  359 (473)
                      ...+....|  -|..|+|+.+|++...+.++..+....       ....+..+|.-+   +++.+|+.
T Consensus        17 l~~~r~~~g--ltq~~lA~~~gvs~~~is~~e~g~~~~-------~~~~~~~ia~~l---~v~~~~l~   72 (80)
T 3kz3_A           17 WEKKKNELG--LSYESVADKMGMGQSAVAALFNGINAL-------NAYNAALLAKIL---KVSVEEFS   72 (80)
T ss_dssp             HHHHHHHHT--CCHHHHHHHTTSCHHHHHHHHTTSSCC-------CHHHHHHHHHHH---TSCGGGTC
T ss_pred             HHHHHHHcC--CCHHHHHHHhCcCHHHHHHHHcCCCCC-------CHHHHHHHHHHh---CCCHHHHh
Confidence            333444455  488999999999999999888775421       123455566555   34444443

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=80.99  E-value=1.9  Score=33.36  Aligned_cols=25  Identities=32%  Similarity=0.397  Sum_probs=23.6

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|.+|+|+.+|||.++|+++++.
T Consensus        22 ~gltq~elA~~~gis~~~is~~E~G   46 (78)
T 3qq6_A           22 KGYSLSELAEKAGVAKSYLSSIERN   46 (78)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            7899999999999999999999875

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=80.94  E-value=0.99  Score=41.27  Aligned_cols=44  Identities=9%  Similarity=0.098  Sum_probs=31.5

Q ss_pred             hCCHHHHHHHHHHhhccCCCCC--CHHHHHHHHCCC-HHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPK--SLSEVGNIFGLS-KERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~l--TlkEIAe~LGIS-~~rVrqi~~R  451 (473)
                      .|+++++.++.....+-...++  |.+|+|+.+|++ .++|++++.+
T Consensus         3 ~lt~~q~~i~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~~   49 (202)
T 1jhf_A            3 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   49 (202)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHHH
Confidence            5888888776432211111356  999999999999 9999998763

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=80.92  E-value=1.9  Score=33.68  Aligned_cols=25  Identities=16%  Similarity=0.288  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|..|+|+.+|||.++|+++++.
T Consensus        30 ~glsq~elA~~~gis~~~is~~e~g   54 (83)
T 2a6c_A           30 SGLTQFKAAELLGVTQPRVSDLMRG   54 (83)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            6899999999999999999999864

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=80.87  E-value=3.7  Score=31.98  Aligned_cols=25  Identities=8%  Similarity=0.088  Sum_probs=21.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .+.|..|||+.+|+|+.+|+..+..
T Consensus        13 ~~~s~~eLa~~lgvs~~tv~r~L~~   37 (81)
T 2htj_A           13 NGGKTAEIAEALAVTDYQARYYLLL   37 (81)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4699999999999999999875543

>3dcf_A Transcriptional regulator of the TETR/ACRR family; YP_290855.1, structural genomics, joint center for structural genomics, JCSG; 2.50A {Thermobifida fusca YX}

Probab=80.85  E-value=14  Score=32.08  Aligned_cols=84  Identities=12%  Similarity=0.074  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHHHhC-CCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHH
Q 011992          287 RLEKEKSKLQSQFG-REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMG  365 (473)
Q Consensus       287 kle~a~~~L~~~lG-RePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lg  365 (473)
                      +|-.+-.+|..+.| ...|..+||+..|++...+.......+..+..++......+............+..+-+...+..
T Consensus        35 ~Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~sK~~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  114 (218)
T 3dcf_A           35 QIIKVATELFREKGYYATSLDDIADRIGFTKPAIYYYFKSKEDVLFAIVNSIVDEALERFHAIAAGPGSPGERIHALLVE  114 (218)
T ss_dssp             HHHHHHHHHHHHTCTTTCCHHHHHHHHTCCHHHHHHHCSSHHHHHHHHHHHHHHHHHHHHHHHHTSSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCcccCcHHHHHHHhCCCHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHccCCCHHHHHHHHHHH
Confidence            56666777777888 45899999999999999999988877777777777766666555555444455555555444444


Q ss_pred             HHHHh
Q 011992          366 LMKSV  370 (473)
Q Consensus       366 L~kAi  370 (473)
                      ++..+
T Consensus       115 ~~~~~  119 (218)
T 3dcf_A          115 HTRTI  119 (218)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            44433

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=80.82  E-value=3.5  Score=35.13  Aligned_cols=42  Identities=10%  Similarity=0.165  Sum_probs=34.4

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .|++.+..||.....    .+.|..|||+.+|++.++|+.++.+-.
T Consensus        35 ~lt~~q~~iL~~l~~----~~~t~~eLa~~l~~~~~~vs~~l~~Le   76 (151)
T 3kp7_A           35 GISAEQSHVLNMLSI----EALTVGQITEKQGVNKAAVSRRVKKLL   76 (151)
T ss_dssp             TCCHHHHHHHHHHHH----SCBCHHHHHHHHCSCSSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc----CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            589998888765533    789999999999999999998665543

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=80.81  E-value=2.6  Score=38.86  Aligned_cols=39  Identities=21%  Similarity=0.347  Sum_probs=31.8

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +++.++.|+.+-..    .+.|..|||+.+|+|.++|+.++.+
T Consensus        18 ~d~~~~~IL~~L~~----~~~s~~eLA~~lglS~stv~~~l~~   56 (192)
T 1uly_A           18 LEDTRRKILKLLRN----KEMTISQLSEILGKTPQTIYHHIEK   56 (192)
T ss_dssp             HSHHHHHHHHHHTT----CCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            57788888766543    5799999999999999999986654

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=80.76  E-value=4.2  Score=35.22  Aligned_cols=50  Identities=4%  Similarity=-0.037  Sum_probs=37.8

Q ss_pred             HHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          400 QHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       400 e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ..+...+.  .|++.+-.||...+.   ..+.|..|||+.+|++.++|..++.+-
T Consensus        33 ~~~~~~l~~~glt~~q~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   84 (162)
T 3k0l_A           33 KYLTEHLSALEISLPQFTALSVLAA---KPNLSNAKLAERSFIKPQSANKILQDL   84 (162)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCGGGHHHHHHHH
T ss_pred             HHHHHHhhhcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            33444443  599999888876553   258999999999999999999866553

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=80.74  E-value=3.6  Score=34.72  Aligned_cols=39  Identities=10%  Similarity=0.151  Sum_probs=28.7

Q ss_pred             CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          410 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       410 perER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ++....||.+-..   ..+.+..|||+.+|+|.++|++++..
T Consensus        41 ~~~rl~IL~~L~~---~~~~s~~eLa~~l~is~stvs~~L~~   79 (122)
T 1u2w_A           41 DENRAKITYALCQ---DEELCVCDIANILGVTIANASHHLRT   79 (122)
T ss_dssp             SHHHHHHHHHHHH---SSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH---CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4445556654431   15799999999999999999987654

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=80.69  E-value=4.7  Score=33.98  Aligned_cols=42  Identities=14%  Similarity=0.122  Sum_probs=33.8

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      .|++.+-.||..-+.   ..+.|..|||+.+|++.++|+.++.+-
T Consensus        28 ~lt~~q~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   69 (145)
T 3g3z_A           28 DLNYNLFAVLYTLAT---EGSRTQKHIGEKWSLPKQTVSGVCKTL   69 (145)
T ss_dssp             TCCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            589999888876543   157999999999999999999866553

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=80.64  E-value=2.8  Score=36.14  Aligned_cols=52  Identities=2%  Similarity=0.012  Sum_probs=38.6

Q ss_pred             HHHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          399 RQHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       399 ~e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      ...+...+.  .|++.+..||...+.   ..+.|..|||+.+|++.++|+.++.+-.
T Consensus        36 ~~~~~~~l~~~~lt~~q~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~Le   89 (159)
T 3s2w_A           36 QIYIGKKIEPYGIGSGQFPFLMRLYR---EDGINQESLSDYLKIDKGTTARAIQKLV   89 (159)
T ss_dssp             HHHHHHHHGGGTCCTTTHHHHHHHHH---SCSEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            334444453  488888888876554   2679999999999999999998766543

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=80.40  E-value=2.5  Score=35.51  Aligned_cols=43  Identities=23%  Similarity=0.289  Sum_probs=34.4

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .|++.+..||...+.   +.+.+..|||+.+|++.++|+.++.+-.
T Consensus        30 ~l~~~~~~iL~~l~~---~~~~~~~~la~~l~~s~~tvs~~l~~L~   72 (145)
T 2a61_A           30 GITPAQFDILQKIYF---EGPKRPGELSVLLGVAKSTVTGLVKRLE   72 (145)
T ss_dssp             TCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCchhHHHHHHHHH
Confidence            589998888876553   2579999999999999999988665533

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=80.33  E-value=2.2  Score=31.76  Aligned_cols=25  Identities=24%  Similarity=0.231  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|..++|+.+|||.++|+.+++.
T Consensus        25 ~g~s~~~lA~~~gis~~~i~~~e~g   49 (74)
T 1y7y_A           25 KGLSQETLAFLSGLDRSYVGGVERG   49 (74)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence            6899999999999999999999864

---

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	473
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	4e-20
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	1e-18
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	7e-18
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	2e-16
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	9e-16
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	3e-13
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	2e-09
d1or7a1	68	a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escheri	1e-04

>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 = 82.5 bits (204), Expect = 4e-20
 Identities = 30/80 (37%), Positives = 51/80 (63%)

Query: 393 VQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA 452
             + LMR+ +  +L  L+P+E  ++R+R+G+ DGKPK+L EVG  F +++ER+RQ+E +A
Sbjct: 3   AMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKA 62

Query: 453 LYRLKQSLGGKASYGYADLL 472
           L +L+     K       L+
Sbjct: 63  LRKLRHPSRSKYLKSLLSLM 82

>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 = 85.0 bits (209), Expect = 1e-18
 Identities = 38/175 (21%), Positives = 72/175 (41%)

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 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
            ++++++ ANLRLV+ +AK+Y  RG+   DL+QEG++GLMK+V+KF+ + G +F+
Sbjct: 262 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 316

>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 = 79.1 bits (194), Expect = 7e-18
 Identities = 46/158 (29%), Positives = 77/158 (48%), Gaps = 30/158 (18%)

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 AKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFA 382
           AK+Y GRG+S  DL+QEG+ GL+++VEKF+ +   +F+
Sbjct: 122 AKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 159

>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 = 2e-16
 Identities = 22/67 (32%), Positives = 41/67 (61%)

Query: 404 NLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGK 463
           ++L  L  +E  ++R+RFGI+     +L EVG  F +++ER+RQ+E++AL +L+     +
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 464 ASYGYAD 470
               + 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 = 69.3 bits (170), Expect = 9e-16
 Identities = 22/57 (38%), Positives = 41/57 (71%)

Query: 402 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQ 458
           +   L+ L+ +E  ++++R G+ DG+  +L EVG  FG+++ER+RQ+E++AL +LK 
Sbjct: 2   LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 58

>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 = 63.0 bits (153), Expect = 3e-13
 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 324 HSGNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCR 380
           +S    RE+LI   L LV  +A   +      + + DL+  G +GL+K+V+    +   R
Sbjct: 6   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKR 65

Query: 381 FA 382
             
Sbjct: 66  AE 67

>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 = 51.4 bits (123), Expect = 2e-09
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQL 448
            +  V K+ + + V+  ++ L  +E+ +++L F     +     EV  I   S  RV QL
Sbjct: 2   VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY----EELPAKEVAKILETSVSRVSQL 57

Query: 449 ESRALYRLKQSL 460
           +++AL RL++ L
Sbjct: 58  KAKALERLREML 69

>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 = 1e-04
 Identities = 14/63 (22%), Positives = 22/63 (34%), Gaps = 4/63 (6%)

Query: 398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK 457
           +RQ V   +  L    R  + LR  ++     S  E+  I       VR    RA   + 
Sbjct: 8   LRQIVFRTIESLPEDLRMAITLRE-LDG---LSYEEIAAIMDCPVGTVRSRIFRAREAID 63

Query: 458 QSL 460
             +
Sbjct: 64  NKV 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	473
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.8
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.53
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.49
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.43
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.42
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.28
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.09
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.93
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.85
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.82
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	98.34
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.29
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.26
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.21
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	98.11
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.95
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.9
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	97.75
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.57
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	97.54
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	95.84
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.61
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	93.94
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	92.11
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	92.06
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.88
d1hlva1	66	DNA-binding domain of centromere binding protein B	91.54
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	90.75
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	90.49
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	89.85
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	89.33
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	88.88
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	88.17
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	87.51
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	87.49
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	87.16
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	86.7
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	86.64
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	86.4
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	86.21
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	86.02
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	85.48
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	85.13
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	85.02
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	84.87
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	84.76
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	84.62
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	84.55
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	84.36
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	84.27
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	83.67
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	83.23
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	83.13
d1y7ya1	69	Restriction-modification controller protein C.AhdI	83.07
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	82.92
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	82.83
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	82.46
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	82.3
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	82.18
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	81.96
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	81.72
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	81.71
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	81.7
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	81.57
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	81.06
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	80.9
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	80.37
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	80.13

>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=99.80  E-value=5.4e-21  Score=175.43  Aligned_cols=135  Identities=33%  Similarity=0.507  Sum_probs=105.3

Q ss_pred             ChhHHhhhcccCccCCCChHHHHHHHHHHHHHHHHHHHHHHHH------------------HHhCCCCC---------HH
Q 011992          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ------------------SQFGREPT---------LI  306 (473)
Q Consensus       254 ~~~lR~~~~~pr~~~lLT~eEE~~L~~~iq~l~kle~a~~~L~------------------~~lGRePT---------~e  306 (473)
                      .||+|.|++.++++|+||+|||++|+++|+....+.....+..                  ...++.|.         ..
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            3699999999999999999999999999988665433322211                  01222222         23


Q ss_pred             HHHHHcCCC---HHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCcccc
Q 011992          307 EWAKAIGLS---CRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCRFAN  383 (473)
Q Consensus       307 EiA~~lGms---~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT  383 (473)
                      ++.......   ...+......|..|+++||..|+++|+++|++|.+.+.+++||+|+|++||++|+++|||++|++|+|
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            333333332   34456677778899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 011992          384 TGVEI  388 (473)
Q Consensus       384 ~~~~~  388 (473)
                      +..++
T Consensus       161 ya~~~  165 (180)
T d1ku2a2         161 YATWW  165 (180)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76544

>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=99.53  E-value=2.4e-15  Score=123.31  Aligned_cols=75  Identities=39%  Similarity=0.737  Sum_probs=70.6

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhhhh
Q 011992          398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYADLL  472 (473)
Q Consensus       398 l~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yldll  472 (473)
                      +++.|..+|+.|+++|+.||.+||||++++++|+.|||+.||||.++|+||+.+|++|||.......++.||+++
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            456789999999999999999999999999999999999999999999999999999999988888899999875

>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=99.49  E-value=3.8e-15  Score=116.71  Aligned_cols=66  Identities=33%  Similarity=0.614  Sum_probs=62.4

Q ss_pred             HHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCchhhhhh
Q 011992          405 LLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKASYGYAD  470 (473)
Q Consensus       405 aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~l~~yld  470 (473)
                      +|+.|+++|+.||.+||||++++++|++|||+.||||.++|+||+.+|++|||.......+..||+
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            467899999999999999999999999999999999999999999999999999888888888886

>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=99.43  E-value=4.5e-14  Score=108.28  Aligned_cols=58  Identities=38%  Similarity=0.726  Sum_probs=54.5

Q ss_pred             HHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          402 VRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       402 L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      |.++|+.|+++|+.||.+||||++++++|++|||+.||||.++|+|++.+|++|||..
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            3457889999999999999999999999999999999999999999999999999964

>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=99.42  E-value=3e-13  Score=105.10  Aligned_cols=69  Identities=29%  Similarity=0.418  Sum_probs=65.9

Q ss_pred             chHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          389 PDISVQKQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       389 pee~le~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      +++.+...+....|..+|+.||+++|.||.++|+    +++|++|||+.||+|+++|++++++|+++||+.|.
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            5777888899999999999999999999999999    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=99.28  E-value=7.3e-12  Score=96.85  Aligned_cols=63  Identities=22%  Similarity=0.153  Sum_probs=59.8

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Q 011992          395 KQLMRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLG  461 (473)
Q Consensus       395 ~~el~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~  461 (473)
                      .++....|.++|+.||+++|.||.++|+    +++|++|||+.||+|.++|+++++||+++||..++
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            4567889999999999999999999999    99999999999999999999999999999999875

>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=99.09  E-value=2.2e-11  Score=119.56  Aligned_cols=81  Identities=35%  Similarity=0.635  Sum_probs=67.5

Q ss_pred             HHHHcCCCHHHHHHH-------HhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCccCCCc
Q 011992          308 WAKAIGLSCRDLKSE-------LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQAGCR  380 (473)
Q Consensus       308 iA~~lGms~eeL~~~-------l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~kg~~  380 (473)
                      +....|++..++...       ......|+.+|+..|+++|++||++|.+++++++||+|+|++||++|+++||+.+|++
T Consensus       235 ie~~~gl~~~elk~i~~~i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~  314 (334)
T d1siga_         235 IEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK  314 (334)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCC
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCc
Confidence            344556665444333       3333479999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCC
Q 011992          381 FANTGVEI  388 (473)
Q Consensus       381 FsT~~~~~  388 (473)
                      |+|+..++
T Consensus       315 f~~~~~~~  322 (334)
T d1siga_         315 FSTYATWW  322 (334)
T ss_dssp             HHHHHHHH
T ss_pred             hHhhhHHH
Confidence            99976655

>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=98.93  E-value=1e-09  Score=89.10  Aligned_cols=58  Identities=28%  Similarity=0.398  Sum_probs=52.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcC---CcchhhHhhhhHHHHHHHhhhhCccCCCccccCC
Q 011992          328 SSREKLINANLRLVVHVAKQYQGR---GISLHDLLQEGSMGLMKSVEKFKPQAGCRFANTG  385 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~---~~saEDLiQEg~lgL~kAiekFDp~kg~~FsT~~  385 (473)
                      ..+++||..|+++|.++|.++.++   +++.|||+|+|++||++|+++|||++|.+|+|+.
T Consensus        10 ~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA   70 (87)
T d1rp3a3          10 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYI   70 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHH
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHH
Confidence            347899999999999999998654   7899999999999999999999999999998753

>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=98.85  E-value=4.4e-09  Score=88.45  Aligned_cols=60  Identities=22%  Similarity=0.217  Sum_probs=51.8

Q ss_pred             HHHHHH-hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCc
Q 011992          401 HVRNLL-TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGGKA  464 (473)
Q Consensus       401 ~L~~aL-~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~~~  464 (473)
                      .|.+.. .-||+++|.||.|||+    +++|+.|||+.||||+++|+++++||+++||+...+-.
T Consensus        10 ~L~d~y~~LLpe~QR~vl~L~~~----e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~ye~kL~   70 (106)
T d1xsva_          10 YLFDFYQSLLTNKQRNYLELFYL----EDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLE   70 (106)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHT----SCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHH----hCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence            344443 3499999999999999    99999999999999999999999999999998654433

>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=98.82  E-value=5.1e-09  Score=88.03  Aligned_cols=52  Identities=25%  Similarity=0.286  Sum_probs=48.5

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLKQSLGG  462 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~L~~  462 (473)
                      .-||+++|.||.|+|+    +++|++|||+.||||+++|+++++||+++||+...+
T Consensus        15 ~lLp~~qR~v~~L~y~----~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~e~k   66 (106)
T d1s7oa_          15 ALLTDKQMNYIELYYA----DDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMK   66 (106)
T ss_dssp             GGSCHHHHHHHHHHHH----TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            4499999999999999    999999999999999999999999999999986544

>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=1e-06  Score=67.98  Aligned_cols=55  Identities=13%  Similarity=0.311  Sum_probs=49.5

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          398 MRQHVRNLLTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       398 l~e~L~~aL~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      ..+.+.+.+..|+++|++|+.+.-     +|++.+|||+.||||..||+....+++.||.
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            356677888899999999999876     6999999999999999999999999998874

>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=98.26  E-value=7.5e-07  Score=69.76  Aligned_cols=44  Identities=34%  Similarity=0.460  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992          282 IQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS  325 (473)
Q Consensus       282 iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~  325 (473)
                      +++.++|+++...|++++||+||.+|||++|||+.++|.+++..
T Consensus         6 r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~   49 (77)
T d1rp3a1           6 REKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDK   49 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            46678999999999999999999999999999999999887653

>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=98.21  E-value=5.3e-07  Score=67.18  Aligned_cols=44  Identities=27%  Similarity=0.345  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhh
Q 011992          282 IQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS  325 (473)
Q Consensus       282 iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~  325 (473)
                      .....++.++..+|.+++||+||.+|||+++|++.+++..++..
T Consensus        11 ~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_          11 KEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45577999999999999999999999999999999999887754

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=98.11  E-value=2.7e-06  Score=64.93  Aligned_cols=47  Identities=19%  Similarity=0.301  Sum_probs=43.9

Q ss_pred             HhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          406 LTLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       406 L~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      +..|+++|++|+.+.-     +|+|.+|||+.||||+.+|++...+++.||.
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     6999999999999999999999999999885

>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=97.95  E-value=8.4e-06  Score=61.72  Aligned_cols=45  Identities=27%  Similarity=0.383  Sum_probs=42.0

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .|+++|++|+.+.-     +|+|.+|||+.||+|..+|+....++++||.
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            59999999998776     7999999999999999999999999999985

>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=97.90  E-value=1.1e-05  Score=61.31  Aligned_cols=45  Identities=29%  Similarity=0.378  Sum_probs=41.6

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .|+++|++|+.+.-     +|+|.+|||+.||+|..||+....++++||-
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            49999999998866     7999999999999999999999999998874

>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=97.75  E-value=2.1e-05  Score=59.03  Aligned_cols=45  Identities=27%  Similarity=0.530  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCC--CHHHHHHHHhhc
Q 011992          282 IQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL--SCRDLKSELHSG  326 (473)
Q Consensus       282 iq~l~kle~a~~~L~~~lGRePT~eEiA~~lGm--s~eeL~~~l~~g  326 (473)
                      +..+.++.++..+|.+++||+||.+|||+++|+  +.+.+...+...
T Consensus         8 ~e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~   54 (60)
T d1ku2a1           8 VETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA   54 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGS
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHc
Confidence            456778899999999999999999999999985  567787776543

>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=97.57  E-value=5.2e-05  Score=60.54  Aligned_cols=45  Identities=22%  Similarity=0.297  Sum_probs=42.3

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALYRLK  457 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR  457 (473)
                      .|+++|++|+.+..     .|++.+|||+.||+|..+|+....++++||.
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            59999999999888     5999999999999999999999999999974

>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=97.54  E-value=4.3e-05  Score=58.58  Aligned_cols=49  Identities=18%  Similarity=0.114  Sum_probs=46.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhhhhHHHHHHHhhhhCcc
Q 011992          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQEGSMGLMKSVEKFKPQ  376 (473)
Q Consensus       328 ~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQEg~lgL~kAiekFDp~  376 (473)
                      ..|++++..|.+.++++|.++.++..+++|++||+++.+|+.++.|++.
T Consensus         7 ~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~   55 (75)
T d1h3la_           7 ARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG   55 (75)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC
Confidence            5799999999999999999999999999999999999999999999753

>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=95.84  E-value=0.0049  Score=46.91  Aligned_cols=44  Identities=16%  Similarity=0.274  Sum_probs=36.6

Q ss_pred             hCCHHHHHHHHH--HhhccCCCCCCHHHHHHHHCC-CHHHHHHHHHH
Q 011992          408 LLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFGL-SKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~L--rY~L~~ge~lTlkEIAe~LGI-S~~rVrqi~~R  451 (473)
                      .|+++|++|+..  .|....|..+|++|||+.+|+ |.++|..++..
T Consensus         2 ~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~   48 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   48 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            599999999864  455566799999999999999 89999987543

>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=95.61  E-value=0.00027  Score=56.33  Aligned_cols=31  Identities=19%  Similarity=0.247  Sum_probs=28.4

Q ss_pred             ccCCCCCCcccccccccccccccccccCCCChhHHhhhc
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLW  262 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D~~~~lR~~~~  262 (473)
                      |.++.+|.+|+|||.+||+     |+|+|   .+|+.||
T Consensus        57 ~yd~~~g~~F~tYA~~~Ir-----gai~d---~lRk~dw   87 (87)
T d1rp3a3          57 NLSTENPKRAEAYIKLRIK-----GAIYD---YLRSLDF   87 (87)
T ss_dssp             TCCCCCTHHHHHHHHHHHH-----HHHHH---HHHTSST
T ss_pred             hhCCCCCCCHHHHHHHHHH-----HHHHH---HHHhCCC
Confidence            5578999999999999999     99999   5999988

>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=93.94  E-value=0.042  Score=38.53  Aligned_cols=38  Identities=16%  Similarity=0.211  Sum_probs=30.9

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLE  449 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~  449 (473)
                      .|++.+.+-+.-.+-    .|.+..+||+.+|||+.||...+
T Consensus         5 ~lt~~q~~~a~~l~~----~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           5 AINKHEQEQISRLLE----KGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             SSCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             cCCHHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHhhC
Confidence            477777776666665    78999999999999999998753

>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=92.11  E-value=0.16  Score=37.15  Aligned_cols=41  Identities=20%  Similarity=0.146  Sum_probs=32.7

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.++.||...-.   +-..++.|||+.+|+|+++|.+++.+
T Consensus         2 klD~~D~~IL~~L~~---n~r~s~~~iA~~lgis~~tv~~Ri~~   42 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVRQ   42 (63)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            367788888876543   25789999999999999999986654

>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=92.06  E-value=0.21  Score=36.38  Aligned_cols=40  Identities=20%  Similarity=0.385  Sum_probs=32.9

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++.++.||..--.   +-..|+.|||+.+|+|..+|+.++.+
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            67788888876554   25789999999999999999987654

>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=91.88  E-value=0.18  Score=36.51  Aligned_cols=40  Identities=15%  Similarity=0.344  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++.++.||.+--.   +...|+.|||+.+|+|+++|.+++.+
T Consensus         1 lD~~D~kIl~~L~~---n~r~s~~~lA~~~gls~~~v~~Ri~~   40 (60)
T d1i1ga1           1 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRKRVKA   40 (60)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45667888775544   25779999999999999999986654

>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=91.54  E-value=0.18  Score=37.59  Aligned_cols=45  Identities=9%  Similarity=0.111  Sum_probs=33.9

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRALY  454 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL~  454 (473)
                      .|+-.++.=+..+|.  .|+.++..|||..+||+.++|+.|+.+--+
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            366677665555554  345578999999999999999999987433

>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=90.75  E-value=0.13  Score=35.37  Aligned_cols=32  Identities=6%  Similarity=0.207  Sum_probs=27.3

Q ss_pred             HHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          415 CIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       415 ~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      +|..|+-     +++.-.+||+.|||++.+|..++..
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     8999999999999999999988764

>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=90.49  E-value=0.39  Score=34.41  Aligned_cols=40  Identities=18%  Similarity=0.353  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++.++.||..--.   +-..++.|||+.+|+|+.+|...+.+
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            45667777765443   25679999999999999999986654

>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=89.85  E-value=0.18  Score=39.11  Aligned_cols=36  Identities=19%  Similarity=0.244  Sum_probs=29.2

Q ss_pred             HHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          414 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       414 R~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      ++++.++..   ++|.|..+||+.|||+.++|++++.+.
T Consensus        12 ~~aV~l~~~---~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          12 RDAVALYEN---SDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHHTT---GGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHH---cCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            456666653   147999999999999999999998765

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=89.33  E-value=0.19  Score=39.41  Aligned_cols=43  Identities=28%  Similarity=0.277  Sum_probs=34.9

Q ss_pred             hCCHHHHHHHHH--HhhccCCCCCCHHHHHHHHC--CCHHHHHHHHH
Q 011992          408 LLNPKERCIVRL--RFGIEDGKPKSLSEVGNIFG--LSKERVRQLES  450 (473)
Q Consensus       408 ~LperER~VL~L--rY~L~~ge~lTlkEIAe~LG--IS~~rVrqi~~  450 (473)
                      .|++|+++||..  .+++..|.+.+.++|++.+|  +|..+|+..+.
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            488999999864  33456789999999999966  58999999664

>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=88.88  E-value=0.33  Score=39.97  Aligned_cols=41  Identities=12%  Similarity=0.000  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       409 LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      |+...|.-|.-.|.    +|++..+||+.||||.++|..++.+=.
T Consensus        17 Ls~dlR~rIv~~~~----~G~s~r~iA~~~~VS~~tV~k~l~r~~   57 (123)
T d1pdnc_          17 LPNNIRLKIVEMAA----DGIRPCVISRQLRVSHGCVSKILNRYQ   57 (123)
T ss_dssp             CCHHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH----hcCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            55555554443455    799999999999999999999887643

>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=88.17  E-value=0.46  Score=33.92  Aligned_cols=32  Identities=19%  Similarity=0.349  Sum_probs=26.6

Q ss_pred             HHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          417 VRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       417 L~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      |...++    ..+|..|||+.||+|.+.|...+..+
T Consensus        24 l~q~lg----RePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_          24 LSKTRG----RAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHT----SCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHcC----CCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            345566    99999999999999999998876543

>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=87.51  E-value=0.75  Score=37.73  Aligned_cols=42  Identities=19%  Similarity=0.223  Sum_probs=34.8

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|+..+-.|+.+-|. . ++++|..|||+.+|+|+++|+..+.+
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            589999999987774 2 35689999999999999999985544

>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=87.49  E-value=0.31  Score=35.21  Aligned_cols=25  Identities=12%  Similarity=0.135  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|+|.+|+|+.+|||.++|+.+++.
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            6799999999999999999999874

>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=87.16  E-value=0.44  Score=34.94  Aligned_cols=43  Identities=21%  Similarity=0.244  Sum_probs=29.1

Q ss_pred             CCHHHHHHHHHHhhc-cCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGI-EDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       409 LperER~VL~LrY~L-~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++....-|...|.| ..+...+..+||+.|||+..+|...+++
T Consensus         3 ls~s~EdYL~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mvkr   46 (63)
T d2isya1           3 LVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSR   46 (63)
T ss_dssp             TSSHHHHHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCchhHHHHHHH
Confidence            444444444444433 2346789999999999999999985443

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.70  E-value=0.39  Score=36.02  Aligned_cols=43  Identities=12%  Similarity=0.108  Sum_probs=37.6

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHH-CCCHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIF-GLSKERVRQLE  449 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~L-GIS~~rVrqi~  449 (473)
                      +.|++.+++|+.+...-.+.+|.+..||+..| |++...|++..
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            46999999999988876667999999999999 89999998754

>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=86.64  E-value=0.61  Score=34.83  Aligned_cols=32  Identities=19%  Similarity=0.355  Sum_probs=27.0

Q ss_pred             HHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          417 VRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       417 L~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      |.-.+|    +.+|..|||+.|||+.+.|.+++..+
T Consensus        19 L~~~lG----R~Pt~~EiA~~lg~s~~e~~~~l~~~   50 (77)
T d1rp3a1          19 LKEKLG----REPTDEEVAKELGISTEELFKTLDKI   50 (77)
T ss_dssp             HHHHHS----SCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHC----cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344565    99999999999999999999987653

>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=86.40  E-value=0.72  Score=36.25  Aligned_cols=47  Identities=15%  Similarity=0.271  Sum_probs=33.1

Q ss_pred             HHHHHHHhhCCHHHHH-HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          400 QHVRNLLTLLNPKERC-IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       400 e~L~~aL~~LperER~-VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      +.+.+.+..|...-|. |+.+-.   + .+++..|||+.+|+|.++|+++++
T Consensus        11 ~~la~~~kaL~~p~Rl~Il~~L~---~-~~~~v~ela~~l~is~stvS~HL~   58 (98)
T d1r1ta_          11 QSLAEFFAVLADPNRLRLLSLLA---R-SELCVGDLAQAIGVSESAVSHQLR   58 (98)
T ss_dssp             HHHHHHHHHHCCHHHHHHHHHHT---T-CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHH---c-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence            4555666666555554 443332   2 579999999999999999999654

>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=86.21  E-value=0.98  Score=35.26  Aligned_cols=48  Identities=19%  Similarity=0.232  Sum_probs=35.7

Q ss_pred             HHHHHHHHhhCCHHHHH-HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          399 RQHVRNLLTLLNPKERC-IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       399 ~e~L~~aL~~LperER~-VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      .+.+.+.+..|...-|. |+.+-..    .+++..||++.+|+|.++|++.++
T Consensus         5 ~e~~a~~fkaL~d~~Rl~Il~~L~~----~~~~v~el~~~l~~s~~~vS~HL~   53 (94)
T d1r1ua_           5 LERVTEIFKALGDYNRIRIMELLSV----SEASVGHISHQLNLSQSNVSHQLK   53 (94)
T ss_dssp             HHHHHHHHHHTCSHHHHHHHHHHHH----CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHc----CCccHHHHHHHHCCCHHHHHHHHH
Confidence            35567777788776665 4433333    579999999999999999999654

>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=86.02  E-value=1.5  Score=35.33  Aligned_cols=50  Identities=10%  Similarity=0.061  Sum_probs=37.2

Q ss_pred             HHHHHHHh--hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          400 QHVRNLLT--LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       400 e~L~~aL~--~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      ..+.+.+.  .|+..+-.||..-+. .+|++.|..|||+.+|++.++|+.++.
T Consensus        16 ~~~~~~l~~~glt~~q~~vL~~l~~-~~~~~it~~ela~~~~~~~~~vs~~l~   67 (135)
T d3broa1          16 TRFDIFAKKYDLTGTQMTIIDYLSR-NKNKEVLQRDLESEFSIKSSTATVLLQ   67 (135)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHH-TTTSCCBHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH-cCCCCCCHHHHHHHHCcCHhHHHHHHH
Confidence            33444443  489999888876664 344679999999999999999986443

>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=85.48  E-value=0.47  Score=34.72  Aligned_cols=31  Identities=13%  Similarity=0.188  Sum_probs=26.7

Q ss_pred             HHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          416 IVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       416 VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      |-.++..    .++|.+|+|+.+||++++|+.+++
T Consensus        11 i~~~r~~----~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          11 LQEHLRN----SGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHT----TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHH----cCCCHHHHHHHHHcCHhHHHHHHc
Confidence            3345555    899999999999999999999986

>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=85.13  E-value=0.51  Score=34.29  Aligned_cols=37  Identities=16%  Similarity=0.284  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          411 PKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       411 erER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      +....||.+-   .++...|.+|+|+.||||+.+|+..+.
T Consensus         5 ~~~~~iL~~L---~~~~~~s~~eLa~~l~vS~~ti~r~i~   41 (63)
T d1biaa1           5 TVPLKLIALL---ANGEFHSGEQLGETLGMSRAAINKHIQ   41 (63)
T ss_dssp             HHHHHHHHHH---TTSSCBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHH---HHCCcCCHHHHHHHHCcCHHHHHHHHH
Confidence            3444454432   345789999999999999999998654

>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=85.02  E-value=0.45  Score=34.46  Aligned_cols=25  Identities=24%  Similarity=0.405  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|.+|+|+.+|||.++|+++++.
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            7899999999999999999999874

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=84.87  E-value=0.69  Score=33.91  Aligned_cols=37  Identities=11%  Similarity=0.108  Sum_probs=28.6

Q ss_pred             HHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          414 RCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       414 R~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      ..|+.+.+.   +.+.|..|||+.+|+|..+|+.++..-+
T Consensus         9 ~~Il~~l~~---~g~~sr~eLa~~~glS~~Tv~~~l~~L~   45 (71)
T d1z05a1           9 GRVYKLIDQ---KGPISRIDLSKESELAPASITKITRELI   45 (71)
T ss_dssp             HHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHH---cCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            455555443   2589999999999999999999876644

>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=84.76  E-value=0.5  Score=36.48  Aligned_cols=35  Identities=20%  Similarity=0.273  Sum_probs=28.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH-----HHHHHHHHhc
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR-----ALYRLKQSLG  461 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R-----AL~KLR~~L~  461 (473)
                      .|+|.+++|+.+|+|..+|+.+++-     .+.+|.+...
T Consensus        23 ~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~   62 (89)
T d2o38a1          23 ARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLN   62 (89)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHH
Confidence            8999999999999999999999972     2455555444

>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=84.62  E-value=0.035  Score=48.44  Aligned_cols=24  Identities=13%  Similarity=-0.043  Sum_probs=21.4

Q ss_pred             ccCCCCCCcccccccccccccccccccCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFD  252 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D  252 (473)
                      |.++.+|.+|+|||.|||+     ++|.+
T Consensus       149 ~fd~~~g~~f~tya~~~i~-----~~i~~  172 (180)
T d1ku2a2         149 KFEYKRRFKFSTYATWWIR-----QAINR  172 (180)
T ss_dssp             HCCGGGCSCHHHHHHHHHH-----HHHHH
T ss_pred             HcCCCCCCCHHHHHHHHHH-----HHHHH
Confidence            6789999999999999999     77755

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.55  E-value=1.3  Score=31.68  Aligned_cols=50  Identities=12%  Similarity=0.100  Sum_probs=41.5

Q ss_pred             CCHHHHHHHHHHhhccCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       409 LperER~VL~LrY~L~~g-e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      +++.+..+|.-.|..+.. ......+||..+||++..|..+...-..+.|.
T Consensus         8 ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           8 FTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             CCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            677888888888875443 56678999999999999999999998888775

>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=84.36  E-value=1.2  Score=34.13  Aligned_cols=51  Identities=16%  Similarity=0.199  Sum_probs=40.4

Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHhhccC---CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          399 RQHVRNLLTLLNPKERCIVRLRFGIED---GKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       399 ~e~L~~aL~~LperER~VL~LrY~L~~---ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      ...|...+..|++.|+.|...  .+++   -..+|.+|||+..|||+++|....++
T Consensus         6 l~~i~~~~~~Ls~~e~~ia~y--il~~~~~~~~~si~~lA~~~~vS~sTi~Rf~kk   59 (83)
T d2o3fa1           6 LAIIQSMKHKLPPSERKLADY--ILAHPHKAIESTVNEISALANSSDAAVIRLCKS   59 (83)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHH--HHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhhCCHHHHHHHHH--HHcCHHHHHHccHHHHHHHHCCCHHHHHHHHHH
Confidence            356778888999999998743  3322   26799999999999999999877655

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.27  E-value=1.1  Score=32.85  Aligned_cols=27  Identities=11%  Similarity=0.133  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      ++++..+||+.|+||.++|..++++-.
T Consensus        29 ~G~s~r~aA~rf~VS~s~v~k~l~r~r   55 (63)
T d1k78a1          29 QGVRPCDISRQLRVSHGCVSKILGRYY   55 (63)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            799999999999999999999887643

>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=83.67  E-value=0.64  Score=36.64  Aligned_cols=44  Identities=20%  Similarity=0.230  Sum_probs=34.5

Q ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 011992          407 TLLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA  452 (473)
Q Consensus       407 ~~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA  452 (473)
                      -.|++.+..||..-+.  .+.++|..|||+.+|++.++|+.++.+-
T Consensus        17 ~gLs~~~~~iL~~L~~--~~~~~t~~eLa~~~~i~~~tvs~~l~~L   60 (109)
T d2d1ha1          17 YKITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVENSLKKL   60 (109)
T ss_dssp             HTCCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCcCHHHHHHHHHHHH--cCCCCCHHHHHHHHCccHhHHHHHHHHH
Confidence            3699999999864432  1246899999999999999999876553

>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=83.23  E-value=0.69  Score=32.88  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|.+|+|+.+|||..+|+++++.
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            7999999999999999999999864

>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=83.13  E-value=0.69  Score=34.32  Aligned_cols=29  Identities=17%  Similarity=0.240  Sum_probs=25.1

Q ss_pred             HHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          418 RLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       418 ~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      .+|-.    .++|.+|+|+.||||..+|.+.+.
T Consensus         8 ~~R~~----~gltQ~elA~~LGvs~~ti~~yE~   36 (67)
T d2auwa1           8 DWMHR----NNLSLTTAAEALGISRRMVSYYRT   36 (67)
T ss_dssp             HHHHH----TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHH----cCCCHHHHHHHhCCCHHHHHHHHc
Confidence            45555    789999999999999999999876

>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=83.07  E-value=0.7  Score=33.58  Aligned_cols=25  Identities=24%  Similarity=0.231  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .++|.+++|+.+|+|+++|+++++.
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

>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=82.92  E-value=0.01  Score=49.80  Aligned_cols=32  Identities=13%  Similarity=0.280  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .|+|++|||+.||.|+..|+.++++|++.+++
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            78999999999999999999999999988765

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=82.83  E-value=6  Score=29.79  Aligned_cols=65  Identities=18%  Similarity=0.186  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHhhcCCcchhhHhh
Q 011992          284 DLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ  360 (473)
Q Consensus       284 ~l~kle~a~~~L~~~lGRePT~eEiA~~lGms~eeL~~~l~~g~~A~e~Li~~yl~lV~sIA~ry~~~~~saEDLiQ  360 (473)
                      ...+|......++...|  -|..++|+.+|++...+.++..+...-       ....+.++|.-|   +++.+|++.
T Consensus         9 ~~~~l~~~i~~~R~~~g--ltq~~lA~~lgis~~~is~~E~g~~~~-------s~~~l~~ia~~l---~v~~~~~~~   73 (87)
T d1lmb3_           9 DARRLKAIYEKKKNELG--LSQESVADKMGMGQSGVGALFNGINAL-------NAYNAALLAKIL---KVSVEEFSP   73 (87)
T ss_dssp             HHHHHHHHHHHHHHHHT--CCHHHHHHHHTSCHHHHHHHHTTSSCC-------CHHHHHHHHHHH---TSCGGGTCH
T ss_pred             HHHHHHHHHHHHHHHcC--CCHHHHHHHhCccHHHHHHHHhccCCC-------cHHHHHHHHHHH---CCCHHHHCh
Confidence            33344445455555666  588999999999999998888766521       234455666665   455666654

>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=82.46  E-value=0.76  Score=32.96  Aligned_cols=24  Identities=13%  Similarity=0.297  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          427 KPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       427 e~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      .++|.+|+|+.+|||.++|+++++
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            789999999999999999999986

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.30  E-value=0.89  Score=34.14  Aligned_cols=52  Identities=17%  Similarity=0.193  Sum_probs=42.2

Q ss_pred             hCCHHHHHHHHHHhhccCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~g-e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      .+++.+..||.-.|-.+.. ......+||..+|++...|..+....+.++|..
T Consensus         9 r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           9 RKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            3677888888888875432 334578899999999999999999999999874

>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=82.18  E-value=0.77  Score=36.78  Aligned_cols=52  Identities=17%  Similarity=0.095  Sum_probs=36.8

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH--HHHHHHHhcc
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRA--LYRLKQSLGG  462 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RA--L~KLR~~L~~  462 (473)
                      .|+|-|.-...-++. +  .|.|.++||+.+|+|..+|++++.-+  -..++..+..
T Consensus        13 ~L~p~e~A~a~~~l~-~--~g~s~~eiA~~~G~s~~~V~~~l~L~~lp~~v~~~~~~   66 (114)
T d1r71a_          13 ELTPREIADFIGREL-A--KGKKKGDIAKEIGKSPAFITQHVTLLDLPEKIADAFNT   66 (114)
T ss_dssp             CCCHHHHHHHHHHHH-H--TTCCHHHHHHHHTCCHHHHHHHHGGGSCCHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHH-H--hCCCHHHHHHHHCCcHHHHHHHHHHhCCCHHHHHHHHc
Confidence            488887766544443 2  57899999999999999999987632  2344444444

>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=81.96  E-value=0.056  Score=51.11  Aligned_cols=24  Identities=13%  Similarity=-0.049  Sum_probs=21.6

Q ss_pred             ccCCCCCCcccccccccccccccccccCC
Q 011992          224 KVSKPQVTNHETYNSRKASVKKKLSEGFD  252 (473)
Q Consensus       224 ~~~~~~~~~f~tYa~~rIr~~~~~gai~D  252 (473)
                      |+++.+|.+|+|||.|||+     |+|.+
T Consensus       306 ~~~~~~~~~f~~~~~~~~~-----~~~~~  329 (334)
T d1siga_         306 KFEYRRGYKFSTYATWWIR-----QAITR  329 (334)
T ss_dssp             HCCGGGCCCHHHHHHHHHH-----HHHHH
T ss_pred             hcCCCCCCchHhhhHHHHH-----HHHHH
Confidence            6788999999999999999     88765

>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=81.72  E-value=1.7  Score=32.03  Aligned_cols=32  Identities=28%  Similarity=0.232  Sum_probs=24.5

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHcCC-CHHHHHH
Q 011992          290 KEKSKLQSQFGREPTLIEWAKAIGL-SCRDLKS  321 (473)
Q Consensus       290 ~a~~~L~~~lGRePT~eEiA~~lGm-s~eeL~~  321 (473)
                      ....+...+.|.+||..|||+.+|+ +...+..
T Consensus        12 ~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~   44 (71)
T d1jhfa1          12 DLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEE   44 (71)
T ss_dssp             HHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHH
Confidence            4445567789999999999999998 5554443

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=81.71  E-value=1.2  Score=32.50  Aligned_cols=51  Identities=12%  Similarity=0.088  Sum_probs=41.2

Q ss_pred             CCHHHHHHHHHHhhccCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQS  459 (473)
Q Consensus       409 LperER~VL~LrY~L~~g-e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~~  459 (473)
                      +++.+..+|.-.|..+.. ......+||..||++...|..+......+.|..
T Consensus         9 ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~   60 (65)
T d1fjla_           9 FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   60 (65)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhc
Confidence            577888888888875432 344568899999999999999999999888863

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=81.70  E-value=1.6  Score=34.35  Aligned_cols=41  Identities=22%  Similarity=0.191  Sum_probs=32.8

Q ss_pred             hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      .|++.|-.|+..-+.   ..+.|..|||+.+|+++++|..++.+
T Consensus        17 Glt~~e~~v~~~L~~---~g~~t~~eia~~~~i~~~~v~~~l~~   57 (109)
T d1sfxa_          17 SFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLKV   57 (109)
T ss_dssp             CCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---cCCCCHHHHHHHhCCCcchHHHHHHH
Confidence            588999888754333   16899999999999999999886544

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.57  E-value=0.49  Score=33.30  Aligned_cols=48  Identities=21%  Similarity=0.287  Sum_probs=37.6

Q ss_pred             hCCHHHHHHHHHHhhccCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 011992          408 LLNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYR  455 (473)
Q Consensus       408 ~LperER~VL~LrY~L~~g-e~lTlkEIAe~LGIS~~rVrqi~~RAL~K  455 (473)
                      .|++.++.||.-.|..+.. .....++||+.+|++...|..+...-..+
T Consensus         3 ~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k   51 (53)
T d1le8a_           3 SISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR   51 (53)
T ss_dssp             CCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhc
Confidence            4889999999998874432 33356889999999999999998766554

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein 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: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=81.06  E-value=1.7  Score=31.79  Aligned_cols=38  Identities=16%  Similarity=0.166  Sum_probs=30.0

Q ss_pred             HHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 011992          413 ERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLESRAL  453 (473)
Q Consensus       413 ER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~RAL  453 (473)
                      .+.|+.+.+.   ..+.|-.|||+.+|+|..+|.++...-+
T Consensus         7 ~~~Il~~i~~---~g~~sr~eLa~~~gLS~~Tvs~iv~~L~   44 (70)
T d1z6ra1           7 AGAVYRLIDQ---LGPVSRIDLSRLAQLAPASITKIVHEML   44 (70)
T ss_dssp             HHHHHHHHHS---SCSCCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3456665554   3789999999999999999999887644

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.90  E-value=1.2  Score=31.63  Aligned_cols=50  Identities=10%  Similarity=0.106  Sum_probs=39.4

Q ss_pred             CCHHHHHHHHHHhhccCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 011992          409 LNPKERCIVRLRFGIEDG-KPKSLSEVGNIFGLSKERVRQLESRALYRLKQ  458 (473)
Q Consensus       409 LperER~VL~LrY~L~~g-e~lTlkEIAe~LGIS~~rVrqi~~RAL~KLR~  458 (473)
                      .++.+..+|...|..+.. .....++||..+||++..|..+...-..++|+
T Consensus         7 ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            577888888888864322 33456899999999999999999888877774

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=80.37  E-value=1.1  Score=38.52  Aligned_cols=37  Identities=19%  Similarity=0.305  Sum_probs=28.7

Q ss_pred             CHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 011992          410 NPKERCIVRLRFGIEDGKPKSLSEVGNIFGLSKERVRQLES  450 (473)
Q Consensus       410 perER~VL~LrY~L~~ge~lTlkEIAe~LGIS~~rVrqi~~  450 (473)
                      +|.-+.||.+-..    .++|..|||+.+|+|.++|+.++.
T Consensus        18 ~p~R~~Il~~L~~----~~~s~~ela~~lg~s~~~v~~hl~   54 (190)
T d1ulya_          18 EDTRRKILKLLRN----KEMTISQLSEILGKTPQTIYHHIE   54 (190)
T ss_dssp             SHHHHHHHHHHTT----CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4555567665444    689999999999999999997654

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.13  E-value=0.67  Score=33.33  Aligned_cols=22  Identities=14%  Similarity=0.280  Sum_probs=20.4

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q 011992          430 SLSEVGNIFGLSKERVRQLESR  451 (473)
Q Consensus       430 TlkEIAe~LGIS~~rVrqi~~R  451 (473)
                      |++|||+..|||..+|+..++.
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~   23 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINK   23 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHCC
Confidence            7899999999999999998875