Citrus Sinensis ID: 012567

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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
Protein Sequence
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSFDRK
Secondary Structure (PSIPRED)
cccccHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHccEEEEEHHcccccccccHHHHHHcHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHccccccccccccccccccccccHHHHccccccccccHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccEccHHHccccccccccccccccccccEEccccccccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHcccccccHHHHHHHHcccccccHHHcccccccHHHHcHHHHHccccEEEEcccccHHHHHHHHcccHcccccccccccccHHHHccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHcccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccEccHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHcccccccccccccccccHHHHHHHHHccccccccHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mttvldveklrlpsleahSNAVAAnrqwtyfgavgpsteenlgtslatetltSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtnTSMWAQLTERERAsiigdsviveaapeeeyseqqplnksadleptHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSvksgstsrrkrpsvqevdysdplrylrattsssrlltANEEMQLSAGIQDLLKLEGLREVlsercggsptFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRgaekfdaskgfkfsTYAHWWIKQAVRKslsdqsrtirlpfhmVEATYRVKEARKQLYSengrhpnneeVAEATGLSMKRLHAVllspkaprsldqkiginqnlkpSVCFILNLAdsliiffpplFIIWFMSFDRK
Flexible Loop (DISEMBL)
mttvldveklrlpsleahsNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtNTSMWAQLTERERASIIGDSVIVEAAPeeeyseqqplnkSADLEPTHEELKLLEeqvsqsiavrsrrqterkARRTRaaekaaanvmsvksgstsrrkrpsvqevdysdplrylRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAaaagvdqrelRRRLNYGilckdkmitsNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKfdaskgfkfstYAHWWIKQAVrkslsdqsrtirlpfhmveatYRVKEARKQLysengrhpnneEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSFDRK
Low Complexity Region (SEG)
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTsdeaviaaasaeavalaraavkvakdaalMVNHHNsakpkskpaisssaDTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSrrqterkarrtraaekaaaNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSliiffpplfiiwfMSFDRK
Disordered region (IsUnstruct)
*******************NAVAANRQWTYFGAVGP*********LATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMV************************************I******************************************************************************************************************LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK*******************************AVL**********QKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSF***
Disordered Region (DISOPRED)
**T**D*EKLRL*********************************************************************************************************************************************************************************************************LRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE*********PTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARK**********NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSF***
Disordered Region (DISEMBL)
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHH******************TSMWAQLTERERASIIGDSVIVEAAP***********KSADLEPTHEELKLLEEQVSQS********************************************VDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSFDRK
Disordered Region (DISPRO)
*TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHH******************TSMWAQLTE****SIIGDSVIVEAAPE*********************LKLLEEQVSQSIAVRSR****************************************YSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSFDR*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSFDRK
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	460	2.2.26 [Sep-21-2011]
O22056	572	RNA polymerase sigma fact	yes	no	0.967	0.777	0.643	1e-146
P26683	390	RNA polymerase sigma fact	yes	no	0.510	0.602	0.447	7e-51
Q9LD95	547	RNA polymerase sigma fact	no	no	0.567	0.477	0.396	1e-47
P38023	399	RNA polymerase sigma fact	yes	no	0.469	0.541	0.467	1e-47
Q31ME3	320	RNA polymerase sigma fact	no	no	0.441	0.634	0.433	1e-43
Q31QG5	320	RNA polymerase sigma fact	no	no	0.478	0.687	0.426	8e-43
P52322	416	RNA polymerase sigma fact	no	no	0.469	0.519	0.380	6e-42
P74565	425	RNA polymerase sigma fact	N/A	no	0.297	0.322	0.514	9e-38
Q03065	332	RNA polymerase sigma-B fa	no	no	0.439	0.608	0.381	1e-37
P33118	329	RNA polymerase sigma fact	yes	no	0.352	0.492	0.441	3e-37

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

 Score =  520 bits (1338), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 299/465 (64%), Positives = 351/465 (75%), Gaps = 20/465 (4%)

Query: 1   MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
           +T++LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL TSDEAV+ 
Sbjct: 49  LTSMLDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVV 108

Query: 60  AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
           AA+AEAVALARAAVKVAKDA L  N +N+        ++SS     S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGI 162

Query: 120 IG-----DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTE 173
           +G     D+ IV        S ++ +    DLE   +E   L E+  S S+AVRS RQTE
Sbjct: 163 LGHLAVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTE 219

Query: 174 RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEM 233
           RKARR +  EK A+ + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE 
Sbjct: 220 RKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEH 279

Query: 234 QLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITS 293
           +LSAGIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI S
Sbjct: 280 ELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKS 339

Query: 294 NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 353
           NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKS
Sbjct: 340 NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKS 399

Query: 354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK 413
           LSDQSR IRLPFHMVEATYRVKEARKQLYSE G+HP NEE+AEATGLSMKRL AVLLSPK
Sbjct: 400 LSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPK 459

Query: 414 APRSLDQKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSFD 458
            PRSLDQKIG+NQNLKPS      +AD   +    + I  FM  D
Sbjct: 460 PPRSLDQKIGMNQNLKPSEV----IADPEAVTSEDILIKEFMRQD 500

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 =  201 bits (512), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 106/237 (44%), Positives = 150/237 (63%), Gaps = 2/237 (0%)

Query: 193 KSG--STSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE 250
           KSG  + SRR+  S ++    D +R         RLL A+EE++L+  I DLL+LE +RE
Sbjct: 59  KSGKAAKSRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRE 118

Query: 251 VLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGM 310
            LSE+    P  ++WA A  +     R RL+ G   KDKM+ SN+RLV+SIAK Y   G+
Sbjct: 119 RLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGL 178

Query: 311 NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA 370
           + QDL+QEG  GL+R AEKFD  KG+KFSTYA WWI+QA+ ++++DQSRTIRLP H+ E 
Sbjct: 179 SFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYET 238

Query: 371 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN 427
             R+K+  K L  E GR P  EE+A    +++++L  +  S + P SL+  IG  ++
Sbjct: 239 ISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEED 295

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

 Score =  191 bits (485), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 104/262 (39%), Positives = 155/262 (59%), Gaps = 1/262 (0%)

Query: 166 VRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSR 225
           VRS+RQ ER+A+  RA +    +        TS +K+   Q  D  D L+       + +
Sbjct: 188 VRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYK-QGADNDDALQLFLWGPETKQ 246

Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
           LLTA EE +L + IQ LLKLE ++  L  + G  PT  +WA A G+    L+  ++ G  
Sbjct: 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRS 306

Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 345
            ++K+IT+N+RLV+ IAK YQ  G+N QDL+QEG  GL++  EKF    G +F+TYA+WW
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWW 366

Query: 346 IKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 405
           I+Q++RKS+   SRTIRLP ++     +V EARK    E    P+ EE+A   G+S ++L
Sbjct: 367 IRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKL 426

Query: 406 HAVLLSPKAPRSLDQKIGINQN 427
             +L + + P S+ Q I  +Q+
Sbjct: 427 DKLLYNTRTPLSMQQPIWSDQD 448

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

 Score =  191 bits (485), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 101/216 (46%), Positives = 139/216 (64%)

Query: 212 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGV 271
           D +R         RLL A+EE++L+  I DLL LE +R+ L E+    P+ A+WAAA   
Sbjct: 89  DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148

Query: 272 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 331
              E RRRL  G   KDKM+ SN+RLV+SIAK Y   G++ QDL+QEG  GL+R AEKFD
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 208

Query: 332 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNN 391
             KG+KFSTYA WWI+QA+ ++++DQSRTIRLP H+ E   R+K+  K L  E GR P  
Sbjct: 209 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTE 268

Query: 392 EEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN 427
           EE+A    +++++L  +  S + P SL+  IG  ++
Sbjct: 269 EEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEED 304

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

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

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

 Score =  177 bits (450), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 88/203 (43%), Positives = 130/203 (64%)

Query: 225 RLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 284
           RLLTA EE+     +Q L+ L   +  L +R G  P+  +WAAA  ++  +L R++  G 
Sbjct: 24  RLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNLEDLDRQIEQGQ 83

Query: 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHW 344
             K KMI +N+RLV+SIAK YQ   M   DL+QEG  GL RG EKFD SKG+KFSTYA+W
Sbjct: 84  RAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDPSKGYKFSTYAYW 143

Query: 345 WIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKR 404
           WI+QA+ ++++ QSRTIRLP H+ E   ++K+ +++L  + GR     E+AE   L +++
Sbjct: 144 WIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQLGRSATASELAEVLELPLEQ 203

Query: 405 LHAVLLSPKAPRSLDQKIGINQN 427
           +   +   + P SLD K+G +Q+
Sbjct: 204 VREYIQMNRQPVSLDVKVGDSQD 226

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 =  175 bits (443), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 95/223 (42%), Positives = 142/223 (63%), Gaps = 3/223 (1%)

Query: 207 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVL-SERCGGSPTFAQ 264
           E   SD +R YLR       LLT  EE+ L   +Q  +KL+ LR+ L SE     P+  +
Sbjct: 5   ETPTSDLVRTYLREIGRVP-LLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLE 63

Query: 265 WAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLV 324
           WAAAAG+   ELR++ + G   K KMI +N+RLV+S+AK Y    M+L DL+QEG  G+ 
Sbjct: 64  WAAAAGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQ 123

Query: 325 RGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSE 384
           RG EKFD +KG++FSTYA+WWI+QA+ +++++++RTIRLP H+ E   ++K+ ++QL  +
Sbjct: 124 RGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKIKKMQRQLSQQ 183

Query: 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN 427
            GR     E+A A  L+  ++   L   + P SLD ++G NQ+
Sbjct: 184 LGRTATLPELAAALDLTPAQVRDYLEKARHPLSLDLRVGDNQD 226

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

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

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

 Score =  172 bits (435), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 97/255 (38%), Positives = 136/255 (53%), Gaps = 39/255 (15%)

Query: 212 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE--------------VLSERCG 257
           D +R         RLL A EE++L+  I DLLKLE +RE               L ER  
Sbjct: 67  DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126

Query: 258 G-------------------------SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 292
                                     +P   +W A +       +RRL +G   K+KM+ 
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186

Query: 293 SNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 352
           SN+RLV+SIAK Y   G++ QDL+QEG  GL+R AEKFD  KG+KFSTYA WWI+QA+ +
Sbjct: 187 SNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITR 246

Query: 353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP 412
           +++DQSRTIRLP H+ E   R+K+  K L  E  R P  EE+A    +++++L  +  S 
Sbjct: 247 AIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSA 306

Query: 413 KAPRSLDQKIGINQN 427
           + P SL+  IG  ++
Sbjct: 307 QLPISLETPIGKEED 321

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

Microcystis aeruginosa (taxid: 1126)

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

 Score =  158 bits (399), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 71/138 (51%), Positives = 97/138 (70%)

Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 345
            KDKM+ SN+RLV+SIAK Y   G++ QDL+QEG  GL+R AEKFD  KG+KFSTYA WW
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248

Query: 346 IKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 405
           I+QA+ ++++DQSRTIRLP H+ E   R+K+  K L  E  R P  EE+AE   +++++L
Sbjct: 249 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTIEKL 308

Query: 406 HAVLLSPKAPRSLDQKIG 423
             +  S + P SL+  IG
Sbjct: 309 RFIAKSAQLPISLETPIG 326

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

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

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

 Score =  158 bits (399), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 77/202 (38%), Positives = 123/202 (60%)

Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
           LL+  +E+  +  +Q ++ +   +E L+E+    PT  +WA    + +  L ++L+ G +
Sbjct: 37  LLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQLKEDVLLQQLSQGQI 96

Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 345
            K KMI +N+RLV+SIAK YQ   +   DL+QEG  GL RG EKFD + G+KFSTYA+WW
Sbjct: 97  AKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFDPTLGYKFSTYAYWW 156

Query: 346 IKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 405
           I+Q + ++++ QSRTIRLP HM +   ++K  +++L  + G      E+A+A  L   ++
Sbjct: 157 IRQGITRAIAQQSRTIRLPIHMADKLNKIKCVQRELSQKLGYIAGVTEIAQALNLEPSQI 216

Query: 406 HAVLLSPKAPRSLDQKIGINQN 427
              L   + P SLD +IG  Q+
Sbjct: 217 REYLQLVRQPVSLDMRIGFEQD 238

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|P33118|RPSB_CORDI RNA polymerase sigma factor SigB OS=Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis) GN=sigB PE=3 SV=2

 Score =  156 bits (395), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 72/163 (44%), Positives = 108/163 (66%), Gaps = 1/163 (0%)

Query: 273 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA 332
           +R+L+  +  G   +  ++ +N+RLV+S+AK Y G GM L DL+QEG  GL+R  EKFD 
Sbjct: 79  KRDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 138

Query: 333 SKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNE 392
           SKGFKFSTYA WWI+QA+ + ++DQSRTIRLP H+VE   ++   ++++Y + GR   NE
Sbjct: 139 SKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQQLGREATNE 198

Query: 393 EVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFI 435
           E+AE +G+   ++  +L   + P SLD  +G ++   P   FI
Sbjct: 199 ELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEE-APLGDFI 240

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

Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis) (taxid: 257309)

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	460
255565968	569	RNA polymerase sigma factor rpoD1, putat	0.906	0.732	0.750	1e-165
296090195	575	unnamed protein product [Vitis vinifera]	0.934	0.747	0.777	1e-156
449454538	580	PREDICTED: RNA polymerase sigma factor s	0.915	0.725	0.696	1e-156
225436223	578	PREDICTED: RNA polymerase sigma factor r	0.934	0.743	0.777	1e-156
224126061	567	predicted protein [Populus trichocarpa]	0.934	0.758	0.742	1e-154
224144900	564	predicted protein [Populus trichocarpa]	0.930	0.758	0.722	1e-153
297843640	572	hypothetical protein ARALYDRAFT_470915 [	0.973	0.783	0.653	1e-146
7363218	575	sigma factor 2 [Sinapis alba]	0.917	0.733	0.666	1e-145
15223259	572	RNApolymerase sigma subunit 2 [Arabidops	0.967	0.777	0.643	1e-145
356509511	558	PREDICTED: RNA polymerase sigma factor r	0.906	0.747	0.668	1e-144

>gi|255565968|ref|XP_002523972.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis] gi|223536699|gb|EEF38340.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]

 Score =  587 bits (1514), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 322/429 (75%), Positives = 366/429 (85%), Gaps = 12/429 (2%)

Query: 4   VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 62
           VLD+EKLRLPS EA S+++A N  WTY            G++LATETL TSDEAVIAAA+
Sbjct: 59  VLDLEKLRLPSFEAPSDSIAPNSPWTY---------ATFGSTLATETLITSDEAVIAAAA 109

Query: 63  AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 122
           AEAVALARAAVKVAKDAAL+V +  SA+ +SK  ++S +  + S W Q TE ERA IIGD
Sbjct: 110 AEAVALARAAVKVAKDAALLVKNFPSAETESK--LTSPSTIDASRWPQFTETERARIIGD 167

Query: 123 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 182
           SV  E  P EE S Q  + +S  LE TH+EL+LL++Q+S+ IAVRSRRQTERKARR RA 
Sbjct: 168 SVATETGPREESSMQSSIKESDYLELTHKELELLQKQLSEGIAVRSRRQTERKARRARAV 227

Query: 183 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 242
           EKAA++V+SVK GSTS++KR S+QEVDYSDPLRYLR TTS+SRLLTA+EE++LSA IQDL
Sbjct: 228 EKAASSVVSVKPGSTSKKKRGSLQEVDYSDPLRYLRGTTSTSRLLTASEELELSAAIQDL 287

Query: 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302
           LKLE L+E L+ER GG PTFAQWAAAAGVDQR LR+R+N+G +CKDKMI SNIRLVISIA
Sbjct: 288 LKLERLQEELAERYGGQPTFAQWAAAAGVDQRTLRKRINHGTICKDKMIKSNIRLVISIA 347

Query: 303 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362
           KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR
Sbjct: 348 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 407

Query: 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKI 422
           LPFHMVEATYRVKEARKQLYSENGRHP++EEVAEA GLSMKRL AVLL+PKAPRSLDQKI
Sbjct: 408 LPFHMVEATYRVKEARKQLYSENGRHPDDEEVAEAAGLSMKRLSAVLLTPKAPRSLDQKI 467

Query: 423 GINQNLKPS 431
           G+N +LKPS
Sbjct: 468 GMNMDLKPS 476

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296090195|emb|CBI40014.3| unnamed protein product [Vitis vinifera]

 Score =  557 bits (1436), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 336/432 (77%), Positives = 366/432 (84%), Gaps = 2/432 (0%)

Query: 2   TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAA 60
           T VLD+EKLRLPSLE+HSN+VAA+R WTY G VGP TE N   +LA ETL TS+EAVIAA
Sbjct: 51  TAVLDIEKLRLPSLESHSNSVAAHRPWTYIGVVGPPTEANFEATLARETLLTSEEAVIAA 110

Query: 61  ASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPA-ISSSADTNTSMWAQLTERERASI 119
           A+AEAVALA+AAVKVAKDAA +V  +NSAK ++KPA   S  DT+     Q TE ER  I
Sbjct: 111 AAAEAVALAKAAVKVAKDAARLVGKNNSAKSETKPASFLSGDDTSQFRRIQFTETERIGI 170

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRT 179
           +GDSV  E    +  S Q     S DLEPT EEL+LLE + S+SI VRS RQ ERKARR 
Sbjct: 171 LGDSVGAETGMVDYNSLQDVTEDSDDLEPTLEELELLEAEFSKSIVVRSNRQVERKARRA 230

Query: 180 RAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGI 239
           RAAEKA+A V+SV+SGSTSRRKR S+QEVDYSDPLRYLR TTS+SRLLTA EE++LS GI
Sbjct: 231 RAAEKASAGVVSVRSGSTSRRKRVSLQEVDYSDPLRYLRGTTSTSRLLTATEELELSEGI 290

Query: 240 QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 299
           QDLLKLE L+E L ER G  PTFAQWAAAAGVDQ+ LRRR NYGI CKDKMI SNIRLVI
Sbjct: 291 QDLLKLEKLQEDLEERFGVKPTFAQWAAAAGVDQKTLRRRTNYGIRCKDKMIKSNIRLVI 350

Query: 300 SIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359
           SIAKNYQGAGMN+QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR
Sbjct: 351 SIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 410

Query: 360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLD 419
           TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL+AVLL+PKAPRSLD
Sbjct: 411 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLNAVLLTPKAPRSLD 470

Query: 420 QKIGINQNLKPS 431
           QKIGINQNLKPS
Sbjct: 471 QKIGINQNLKPS 482

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454538|ref|XP_004145011.1| PREDICTED: RNA polymerase sigma factor sigB-like [Cucumis sativus] gi|449473951|ref|XP_004154029.1| PREDICTED: RNA polymerase sigma factor sigB-like [Cucumis sativus]

 Score =  556 bits (1434), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 299/429 (69%), Positives = 351/429 (81%), Gaps = 8/429 (1%)

Query: 3   TVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAAS 62
           T LDV++L+LP  + ++++V+  R  +Y GAV         +SLA+  LTS+EA IAAA+
Sbjct: 67  TTLDVDRLKLPPFDTNTDSVSVERLRSYLGAVE--------SSLASTLLTSEEASIAAAA 118

Query: 63  AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 122
           AEAV LA+AAVKVA+DAAL+ N+ NS++  +K   S   D     WAQ  E ERA IIG+
Sbjct: 119 AEAVTLAKAAVKVARDAALLANNINSSRAGTKSQSSPKPDALHFKWAQFMESERADIIGE 178

Query: 123 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 182
            V V   P E  + +    +S D+EPT EEL+LL++++S+SI V+S+RQTERKARRTRAA
Sbjct: 179 PVGVNKRPMEGDALEPSTTESDDMEPTSEELELLQDELSESITVKSKRQTERKARRTRAA 238

Query: 183 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 242
           EK   +V+S KSGS+SR+KR SVQEVDYSDPLRYLRATT++SRLLTA EE++LS GIQDL
Sbjct: 239 EKTVTSVLSFKSGSSSRKKRNSVQEVDYSDPLRYLRATTNTSRLLTATEELELSEGIQDL 298

Query: 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302
           LKLE L+E L ER G  PTFAQWAAAAGV+QR LR+RLNYG LCKDKMI SNIRLVISIA
Sbjct: 299 LKLERLQEELGERYGNEPTFAQWAAAAGVNQRTLRKRLNYGTLCKDKMIKSNIRLVISIA 358

Query: 303 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362
           KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK LSDQSRTIR
Sbjct: 359 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKFLSDQSRTIR 418

Query: 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKI 422
           LPFHMVEATYRVKEARKQL  ENGRHP+++E+AEA GLSMKRL AVL++PKAPRSL+QKI
Sbjct: 419 LPFHMVEATYRVKEARKQLLHENGRHPDDKEIAEAAGLSMKRLAAVLMTPKAPRSLEQKI 478

Query: 423 GINQNLKPS 431
           GINQNLKPS
Sbjct: 479 GINQNLKPS 487

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225436223|ref|XP_002273602.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Vitis vinifera]

 Score =  556 bits (1434), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 336/432 (77%), Positives = 366/432 (84%), Gaps = 2/432 (0%)

Query: 2   TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAA 60
           T VLD+EKLRLPSLE+HSN+VAA+R WTY G VGP TE N   +LA ETL TS+EAVIAA
Sbjct: 54  TAVLDIEKLRLPSLESHSNSVAAHRPWTYIGVVGPPTEANFEATLARETLLTSEEAVIAA 113

Query: 61  ASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPA-ISSSADTNTSMWAQLTERERASI 119
           A+AEAVALA+AAVKVAKDAA +V  +NSAK ++KPA   S  DT+     Q TE ER  I
Sbjct: 114 AAAEAVALAKAAVKVAKDAARLVGKNNSAKSETKPASFLSGDDTSQFRRIQFTETERIGI 173

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRT 179
           +GDSV  E    +  S Q     S DLEPT EEL+LLE + S+SI VRS RQ ERKARR 
Sbjct: 174 LGDSVGAETGMVDYNSLQDVTEDSDDLEPTLEELELLEAEFSKSIVVRSNRQVERKARRA 233

Query: 180 RAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGI 239
           RAAEKA+A V+SV+SGSTSRRKR S+QEVDYSDPLRYLR TTS+SRLLTA EE++LS GI
Sbjct: 234 RAAEKASAGVVSVRSGSTSRRKRVSLQEVDYSDPLRYLRGTTSTSRLLTATEELELSEGI 293

Query: 240 QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 299
           QDLLKLE L+E L ER G  PTFAQWAAAAGVDQ+ LRRR NYGI CKDKMI SNIRLVI
Sbjct: 294 QDLLKLEKLQEDLEERFGVKPTFAQWAAAAGVDQKTLRRRTNYGIRCKDKMIKSNIRLVI 353

Query: 300 SIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359
           SIAKNYQGAGMN+QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR
Sbjct: 354 SIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 413

Query: 360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLD 419
           TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL+AVLL+PKAPRSLD
Sbjct: 414 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLNAVLLTPKAPRSLD 473

Query: 420 QKIGINQNLKPS 431
           QKIGINQNLKPS
Sbjct: 474 QKIGINQNLKPS 485

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224126061|ref|XP_002319746.1| predicted protein [Populus trichocarpa] gi|222858122|gb|EEE95669.1| predicted protein [Populus trichocarpa]

 Score =  552 bits (1423), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 320/431 (74%), Positives = 367/431 (85%), Gaps = 1/431 (0%)

Query: 2   TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTS-DEAVIAA 60
           T VLD+EKLRLPSLE HS++++ANR WTY G +GP  +   GTSLA ETL + DEAVIAA
Sbjct: 44  TAVLDLEKLRLPSLEPHSDSISANRPWTYIGGIGPQKKPPFGTSLAAETLIANDEAVIAA 103

Query: 61  ASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASII 120
           A+AEAVALARAAVKVAKDAA M  +++S K ++K  I+S+ D+ +SMW+ LTE+ERA II
Sbjct: 104 AAAEAVALARAAVKVAKDAAEMAKNYSSMKKETKIPIASTTDSFSSMWSLLTEKERADII 163

Query: 121 GDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTR 180
           GDSV  E    EEYS Q P  +   LEPT EEL LL++Q+S+ IAVRS+RQTERKARR R
Sbjct: 164 GDSVSAETRLREEYSVQYPTEEYDCLEPTQEELALLQKQLSEGIAVRSKRQTERKARRAR 223

Query: 181 AAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQ 240
           AAEKAAANV+SVKSGSTS++KR  +QEVD SDPLR+ R  +SSSRLL+A EE++LS GIQ
Sbjct: 224 AAEKAAANVVSVKSGSTSKKKRVPLQEVDQSDPLRFFRGASSSSRLLSATEEVELSEGIQ 283

Query: 241 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 300
           DLLKLE + E L ER GG P+FAQWAAAAGVDQ  LR+RLNYGILCKDKMI SN+RLVIS
Sbjct: 284 DLLKLERIEEELKERFGGEPSFAQWAAAAGVDQLTLRKRLNYGILCKDKMIKSNVRLVIS 343

Query: 301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360
           IAKNYQG GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD+SRT
Sbjct: 344 IAKNYQGTGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDRSRT 403

Query: 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQ 420
           IRLPFHMV+ATYRVKEARKQLYSENGRHP+++EVAEA GLSMKRL AVLL+PKAPRSLDQ
Sbjct: 404 IRLPFHMVDATYRVKEARKQLYSENGRHPDDKEVAEAAGLSMKRLSAVLLTPKAPRSLDQ 463

Query: 421 KIGINQNLKPS 431
           K+G N +LK S
Sbjct: 464 KMGFNMDLKLS 474

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144900|ref|XP_002325455.1| predicted protein [Populus trichocarpa] gi|222862330|gb|EEE99836.1| predicted protein [Populus trichocarpa]

 Score =  548 bits (1412), Expect = e-153,   Method: Compositional matrix adjust.
 Identities = 310/429 (72%), Positives = 357/429 (83%), Gaps = 1/429 (0%)

Query: 4   VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLT-SDEAVIAAAS 62
           VL++EKLRLPSLE+HS+++AANR WTY G +GP  E   GTSLATETL  +DEAVIAAA+
Sbjct: 43  VLNLEKLRLPSLESHSDSIAANRPWTYIGGIGPPKEPLFGTSLATETLIINDEAVIAAAA 102

Query: 63  AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 122
           AEAVALARAAVKVAKDAA M  ++ S   ++K  I+S+AD+ +SMW+ LT +ERA IIG 
Sbjct: 103 AEAVALARAAVKVAKDAAEMAKNYCSVNTETKIPIASTADSFSSMWSLLTGKERADIIGV 162

Query: 123 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 182
           S   E    EE S Q P  +S    PTHEEL LLE+Q+S+SI VRS+RQT+RKA+R RAA
Sbjct: 163 SFSAETGLREECSTQYPTEESDCFGPTHEELALLEKQLSESIVVRSKRQTQRKAKRARAA 222

Query: 183 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 242
           EKAAAN + +KSGS  ++KR  VQEVD SDPLR+ R  ++SSRLL+A EE++LS GIQDL
Sbjct: 223 EKAAANFVFMKSGSACKKKRVPVQEVDQSDPLRFFRGASTSSRLLSATEEVELSEGIQDL 282

Query: 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302
           LKLE + E L ER GG PTFAQWAAAA VDQ  LR+RLNY ILCKDKMI SNIRLVISIA
Sbjct: 283 LKLERIEEELKERFGGKPTFAQWAAAARVDQITLRKRLNYAILCKDKMIKSNIRLVISIA 342

Query: 303 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 362
           KNYQGAGMNLQDLVQEGCRGLVRG EKFDASKGFKFSTYAHWWI+QAVR+SLSDQSRTIR
Sbjct: 343 KNYQGAGMNLQDLVQEGCRGLVRGVEKFDASKGFKFSTYAHWWIRQAVRRSLSDQSRTIR 402

Query: 363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKI 422
           LPFHMV+ATYRVKEARKQ YSENGRHP+++EVAEATGLSMKRL AVLL+PKAPRSLDQK+
Sbjct: 403 LPFHMVDATYRVKEARKQFYSENGRHPDDKEVAEATGLSMKRLSAVLLTPKAPRSLDQKM 462

Query: 423 GINQNLKPS 431
           G N +LK S
Sbjct: 463 GFNMDLKLS 471

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843640|ref|XP_002889701.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp. lyrata] gi|297335543|gb|EFH65960.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp. lyrata]

 Score =  525 bits (1351), Expect = e-146,   Method: Compositional matrix adjust.
 Identities = 302/462 (65%), Positives = 350/462 (75%), Gaps = 14/462 (3%)

Query: 1   MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
           +T++LDV KLRLPS +  S++  ++RQWTY    GPSTE     +LA+ETL TSDEAV+ 
Sbjct: 49  LTSMLDVAKLRLPSFDTDSDSRISDRQWTYTRTDGPSTEAKYLEALASETLLTSDEAVVV 108

Query: 60  AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
           AA+AEAVALARAAVKVAKDA L  N +N+        ISS+AD   S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAAVKVAKDATLFKNSNNT-----NLLISSTADKR-SKWDQFTEKERAGI 162

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSA--DLEPTHEELKLLEEQV-SQSIAVRSRRQTERKA 176
           +G   + +     +       NK +  DLE   +E   L E+  S S+AVRS RQTERKA
Sbjct: 163 LGHLAVSDNGIVSDKITAPASNKESPGDLESEKQEEVELLEEQPSVSLAVRSTRQTERKA 222

Query: 177 RRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLS 236
           RR +  EK A+ + SVK+GS  R+KR   QEVD++DPLRYLR TTSSS+LLT  EE +LS
Sbjct: 223 RRAKGLEKTASGIPSVKTGSNPRKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELS 282

Query: 237 AGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIR 296
           AGIQDLLKLE L+  L+ERCG  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIR
Sbjct: 283 AGIQDLLKLERLQTELTERCGRQPTFAQWASAAGVDQKSLRKRIHHGTLCKDKMIKSNIR 342

Query: 297 LVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356
           LVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKSLSD
Sbjct: 343 LVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSD 402

Query: 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416
           QSR IRLPFHMVEATYRVKEARKQLYSE G+HP NEE+AEATGLSMKRL AVLLSPK PR
Sbjct: 403 QSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPR 462

Query: 417 SLDQKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSFD 458
           SLDQKIG+NQNLKPS      +AD   +    + I  FM  D
Sbjct: 463 SLDQKIGMNQNLKPSEV----IADPEAVTSEDILIKEFMRQD 500

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|7363218|emb|CAB83106.1| sigma factor 2 [Sinapis alba]

 Score =  523 bits (1346), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 292/438 (66%), Positives = 340/438 (77%), Gaps = 16/438 (3%)

Query: 1   MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
           +T+ LDV KLRLPS +  S++  ++R WTY   +GPSTE     +LA+ETL TSDEAV+A
Sbjct: 49  LTSTLDVAKLRLPSFDTDSDSRISDRPWTYTRTIGPSTEAKYLEALASETLLTSDEAVVA 108

Query: 60  AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
           AA+AEAVALARAA+KVAKDA L  N HN+     K ++SS+AD   S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAALKVAKDATLFGNSHNT-----KLSVSSAADKR-SKWDQFTEKERAGI 162

Query: 120 IG-----DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTER 174
           +G     D+ +V        S +     S DL P     K   E++S S AVRS RQTER
Sbjct: 163 LGHLAVSDTGVVSDRITAPGSLECNKEASDDLTPAE---KQEVEKLSVSSAVRSTRQTER 219

Query: 175 KARRTRAAEKAAANVMS-VKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEM 233
           KARR +  EK A+ + S VK+GS+SR+KR + QE+D++DPLRYLR TTSSS+LLTA EE 
Sbjct: 220 KARRVKGLEKTASGMQSSVKTGSSSRKKRVASQEIDHNDPLRYLRMTTSSSKLLTAREEQ 279

Query: 234 QLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITS 293
           QLS GIQDLLKLE L+  L+ERCG  PTF+QWA+AAGVD++ LR+R+ +G  CKD+MI S
Sbjct: 280 QLSEGIQDLLKLERLQAELTERCGHQPTFSQWASAAGVDKKTLRKRITHGTQCKDRMIKS 339

Query: 294 NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 353
           NIRLVISIAKNYQGAGM+ QDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKS
Sbjct: 340 NIRLVISIAKNYQGAGMDFQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKS 399

Query: 354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK 413
           LSDQSR IRLPFHMVEATYRVKEARKQLYSE G+ P NEEVAEATGLSMKRL AVLLSPK
Sbjct: 400 LSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKQPKNEEVAEATGLSMKRLMAVLLSPK 459

Query: 414 APRSLDQKIGINQNLKPS 431
            PRSLDQKIGIN NLKPS
Sbjct: 460 PPRSLDQKIGINLNLKPS 477

Source: Sinapis alba

Species: Sinapis alba

Genus: Sinapis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15223259|ref|NP_172330.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana] gi|75219074|sp|O22056.2|SIGB_ARATH RecName: Full=RNA polymerase sigma factor sigB; Short=Sigma factor B; Short=Sigma-B; AltName: Full=Protein ABERRANT CHLOROPLAST 1; AltName: Full=RNA polymerase sigma factor sig1; Short=Atsig1; Short=Sigma factor 1; AltName: Full=RNA polymerase sigma factor sig2; Short=Atsig2; Short=Sigma factor 2; AltName: Full=RNA polymerase sigma factor sigA; Short=Sigma factor A; Short=Sigma-A; Flags: Precursor gi|6664315|gb|AAF22897.1|AC006932_14 T27G7.22 [Arabidopsis thaliana] gi|9802550|gb|AAF99752.1|AC003981_2 F22O13.2 [Arabidopsis thaliana] gi|2443357|dbj|BAA22427.1| SigB [Arabidopsis thaliana] gi|2597831|emb|CAA75584.1| sigma factor [Arabidopsis thaliana] gi|2879922|dbj|BAA24825.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana] gi|5478446|dbj|BAA82449.1| sigma factor SigB [Arabidopsis thaliana] gi|133778838|gb|ABO38759.1| At1g08540 [Arabidopsis thaliana] gi|332190182|gb|AEE28303.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana]

 Score =  520 bits (1338), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 299/465 (64%), Positives = 351/465 (75%), Gaps = 20/465 (4%)

Query: 1   MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
           +T++LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL TSDEAV+ 
Sbjct: 49  LTSMLDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVV 108

Query: 60  AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
           AA+AEAVALARAAVKVAKDA L  N +N+        ++SS     S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGI 162

Query: 120 IG-----DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTE 173
           +G     D+ IV        S ++ +    DLE   +E   L E+  S S+AVRS RQTE
Sbjct: 163 LGHLAVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTE 219

Query: 174 RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEM 233
           RKARR +  EK A+ + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE 
Sbjct: 220 RKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEH 279

Query: 234 QLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITS 293
           +LSAGIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI S
Sbjct: 280 ELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKS 339

Query: 294 NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS 353
           NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKS
Sbjct: 340 NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKS 399

Query: 354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK 413
           LSDQSR IRLPFHMVEATYRVKEARKQLYSE G+HP NEE+AEATGLSMKRL AVLLSPK
Sbjct: 400 LSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPK 459

Query: 414 APRSLDQKIGINQNLKPSVCFILNLADSLIIFFPPLFIIWFMSFD 458
            PRSLDQKIG+NQNLKPS      +AD   +    + I  FM  D
Sbjct: 460 PPRSLDQKIGMNQNLKPSEV----IADPEAVTSEDILIKEFMRQD 500

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509511|ref|XP_003523491.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  516 bits (1330), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 289/432 (66%), Positives = 342/432 (79%), Gaps = 15/432 (3%)

Query: 2   TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAA 60
           +T+L +EK +L +L+A S+    N  W Y  A       N  ++L+ E+L T++EAVI A
Sbjct: 47  STLLSLEK-KL-ALDAPSDP---NTSWPYIAAA------NFKSTLSAESLLTNEEAVIVA 95

Query: 61  ASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMW-AQLTERERASI 119
           A++EA+ALA+AA KVAKDAAL+V     A+ + K  +SS +D     W  Q+ E E    
Sbjct: 96  AASEALALAKAAAKVAKDAALLVKKKPPAEAEYKSHVSSKSDDLLLKWFKQMEEVEDG-- 153

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRT 179
           + +  +   A   E  +  P  + +DLEP+HEEL+ L+EQ+S SIAVRSRRQTERKA+R 
Sbjct: 154 VAEESMGAGAEIMEGVDVSPSEEESDLEPSHEELERLQEQLSDSIAVRSRRQTERKAKRV 213

Query: 180 RAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGI 239
           RA EKA  N  S K GS+SRRKR S+QEVDYSDPLRYLR TTS+SRLLT  EE++LSAGI
Sbjct: 214 RATEKATTNFTSFKPGSSSRRKRVSMQEVDYSDPLRYLRTTTSASRLLTPTEEIKLSAGI 273

Query: 240 QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 299
           QDLLKLE ++E L+ER G  PTFAQWAA AGVDQ+ LR+RLNYGI CKDKMI SNIRLVI
Sbjct: 274 QDLLKLEKIQEDLAERFGSQPTFAQWAAVAGVDQKTLRKRLNYGIFCKDKMIKSNIRLVI 333

Query: 300 SIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359
           SIAKNYQG+GMNLQDLVQEGCRGLV+GAEKFD +KGFKFSTYAHWWIKQAVRKSLSDQSR
Sbjct: 334 SIAKNYQGSGMNLQDLVQEGCRGLVKGAEKFDGTKGFKFSTYAHWWIKQAVRKSLSDQSR 393

Query: 360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLD 419
           TIRLPFHMVEATYRVKEARKQLYSENGR P++EEVAEATGLSMKRL+AVL++PKAPRSL+
Sbjct: 394 TIRLPFHMVEATYRVKEARKQLYSENGRQPDDEEVAEATGLSMKRLNAVLMTPKAPRSLE 453

Query: 420 QKIGINQNLKPS 431
           QKIGINQNLKPS
Sbjct: 454 QKIGINQNLKPS 465

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	460
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.926	0.744	0.585	3.5e-123
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.5	0.420	0.406	1.5e-42
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.595	0.479	0.341	2.2e-41
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.330	0.410	0.444	2.8e-36
TIGR_CMR|BA_4515	373	BA_4515 "RNA polymerase sigma-	0.297	0.367	0.467	2.1e-34
UNIPROTKB|O48655	519	rsigA "Plastid RNA polymerase	0.443	0.393	0.388	4.6e-34
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.467	0.407	0.380	1.5e-33
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.302	0.240	0.446	1.9e-33
TAIR|locus:2084420	571	SIGC "AT3G53920" [Arabidopsis	0.423	0.341	0.346	2.1e-33
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.328	0.467	0.430	3.7e-32

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

 Score = 1211 (431.4 bits), Expect = 3.5e-123, P = 3.5e-123
 Identities = 254/434 (58%), Positives = 297/434 (68%)

Query:     1 MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTXXXXXXXX 60
             +T++LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL         
Sbjct:    49 LTSMLDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVV 108

Query:    61 XXXXXXXXXXXXXXXXXXXXXMVNHHNXXXXXXXXXXXXXXDTNTSMWAQLTERERASII 120
                                  +  + N                  S W Q TE+ERA I+
Sbjct:   109 AAAAEAVALARAAVKVAKDATLFKNSNNTNLLTSSTAD-----KRSKWDQFTEKERAGIL 163

Query:   121 GDSVIVEAAPEEEYSEQQPLNKSA--DLEPT-HEELKLLEEQVSQSIAVRSXXXXXXXXX 177
             G   + +     +       NK +  DLE    EE++LLEEQ S S+AVRS         
Sbjct:   164 GHLAVSDNGIVSDKITASASNKESIGDLESEKQEEVELLEEQPSVSLAVRSTRQTERKAR 223

Query:   178 XXXXXXXXXXNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 237
                        + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSA
Sbjct:   224 RAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSA 283

Query:   238 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 297
             GIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRL
Sbjct:   284 GIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRL 343

Query:   298 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 357
             VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKSLSDQ
Sbjct:   344 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQ 403

Query:   358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRS 417
             SR IRLPFHMVEATYRVKEARKQLYSE G+HP NEE+AEATGLSMKRL AVLLSPK PRS
Sbjct:   404 SRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRS 463

Query:   418 LDQKIGINQNLKPS 431
             LDQKIG+NQNLKPS
Sbjct:   464 LDQKIGMNQNLKPS 477

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

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

 Score = 450 (163.5 bits), Expect = 1.5e-42, P = 1.5e-42
 Identities = 94/231 (40%), Positives = 140/231 (60%)

Query:   197 TSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERC 256
             TS +K+   Q  D  D L+       + +LLTA EE +L + IQ LLKLE ++  L  + 
Sbjct:   219 TSAKKKYK-QGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQN 277

Query:   257 GGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLV 316
             G  PT  +WA A G+    L+  ++ G   ++K+IT+N+RLV+ IAK YQ  G+N QDL+
Sbjct:   278 GCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLL 337

Query:   317 QEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKE 376
             QEG  GL++  EKF    G +F+TYA+WWI+Q++RKS+   SRTIRLP ++     +V E
Sbjct:   338 QEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSE 397

Query:   377 ARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN 427
             ARK    E    P+ EE+A   G+S ++L  +L + + P S+ Q I  +Q+
Sbjct:   398 ARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQD 448

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 = 439 (159.6 bits), Expect = 2.2e-41, P = 2.2e-41
 Identities = 96/281 (34%), Positives = 147/281 (52%)

Query:   143 SADLEPTHEELKLLEEQVSQSIAVRSXXXXXXXXXXXXXXXXXXXNVMSVKSGSTSRRKR 202
             S D   ++EEL     Q    + VRS                   +V      S  + K 
Sbjct:   194 SVDSSKSNEEL-----QSKGQVFVRSTRLLERRSKRRYAPRASIADVSCSADNSKKKEKS 248

Query:   203 PSVQEV-DYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPT 261
                  V +  +P +       ++  LTA EE  L + IQ L+K+E     L  +CG  PT
Sbjct:   249 KKYGRVLEPDEPFKLFLRDRETTEFLTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPT 308

Query:   262 FAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCR 321
              A+WA A G+  +EL+  +  G  C++KM  SN RLVI +A+ Y+G G+++QDLVQ+GC 
Sbjct:   309 LAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCS 368

Query:   322 GLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 381
             GL++  EKF+ SKG +F TYA+WWI+Q+++KS+   SR IRLP  +     +V +AR + 
Sbjct:   369 GLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMEC 428

Query:   382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKI 422
               E G  P N  VA   G+++++L  +    + PRS+   +
Sbjct:   429 IME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHV 468

GO:0009536 "plastid" evidence=RCA

TIGR_CMR|CHY_0455 CHY_0455 "RNA polymerase sigma factor RpoD" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 342 (125.4 bits), Expect = 2.8e-36, Sum P(3) = 2.8e-36
 Identities = 68/153 (44%), Positives = 99/153 (64%)

Query:   272 DQRELRRRLNYGIL-CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 330
             ++ EL +R   G    K K+  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKF
Sbjct:   118 EEIELAKRKEEGDEEAKRKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKF 177

Query:   331 DASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN 390
             D  KG+KFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++    + L  E GR P 
Sbjct:   178 DYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPT 237

Query:   391 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIG 423
              EE+A+  G+S  ++  ++   + P SL+  IG
Sbjct:   238 PEEIAKEMGISEDKVREIMKIAQEPVSLETPIG 270

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|BA_4515 BA_4515 "RNA polymerase sigma-43 factor" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 343 (125.8 bits), Expect = 2.1e-34, Sum P(2) = 2.1e-34
 Identities = 64/137 (46%), Positives = 94/137 (68%)

Query:   287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346
             K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD  KGFKFSTYA WWI
Sbjct:   137 KRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWI 196

Query:   347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 406
             +QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P+ EE+ E   L+ +++ 
Sbjct:   197 RQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVR 256

Query:   407 AVLLSPKAPRSLDQKIG 423
              +L   + P SL+  IG
Sbjct:   257 EILKIAQEPVSLETPIG 273

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

GO:0016987 "sigma factor activity" evidence=ISS

UNIPROTKB|O48655 rsigA "Plastid RNA polymerase sigma factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 370 (135.3 bits), Expect = 4.6e-34, P = 4.6e-34
 Identities = 80/206 (38%), Positives = 123/206 (59%)

Query:   216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRE 275
             YLR T S   LLT  + + LS  I+D + L+  R  L E+ G  P++ Q A +  +   E
Sbjct:   207 YLRGTVSKE-LLTHKQVVHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPE 265

Query:   276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKG 335
             LR R++   L ++ +  SN+RLVISIA+ Y   G+ L DL+Q G  GL+RG EKFDAS+G
Sbjct:   266 LRSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRG 325

Query:   336 FKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVA 395
             F+ STY +WWI+Q V ++L++ S+T RLP ++ E    ++ A+ +L  + G  P  E +A
Sbjct:   326 FRISTYVYWWIRQGVSRALAENSKTFRLPTYLHERLIAIRGAKYEL-EDQGIAPTIENIA 384

Query:   396 EATGLSMKRLHAVLLSPKAPRSLDQK 421
              +  +S K++     +     SLDQ+
Sbjct:   385 GSLNISEKKVLNATEAVNKVLSLDQQ 410

GO:0009416 "response to light stimulus" evidence=IEP

UNIPROTKB|P0A602 rpoD "RNA polymerase sigma factor RpoD" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 365 (133.5 bits), Expect = 1.5e-33, P = 1.5e-33
 Identities = 86/226 (38%), Positives = 133/226 (58%)

Query:   199 RRKRPSVQEVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCG 257
             R+ R   +    +D +R YL+     + LL A EE++L+  I+  L    L   LSER  
Sbjct:   213 RQARKDAELTASADSVRAYLKQIGKVA-LLNAEEEVELAKRIEAGLYATQLMTELSERGE 271

Query:   258 GSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
               P  AQ        +R++      G   K+ ++ +N+RLV+S+AK Y G GM   DL+Q
Sbjct:   272 KLPA-AQ--------RRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQ 322

Query:   318 EGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEA 377
             EG  GL+R  EKFD +KG+KFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   
Sbjct:   323 EGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRI 382

Query:   378 RKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIG 423
             +++L  + GR P  EE+A+   ++ +++  +    + P SLDQ IG
Sbjct:   383 QRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIG 428

GO:0003677 "DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005618 "cell wall" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009405 "pathogenesis" evidence=IMP

GO:0009415 "response to water stimulus" evidence=IEP

GO:0016987 "sigma factor activity" evidence=IDA

GO:0040007 "growth" evidence=IMP

GO:0052572 "response to host immune response" evidence=IEP

TIGR_CMR|GSU_3089 GSU_3089 "RNA polymerase sigma factor RpoD" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 341 (125.1 bits), Expect = 1.9e-33, Sum P(2) = 1.9e-33
 Identities = 62/139 (44%), Positives = 94/139 (67%)

Query:   285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHW 344
             L K +++ +N+RLV+SIAK Y   G+   DL+QEG  GL++  +KF+  +G+KFSTYA W
Sbjct:   339 LAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATW 398

Query:   345 WIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKR 404
             WI+QA+ ++++DQ+RTIR+P HM+E   ++    +QL  E GR P+ EE+AE   L + +
Sbjct:   399 WIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMNLPLDK 458

Query:   405 LHAVLLSPKAPRSLDQKIG 423
             +  VL   K P SL+  IG
Sbjct:   459 VRKVLKIAKEPISLETPIG 477

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

GO:0016987 "sigma factor activity" evidence=ISS

TAIR|locus:2084420 SIGC "AT3G53920" [Arabidopsis thaliana (taxid:3702)]

 Score = 367 (134.2 bits), Expect = 2.1e-33, P = 2.1e-33
 Identities = 68/196 (34%), Positives = 128/196 (65%)

Query:   229 ANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288
             +  E ++S G++ +  +E +R  L E  G   + + WAAAAG++++ L R L+YG  C+D
Sbjct:   275 SRNETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRD 334

Query:   289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ 348
             +++ S   LV+ +A+NY+G G+  +DL+Q G  G+++GAE+FD ++G+KFSTY  +WI++
Sbjct:   335 ELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRK 394

Query:   349 AVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENG-RHPNNEEVAEATGLSMKRLHA 407
             ++   +S  +R + +P  ++     +++ARK L + +G ++  +EE+A+ TG S+K++ A
Sbjct:   395 SMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGIKYAADEEIAKLTGHSVKKIRA 454

Query:   408 VLLSPKAPRSLDQKIG 423
                  K   S+D+K+G
Sbjct:   455 ANQCLKVVGSIDKKVG 470

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;IMP

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

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0019685 "photosynthesis, dark reaction" evidence=NAS

GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA;TAS

GO:0071482 "cellular response to light stimulus" evidence=IEP

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 65/151 (43%), Positives = 102/151 (67%)

Query:   273 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA 332
             +R+L   +  G   +  ++ +N+RLV+S+AK Y G GM L DL+QEG  GL+R  EKFD 
Sbjct:    73 KRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 132

Query:   333 SKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNE 392
             +KGFKFSTYA WWI+QA+ + ++DQSRTIRLP H+VE   ++   +++++   GR   +E
Sbjct:   133 TKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDE 192

Query:   393 EVAEATGLSMKRLHAVLLSPKAPRSLDQKIG 423
             E+A  +G+ + +++ +L   + P SLD  +G
Sbjct:   193 ELAAESGIPIDKINDLLEHSRDPVSLDMPVG 223

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

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

GO:0016987 "sigma factor activity" evidence=IGI

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

GO:0040007 "growth" evidence=IMP

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

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O22056	SIGB_ARATH	No assigned EC number	0.6430	0.9673	0.7779	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_fgenesh4_pm.C_LG_XIII0293	hypothetical protein (568 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.29520003	annotation not avaliable (742 aa)					•		•		0.499
	fgenesh4_pm.C_LG_X000986	hypothetical protein (932 aa)							•		0.472
	gw1.XIV.2088.1	hypothetical protein (955 aa)			•	•			•		0.429
	estExt_fgenesh4_pg.C_13160002	hypothetical protein (165 aa)			•				•		0.415
	estExt_Genewise1_v1.C_LG_X3691	SubName- Full=Putative uncharacterized protein; (165 aa)			•				•		0.410
	grail3.3134000101	Predicted protein (100 aa)							•		0.406
	eugene3.00020721	hypothetical protein (1053 aa)			•						0.404

---

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	460
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	9e-70
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	6e-66
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	6e-57
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	1e-53
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	1e-51
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-46
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	3e-46
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	5e-45
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	1e-44
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	3e-40
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	7e-38
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	8e-36
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	1e-30
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	1e-18
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	4e-18
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	9e-18
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	4e-17
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	6e-17
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	3e-16
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	7e-16
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	9e-15
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	9e-15
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	4e-14
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	1e-13
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	5e-13
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	1e-12
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	2e-09
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	3e-09
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	1e-08
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	2e-08
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	2e-08
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	3e-08
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	3e-08
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	3e-08
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	4e-08
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	2e-06
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	7e-06
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	6e-05

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

 Score =  223 bits (570), Expect = 9e-70
 Identities = 96/216 (44%), Positives = 145/216 (67%), Gaps = 2/216 (0%)

Query: 212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAG 270
           D +R YL+       LLT  EE++L+  +Q ++ LE LRE L E+ G  P+  +WAAAAG
Sbjct: 1   DLVRLYLQ-EIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAG 59

Query: 271 VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 330
           + + ELR+RL  G   K+KMI +N+RLV+S+AK YQ  G+ L DL+QEG  GL R  EKF
Sbjct: 60  LSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKF 119

Query: 331 DASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN 390
           D ++G+KFSTYA+WWI+Q + +++++QSRTIRLP H+ E   ++K+ +++L  + GR P+
Sbjct: 120 DPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPS 179

Query: 391 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ 426
             E+AEA  L  +++  +L   + P SLD  +G  +
Sbjct: 180 EAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEE 215

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 =  215 bits (550), Expect = 6e-66
 Identities = 104/285 (36%), Positives = 150/285 (52%), Gaps = 11/285 (3%)

Query: 139 PLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTS 198
                 +L    E+ +        S                + A+  A            
Sbjct: 1   TPELEDELLLLEEDRQPAATDDLDSDEDEESSSENADELSEKEAKAKA-----------L 49

Query: 199 RRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGG 258
            R +   ++V   D +R         RLL  +EE++L+  I DLL+LE LRE      G 
Sbjct: 50  ARIKIGPKKVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGR 109

Query: 259 SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQE 318
            P+  +WA    +   + RRRL  G   K+KM+ SN+RLV+SIAK Y   G++ QDL+QE
Sbjct: 110 EPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQE 169

Query: 319 GCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEAR 378
           G  GL+R AEKFD  KG+KFSTYA WWI+QA+ ++++DQSRTIRLP H+ E   R+K+  
Sbjct: 170 GSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTT 229

Query: 379 KQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIG 423
           K L  E GR P  EE+AE+  +++++L  +  S + P SL+  IG
Sbjct: 230 KVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIG 274

Length = 373

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

 Score =  190 bits (485), Expect = 6e-57
 Identities = 93/218 (42%), Positives = 141/218 (64%), Gaps = 2/218 (0%)

Query: 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAA 269
           +D +R YLR       LLT  EE+     +Q L+ L+ +RE L+E  G  PT A+WA AA
Sbjct: 7   TDLVRTYLREIGRVP-LLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAA 65

Query: 270 GVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 329
            + + ELR  +  G   K KM+ +N+RLV+S+AK Y    ++L DL+QEG  G+ RG EK
Sbjct: 66  KLSEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEK 125

Query: 330 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 389
           FD +KG++FSTYA+WWI+QA+ ++++++SRTIRLP H+ E   ++K+A++QL  + GR  
Sbjct: 126 FDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAA 185

Query: 390 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN 427
              E+AE   L+ K++   L   + P SLD ++G NQ+
Sbjct: 186 TIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQD 223

Length = 317

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

 Score =  179 bits (456), Expect = 1e-53
 Identities = 64/137 (46%), Positives = 96/137 (70%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346
           K +++ SN+RLV+SIAK Y   G++  DL+QEG  GL++  EKFD  KG+KFSTYA WWI
Sbjct: 2   KKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWI 61

Query: 347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 406
           +QA+ ++++DQ+RTIR+P HMVE   ++ +A +QL  E GR P +EE+AE  G+  +++ 
Sbjct: 62  RQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVR 121

Query: 407 AVLLSPKAPRSLDQKIG 423
            +    + P SL+  IG
Sbjct: 122 EIKKIAQEPISLETPIG 138

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|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated

 Score =  176 bits (449), Expect = 1e-51
 Identities = 80/202 (39%), Positives = 127/202 (62%)

Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
           LLT  +E+     +Q ++ L   +E L+++ G  P+  +WA A  + + EL++ L  G  
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 345
            K KMI +N+RLV++IAK YQ   M   DL+QEG  GL RG EKFD ++G+KFSTYA+WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 346 IKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 405
           I+QA+ ++++ Q+RTIRLP H+ E   ++K+ +++L  + GR     E+A+   L   ++
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQI 211

Query: 406 HAVLLSPKAPRSLDQKIGINQN 427
              L   + P SLD ++G NQ+
Sbjct: 212 REYLSMARQPISLDVRVGDNQD 233

Length = 327

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

 Score =  167 bits (425), Expect = 2e-46
 Identities = 102/393 (25%), Positives = 173/393 (44%), Gaps = 56/393 (14%)

Query: 44  TSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADT 103
           + +  +T  + E+ I     +  A A AA   AK         +S K + K A+    D 
Sbjct: 60  SGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLK-DELDSSKKAEKKNALDKDDDL 118

Query: 104 NTSMWAQLTE--RERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVS 161
           N      +     +      D  + +   +++  ++       D +   E+ +  E +  
Sbjct: 119 NYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKEL 178

Query: 162 QSIAVRSRRQTE-------RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPL 214
           + ++       +       R+AR+       A                         DP+
Sbjct: 179 EKLSDDDDFVWDEDDSEALRQARKDAKLTATA-------------------------DPV 213

Query: 215 R-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 273
           + YL+      +LL A EE++L+  I+      GL        G               +
Sbjct: 214 KAYLK-QIGKVKLLNAEEEVELAKRIE-----AGLYAEELLAEGEKLDPEL--------R 259

Query: 274 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 333
           R+L+     G   K+ ++ +N+RLV+S+AK Y   G++  DL+QEG  GL++  EKFD +
Sbjct: 260 RDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYT 319

Query: 334 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 393
           KG+KFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++    ++L  E GR P  EE
Sbjct: 320 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEE 379

Query: 394 VAEATGLSMKRLHAVLLSPK---APRSLDQKIG 423
           +A+  G + ++   V    K    P SLD+ IG
Sbjct: 380 LAKEMGFTPEK---VREIQKYNREPISLDKTIG 409

Length = 509

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

 Score =  163 bits (414), Expect = 3e-46
 Identities = 84/219 (38%), Positives = 120/219 (54%), Gaps = 20/219 (9%)

Query: 225 RLLTANEEMQLSAGIQDLLKLEGLREVL-SERCGGSPTFAQWAAAAGVDQ---------- 273
            LL    E++L+  ++D   L  L E L   + G  P+      A  +            
Sbjct: 22  PLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPL 81

Query: 274 ------RELRRRLNYGIL---CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLV 324
                 + L RRL  G      K K++ SN+RLV+SIAK Y G G+   DL+QEG  GL+
Sbjct: 82  LTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLM 141

Query: 325 RGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSE 384
           +  EKFD  KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P H VE   +++  +++L  E
Sbjct: 142 KAVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQE 201

Query: 385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIG 423
            GR P  EE+AE  G+S  ++  +L     P SLD  IG
Sbjct: 202 LGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIG 240

Length = 342

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

 Score =  159 bits (404), Expect = 5e-45
 Identities = 78/202 (38%), Positives = 121/202 (59%), Gaps = 21/202 (10%)

Query: 226 LLTANEEMQLS----AGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281
           LLTA +E++L+    AG+     LE  + +   R                 +R+L   + 
Sbjct: 40  LLTAADEVELAKRIEAGLYAEHLLETRKRLSEAR-----------------KRDLAAVVR 82

Query: 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTY 341
            G   +  ++ +N+RLV+S+AK Y G GM L DL+QEG  GL+R  EKFD +KGFKFSTY
Sbjct: 83  DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTY 142

Query: 342 AHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLS 401
           A WWI+QA+ + ++DQSRTIRLP H+VE   ++   +++L+ + GR   +EE+AE +G+ 
Sbjct: 143 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIP 202

Query: 402 MKRLHAVLLSPKAPRSLDQKIG 423
            +++  +L   + P SLD  +G
Sbjct: 203 EEKIADLLEHSRDPVSLDMPVG 224

Length = 324

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

 Score =  160 bits (407), Expect = 1e-44
 Identities = 83/233 (35%), Positives = 132/233 (56%), Gaps = 32/233 (13%)

Query: 215 RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQR 274
           RY++       ++ AN   +    I+  L+L  +RE L+   G  P+  +WA  A +   
Sbjct: 89  RYMKL------IVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADISLA 142

Query: 275 ELRRRLNY----------------------GILCKDKMITSNIRLVISIAKNYQGAGMNL 312
           +L+  L                        G+  K+ MI +N+RLV+S+AK YQ  G+ L
Sbjct: 143 DLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLEL 202

Query: 313 QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY 372
            DLVQEG  GL R  EKFD +KG++FSTYA+WWI+Q + ++++ QSRTIRLP H+ E   
Sbjct: 203 LDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLN 262

Query: 373 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR--SLDQKIG 423
           ++K+A++++  E GR P  E++A+   ++  ++  VLL  + PR  SL+ K+G
Sbjct: 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL--RVPRSVSLETKVG 313

Length = 415

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

 Score =  147 bits (374), Expect = 3e-40
 Identities = 65/137 (47%), Positives = 93/137 (67%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346
           K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD  KGFKFSTYA WWI
Sbjct: 131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWI 190

Query: 347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 406
           +QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  E GR P  EE+AE   +  +++ 
Sbjct: 191 RQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVR 250

Query: 407 AVLLSPKAPRSLDQKIG 423
            +L   + P SL+  IG
Sbjct: 251 EILKIAQEPVSLETPIG 267

Length = 367

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

 Score =  139 bits (351), Expect = 7e-38
 Identities = 58/139 (41%), Positives = 88/139 (63%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346
           +  MI SN+RLV+SIAK+Y   G+ L DL++EG  GL+   EKFD  +GF+FSTYA WWI
Sbjct: 48  RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWI 107

Query: 347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 406
           +Q + +++ +Q+RTIRLP H+++       A +QL  + GR P+ EE+AE     ++ + 
Sbjct: 108 RQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVS 167

Query: 407 AVLLSPKAPRSLDQKIGIN 425
            VL   +   SLD  +  +
Sbjct: 168 RVLALNERITSLDAPLDDD 186

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

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

 Score =  139 bits (353), Expect = 8e-36
 Identities = 66/140 (47%), Positives = 94/140 (67%), Gaps = 6/140 (4%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQ--DLVQEGCRGLVRGAEKFDASKGFKFSTYAHW 344
           K +M+ +N+RLVISIAK Y   G  LQ  DL+QEG  GL++  +KF+  +G+KFSTYA W
Sbjct: 382 KKEMVEANLRLVISIAKKYTNRG--LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 439

Query: 345 WIKQAVRKSLSDQSRTIRLPFHMVEATYR-VKEARKQLYSENGRHPNNEEVAEATGLSMK 403
           WI+QA+ +S++DQ+RTIR+P HM+E   +  + +R Q+  E GR P  EE+AE  G+   
Sbjct: 440 WIRQAITRSIADQARTIRIPVHMIETINKLNRISR-QMLQEIGREPTPEELAERLGMPED 498

Query: 404 RLHAVLLSPKAPRSLDQKIG 423
           ++  VL   K P SL+  IG
Sbjct: 499 KVRKVLKIAKEPISLETPIG 518

Length = 619

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

 Score =  120 bits (303), Expect = 1e-30
 Identities = 51/111 (45%), Positives = 74/111 (66%)

Query: 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ 348
           +MI SN+RLV+ IAK Y   G+ L DL++EG  GL+R  EKFD  +GF+FSTYA WWI+Q
Sbjct: 90  RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 149

Query: 349 AVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG 399
            + +++ +Q+RTIRLP H+V+       A ++L  +    P+ EE+AE   
Sbjct: 150 TIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLD 200

Length = 325

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

 Score = 79.9 bits (198), Expect = 1e-18
 Identities = 29/71 (40%), Positives = 44/71 (61%)

Query: 290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349
           ++   + LV S+A+ Y G G + +DLVQEG  GL+R  E+FD  +G  FST+ +  I+ A
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 350 VRKSLSDQSRT 360
           +  +L  Q RT
Sbjct: 61  IIDALRKQRRT 71

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

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

 Score = 83.3 bits (206), Expect = 4e-18
 Identities = 49/152 (32%), Positives = 82/152 (53%), Gaps = 2/152 (1%)

Query: 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 330
           + REL  R+  G    ++K+I  N+RLV+S+ + +   G  + DL Q GC GL++  + F
Sbjct: 20  EMRELFIRMQSGDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNF 79

Query: 331 DASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN 390
           D S+  KFSTYA   I   +R+ L D +  IR+   + +  Y+  + R +L SEN + P 
Sbjct: 80  DLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKLISENSKEPT 138

Query: 391 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKI 422
             E+A+   +  + +   L + + P SL + I
Sbjct: 139 VSEIAKELKVPQEEVVFALDAIQDPVSLFEPI 170

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

 Score = 81.9 bits (203), Expect = 9e-18
 Identities = 46/138 (33%), Positives = 75/138 (54%), Gaps = 2/138 (1%)

Query: 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347
           +K++  N+ LV SIA+ ++  G   +DLVQ G  GLV+  ++FD S G KFST+A   I 
Sbjct: 6   EKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIM 65

Query: 348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHA 407
             +++   D +  +R+P  + E   ++ +A ++L    GR P   E+AE  G+S + +  
Sbjct: 66  GEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVVE 125

Query: 408 VLLSPKA--PRSLDQKIG 423
            L +  A    SLD  I 
Sbjct: 126 ALEAGNAYQALSLDASIE 143

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

 Score = 80.1 bits (198), Expect = 4e-17
 Identities = 51/163 (31%), Positives = 82/163 (50%), Gaps = 7/163 (4%)

Query: 266 AAAAGVDQRELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAG-MNLQDLVQEGCR 321
            A   + + E  + L Y   G     ++I   + LV SIA+ ++  G     DL+Q G  
Sbjct: 1   NAPQPLSKEEEEKLLEYYAEGDEEARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMI 60

Query: 322 GLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 381
           GL++  E++D SKG KFSTYA   I+  +   L     ++++P  + E   R++EA  +L
Sbjct: 61  GLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDEL 119

Query: 382 YSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKI 422
             E GR P +EE+AE  G+  +     LL+       SLD+ +
Sbjct: 120 EQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDV 162

Length = 247

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

 Score = 80.0 bits (198), Expect = 6e-17
 Identities = 49/147 (33%), Positives = 82/147 (55%), Gaps = 2/147 (1%)

Query: 273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 331
            REL  R+  G    ++K+I  N+RLV+S+ + +   G N+ DL Q GC GL++  + FD
Sbjct: 24  MRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFD 83

Query: 332 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNN 391
            S+  KFSTYA   I   +R+ L D +  IR+   + +  Y+  + R++L +EN + P  
Sbjct: 84  LSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTV 142

Query: 392 EEVAEATGLSMKRLHAVLLSPKAPRSL 418
           EE+A+   +  + +   L + + P SL
Sbjct: 143 EEIAKELEVPREEVVFALDAIQDPVSL 169

Length = 258

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

 Score = 78.0 bits (193), Expect = 3e-16
 Identities = 41/115 (35%), Positives = 68/115 (59%), Gaps = 2/115 (1%)

Query: 311 NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA 370
             +DLVQ G  GL+R  E+FD SKG  FS++A  +I+  ++  L D+S T+R+P    E 
Sbjct: 52  PYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQEL 111

Query: 371 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIG 423
             + K+ R++L  E GR P ++E+A+A  +S++    + L+   + P SLD  + 
Sbjct: 112 QRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVN 166

Length = 256

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

 Score = 76.3 bits (188), Expect = 7e-16
 Identities = 50/135 (37%), Positives = 76/135 (56%), Gaps = 1/135 (0%)

Query: 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347
           DK+I  N+RLV SI K +   G   +DL Q GC GLV+  +KFD S   KFSTYA   I 
Sbjct: 14  DKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIM 73

Query: 348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHA 407
             +++ L D    I++   + E   +++  +++L  E GR P   E+AEA G+S + +  
Sbjct: 74  GEIKRFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVM 132

Query: 408 VLLSPKAPRSLDQKI 422
            L S ++P+SL   +
Sbjct: 133 ALESARSPQSLYDTV 147

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|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH

 Score = 73.8 bits (182), Expect = 9e-15
 Identities = 26/77 (33%), Positives = 47/77 (61%), Gaps = 2/77 (2%)

Query: 273 QRELRRRLNYG--ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 330
           + +L +RL     +    K++ S++R V+ IA+ Y+G G+   DL+QEG  GL++  ++F
Sbjct: 21  EYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

Query: 331 DASKGFKFSTYAHWWIK 347
           D  +G +  ++A  WIK
Sbjct: 81  DPERGVRLVSFAVHWIK 97

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

 Score = 73.5 bits (181), Expect = 9e-15
 Identities = 41/135 (30%), Positives = 75/135 (55%), Gaps = 1/135 (0%)

Query: 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347
           D ++  N+RLV S+ + +   G    DL Q GC GL++  +KFD S   KFSTYA   I 
Sbjct: 35  DTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMII 94

Query: 348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHA 407
             +++ L D   T+++   + E   ++++ + +L  E GR P  EE+AE  G++ + +  
Sbjct: 95  GEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVL 153

Query: 408 VLLSPKAPRSLDQKI 422
              + ++P+S+ + +
Sbjct: 154 AQEASRSPQSIHETV 168

Length = 252

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

 Score = 72.1 bits (178), Expect = 4e-14
 Identities = 22/59 (37%), Positives = 39/59 (66%)

Query: 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347
           +++ S++R V+ IA+ Y+G G+   DL+QEG  GL++  ++FD   G +  ++A  WIK
Sbjct: 52  QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIK 110

Length = 284

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

 Score = 70.8 bits (174), Expect = 1e-13
 Identities = 25/59 (42%), Positives = 43/59 (72%)

Query: 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347
           ++I++++RLVIS+A  ++  G+ + DL+QEG  GL+  A +F+  +  +FSTYA WWI+
Sbjct: 44  RIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIR 102

Length = 289

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

 Score = 68.1 bits (167), Expect = 5e-13
 Identities = 35/106 (33%), Positives = 54/106 (50%), Gaps = 11/106 (10%)

Query: 308 AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV----RKSLSDQSRTIRL 363
           + + L DL+Q G  GL+   E++D S+G KF TYA   I+ A+    R+ L    R++R 
Sbjct: 22  SSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRR-LDWVPRSLRQ 80

Query: 364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 409
               +E       A ++L +  GR P  EE+AE  G+ +K     L
Sbjct: 81  KARKLE------RAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120

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|146934 pfam04539, Sigma70_r3, Sigma-70 region 3

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 21/59 (35%), Positives = 36/59 (61%)

Query: 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN 427
           E   ++K A+++L  E GR P  EE+AE  G+S +++  VL + + P SLD  +G  ++
Sbjct: 1   ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEED 59

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

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

 Score = 57.6 bits (140), Expect = 2e-09
 Identities = 23/56 (41%), Positives = 35/56 (62%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
           ++ +I  N+RLV  I K ++  G ++ DL+  G  GL++  E FDA KG K +TYA
Sbjct: 51  RNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA 106

Length = 233

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

 Score = 57.4 bits (139), Expect = 3e-09
 Identities = 33/101 (32%), Positives = 53/101 (52%), Gaps = 9/101 (8%)

Query: 313 QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV---RKSLSDQSRTIRLPFHMVE 369
            DLV  G  GL+   EKFD  +  KF TYA   I+ A+    +S+    R++R     +E
Sbjct: 62  DDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRSVRQKARQIE 121

Query: 370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410
               + EAR       GR P++EE+A+  G+S++  +++L 
Sbjct: 122 RAIAMLEARL------GRTPSDEEIADELGISLEEYNSLLS 156

Length = 268

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

 Score = 55.6 bits (134), Expect = 1e-08
 Identities = 40/139 (28%), Positives = 65/139 (46%), Gaps = 2/139 (1%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346
           +D+++T  + L   IA+ + G G    DLVQ    GLV    +FD   G  F ++A   I
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTI 101

Query: 347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 406
              VR+   D S ++++P  + E   R+  A  +L    GR P   E+A   G+  + + 
Sbjct: 102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVV 161

Query: 407 AVLLSPKA--PRSLDQKIG 423
             L++  A    S+D   G
Sbjct: 162 EGLVAGSAYNTLSIDSGGG 180

Length = 264

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

 Score = 54.9 bits (132), Expect = 2e-08
 Identities = 35/115 (30%), Positives = 59/115 (51%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346
           ++K++     LV SIA  Y   G   +DLVQ G  GL+    ++D S G  F  +A   I
Sbjct: 31  QEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTI 90

Query: 347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLS 401
              +++ L D++ ++ +P  + E   ++K+A  +L     R P   E+A+  GLS
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLS 145

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

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

 Score = 54.1 bits (131), Expect = 2e-08
 Identities = 37/111 (33%), Positives = 56/111 (50%), Gaps = 17/111 (15%)

Query: 307 GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ-------SR 359
            A ++L DL+Q G  GL+  A ++D  +G  F TYA     Q +R ++ D+        R
Sbjct: 33  PASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYA----GQRIRGAMLDELRSLDWVPR 88

Query: 360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL 410
           ++R     V       +A +QL  E GR P + EVAE  GLS++    +LL
Sbjct: 89  SVRRNAREVA------QAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLL 133

Length = 236

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

 Score = 54.3 bits (131), Expect = 3e-08
 Identities = 32/97 (32%), Positives = 48/97 (49%), Gaps = 3/97 (3%)

Query: 313 QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY 372
            DL   G  GL    EKFD S+  KF TYA + I+ A+   L  +     LP  M E T 
Sbjct: 53  DDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED---WLPRSMREKTK 109

Query: 373 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 409
           +V+ A ++L     R+   +EVA   G++ + + A +
Sbjct: 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM 146

Length = 251

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

 Score = 52.7 bits (127), Expect = 3e-08
 Identities = 28/144 (19%), Positives = 52/144 (36%), Gaps = 10/144 (6%)

Query: 288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 347
           +++    + LV   A+ Y G   + +DLVQE    L+   ++FD      F  +     +
Sbjct: 4   EELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIAR 61

Query: 348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA-TGLSMKRLH 406
             +   L  + R  R    + E         ++L  E       E + EA   L  +   
Sbjct: 62  NLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEE----EREALREALEKLPERERE 117

Query: 407 AVLLSPKAPRSLDQ---KIGINQN 427
            ++L      S  +    +GI+  
Sbjct: 118 VLVLRYLEGLSYKEIAEILGISVG 141

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|131882 TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor

 Score = 54.1 bits (130), Expect = 3e-08
 Identities = 28/86 (32%), Positives = 47/86 (54%), Gaps = 1/86 (1%)

Query: 276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASK 334
           L ++L  G    K  +I  N+RLV+ IA+ ++  G+ ++DLV  G  GL++    F+ SK
Sbjct: 42  LLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSK 101

Query: 335 GFKFSTYAHWWIKQAVRKSLSDQSRT 360
             K +TYA   I+  +   L   ++T
Sbjct: 102 KIKLATYASRCIENEILMYLRRNNKT 127

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|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor

 Score = 53.6 bits (129), Expect = 4e-08
 Identities = 20/58 (34%), Positives = 33/58 (56%)

Query: 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
             ++ +I  N+RLV  I K +   G ++ DL+  G  GL++  + FD  KG + +TYA
Sbjct: 48  EARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYA 105

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

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

 Score = 48.9 bits (117), Expect = 2e-06
 Identities = 32/105 (30%), Positives = 56/105 (53%)

Query: 297 LVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 356
           LV S+A  Y     + +DLVQ G  GL+    ++D S G  F  +A   I   +++ L D
Sbjct: 41  LVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRD 100

Query: 357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLS 401
           ++ ++ +P  + E   ++K+A  +L +E  R P   E+A+  G+S
Sbjct: 101 KTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVS 145

Length = 257

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

 Score = 46.8 bits (112), Expect = 7e-06
 Identities = 20/56 (35%), Positives = 35/56 (62%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
           +  +I  N+RLV+ IA+ ++  G+N++DL+  G  GL++    F+  K  K +TYA
Sbjct: 54  RSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109

Length = 234

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

 Score = 44.2 bits (104), Expect = 6e-05
 Identities = 36/131 (27%), Positives = 59/131 (45%), Gaps = 8/131 (6%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGM----NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
           +D +I   + LV ++A     +GM      +DL   G  GLVR  E+FD  K  +F  YA
Sbjct: 25  RDVLIEFYLPLVKNVAHRL-ISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYA 83

Query: 343 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM 402
            + IK A+   L  Q     +P  + +   ++ +A   L    G+ P + E+ E   +S 
Sbjct: 84  LFLIKAAIIDDLRKQD---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQ 140

Query: 403 KRLHAVLLSPK 413
           + L     S +
Sbjct: 141 QELSGWFSSAR 151

Length = 257

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	460
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; 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
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	99.97
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.97
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.97
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	99.97
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.96
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	99.96
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	99.96
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	99.96
PRK08215	258	sporulation sigma factor SigG; Reviewed	99.94
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	99.93
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	99.93
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	99.93
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	99.92
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	99.92
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	99.91
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	99.91
PRK05572	252	sporulation sigma factor SigF; Validated	99.9
PRK07670	251	RNA polymerase sigma factor SigD; Validated	99.88
PRK08583	257	RNA polymerase sigma factor SigB; Validated	99.88
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	99.88
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	99.87
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	99.83
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.81
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.72
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.72
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.71
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.68
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.66
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.66
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.64
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.64
PRK12513	194	RNA polymerase sigma factor; Provisional	99.63
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.62
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.61
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.6
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.6
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.6
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.6
PRK12514	179	RNA polymerase sigma factor; Provisional	99.6
PRK12537	182	RNA polymerase sigma factor; Provisional	99.59
PRK12524	196	RNA polymerase sigma factor; Provisional	99.59
PRK11922	231	RNA polymerase sigma factor; Provisional	99.59
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.58
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.58
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.58
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.58
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.57
PRK12538	233	RNA polymerase sigma factor; Provisional	99.56
PRK12534	187	RNA polymerase sigma factor; Provisional	99.56
PRK12531	194	RNA polymerase sigma factor; Provisional	99.56
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.56
PRK12519	194	RNA polymerase sigma factor; Provisional	99.56
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.55
PRK12526	206	RNA polymerase sigma factor; Provisional	99.54
PRK12536	181	RNA polymerase sigma factor; Provisional	99.53
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.53
PRK12542	185	RNA polymerase sigma factor; Provisional	99.52
PRK12539	184	RNA polymerase sigma factor; Provisional	99.52
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.51
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.51
PRK12515	189	RNA polymerase sigma factor; Provisional	99.51
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.5
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.5
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.49
PRK12522	173	RNA polymerase sigma factor; Provisional	99.48
PRK12512	184	RNA polymerase sigma factor; Provisional	99.48
PRK12520	191	RNA polymerase sigma factor; Provisional	99.48
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.47
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.47
PRK11924	179	RNA polymerase sigma factor; Provisional	99.47
PRK12543	179	RNA polymerase sigma factor; Provisional	99.46
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.46
PRK12516	187	RNA polymerase sigma factor; Provisional	99.46
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.45
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.44
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.42
PRK12518	175	RNA polymerase sigma factor; Provisional	99.42
PRK12547	164	RNA polymerase sigma factor; Provisional	99.42
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.41
PRK12535	196	RNA polymerase sigma factor; Provisional	99.41
PRK12529	178	RNA polymerase sigma factor; Provisional	99.41
PRK12533	216	RNA polymerase sigma factor; Provisional	99.41
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.4
PRK12541	161	RNA polymerase sigma factor; Provisional	99.4
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.39
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.38
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.38
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.37
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.36
PRK12540	182	RNA polymerase sigma factor; Provisional	99.36
PRK12528	161	RNA polymerase sigma factor; Provisional	99.36
PRK12532	195	RNA polymerase sigma factor; Provisional	99.35
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.35
PRK12545	201	RNA polymerase sigma factor; Provisional	99.34
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.33
PRK12530	189	RNA polymerase sigma factor; Provisional	99.32
PRK12517	188	RNA polymerase sigma factor; Provisional	99.32
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.32
PRK12544	206	RNA polymerase sigma factor; Provisional	99.31
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.31
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.31
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.3
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.3
PRK12546	188	RNA polymerase sigma factor; Provisional	99.29
PRK12511	182	RNA polymerase sigma factor; Provisional	99.27
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.24
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.2
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.2
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.18
PRK12525	168	RNA polymerase sigma factor; Provisional	99.18
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.09
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.04
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.03
PRK09191	261	two-component response regulator; Provisional	99.02
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	98.99
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	98.98
PRK09047	161	RNA polymerase factor sigma-70; Validated	98.91
PF07638	185	Sigma70_ECF: ECF sigma factor	98.4
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.07
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	97.77
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	96.3
PRK07670	251	RNA polymerase sigma factor SigD; Validated	96.03
PRK05901	509	RNA polymerase sigma factor; Provisional	95.86
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	95.44
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	95.37
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	95.33
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	95.17
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	95.12
PRK07598	415	RNA polymerase sigma factor SigC; Validated	95.03
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	94.96
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	94.85
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	94.84
PRK05949	327	RNA polymerase sigma factor; Validated	94.81
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	94.78
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	94.58
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	94.5
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	94.32
PRK07405	317	RNA polymerase sigma factor SigD; Validated	94.31
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	93.88
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	93.56
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	93.22
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	93.22
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	92.7
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	92.49
PRK08215	258	sporulation sigma factor SigG; Reviewed	91.56
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	91.2
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	91.18
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	90.86
PRK05572	252	sporulation sigma factor SigF; Validated	90.41
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	90.36
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	90.25
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	89.17
PHA02547	179	55 RNA polymerase sigma factor; Provisional	88.68
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	88.38
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	82.15
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	80.27
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	80.23

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=5.4e-47  Score=393.87  Aligned_cols=230  Identities=37%  Similarity=0.651  Sum_probs=217.3

Q ss_pred             CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH--------------------HHhHHHHHhhhcCCCCcHHHHHH
Q 012567          209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAA  267 (460)
Q Consensus       209 ~~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~--------------------le~~~~~L~~~~g~~pt~~ewA~  267 (460)
                      .++|+++ ||++| |++||||++||++|+++||.++.                    |++++..|.+++|++||..|||.
T Consensus        57 ~~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~  135 (415)
T PRK07598         57 RSTDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAK  135 (415)
T ss_pred             CCCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            3479999 99999 99999999999999999999999                    99999999999999999999995


Q ss_pred             HhC----------------------CCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHH
Q 012567          268 AAG----------------------VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR  325 (460)
Q Consensus       268 a~g----------------------~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLir  325 (460)
                      ++|                      ++..+|+..++.|..|+++||.+|+++|+++|++|.++|++++||+|||++|||+
T Consensus       136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~r  215 (415)
T PRK07598        136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER  215 (415)
T ss_pred             HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence            555                      5566666777889999999999999999999999999999999999999999999


Q ss_pred             HHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHH
Q 012567          326 GAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL  405 (460)
Q Consensus       326 AiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~V  405 (460)
                      |+++|||.+|++|+||++||||++|.++++++++++++|.++.+.+++++++...|..++|+.|+..|||+.|||++++|
T Consensus       216 avekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~v  295 (415)
T PRK07598        216 AVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQV  295 (415)
T ss_pred             HHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCCcccccccccCCCCCcccccccCCC
Q 012567          406 HAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLA  439 (460)
Q Consensus       406 k~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~  439 (460)
                      +.++..++.++|||.+++++++.++.|+++++..
T Consensus       296 r~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~~~  329 (415)
T PRK07598        296 REVLLRVPRSVSLETKVGKDKDTELGDLLETDDI  329 (415)
T ss_pred             HHHHHHccCCcccccccCCCccccHHHhccCCCC
Confidence            9999999999999999998888889998876543

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.8e-44  Score=371.92  Aligned_cols=229  Identities=43%  Similarity=0.721  Sum_probs=221.6

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHH
Q 012567          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (460)
Q Consensus       210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e  288 (460)
                      ..|++. ||+++ +++|+||+|||++|+++|++++.+++++.+|++.+|++|+..+||.++|++..+|..++..|..|++
T Consensus        61 ~~d~l~~Yl~~i-~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~  139 (373)
T PRK07406         61 TEDSIRVYLQEI-GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE  139 (373)
T ss_pred             CCCHHHHHHHHh-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence            368899 99999 9999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH
Q 012567          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (460)
Q Consensus       289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~  368 (460)
                      .||..|+++|+++|++|.++|.+++||+|||++|||+++++|||.+|++|+|||+||||++|.++|+++++++|+|.++.
T Consensus       140 ~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~  219 (373)
T PRK07406        140 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY  219 (373)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCC
Q 012567          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLA  439 (460)
Q Consensus       369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~  439 (460)
                      +.+++++++...|...+|+.||.+|||+.||+++++|..++..+...+|||.+++++++.++.|+++|+..
T Consensus       220 ~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~~  290 (373)
T PRK07406        220 ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGE  290 (373)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCCC
Confidence            99999999999999999999999999999999999999999888889999999988878889999987643

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

Probab=100.00  E-value=5.7e-44  Score=358.60  Aligned_cols=226  Identities=42%  Similarity=0.727  Sum_probs=217.3

Q ss_pred             CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHH
Q 012567          212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM  290 (460)
Q Consensus       212 d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~L  290 (460)
                      |++. ||+++ +++|+||+|||.+|+++++.++.+++++..|+++.|++||..+||+++|++..+|+..++.|..|++.|
T Consensus         1 ~~~~~yl~~~-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L   79 (298)
T TIGR02997         1 DLVRLYLQEI-GRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM   79 (298)
T ss_pred             CcHHHHHHHc-cccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence            4678 99999 999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHH
Q 012567          291 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA  370 (460)
Q Consensus       291 I~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~  370 (460)
                      |.+|+++|+++|++|.++|.+++||+||||+|||+|+++|||.+|++|+||++||||++|.+++.++++++|+|.++...
T Consensus        80 v~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~  159 (298)
T TIGR02997        80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEK  159 (298)
T ss_pred             HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCC
Q 012567          371 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNL  438 (460)
Q Consensus       371 i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~  438 (460)
                      +++++++...+...+|+.||.+|||+.||+++++|..++......+|||.+++++++.++.++++|+.
T Consensus       160 ~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~  227 (298)
T TIGR02997       160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDG  227 (298)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCCC
Confidence            99999999999999999999999999999999999999998889999999998776677888887743

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=1e-43  Score=361.34  Aligned_cols=228  Identities=37%  Similarity=0.647  Sum_probs=221.3

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHH
Q 012567          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (460)
Q Consensus       210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e  288 (460)
                      .+|++. ||+++ +++|+||++||++|+++|+.++.+++.+..|.+.+|++|+..+|+.++++++.+|+..++.|..|++
T Consensus        16 ~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~   94 (327)
T PRK05949         16 SADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ   94 (327)
T ss_pred             CCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence            478999 99999 9999999999999999999999999999999999999999999999999999999999999989999


Q ss_pred             HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH
Q 012567          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (460)
Q Consensus       289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~  368 (460)
                      .||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|+++++++|+|.++.
T Consensus        95 ~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~  174 (327)
T PRK05949         95 KMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHIT  174 (327)
T ss_pred             HHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCC
Q 012567          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNL  438 (460)
Q Consensus       369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~  438 (460)
                      +.+++++++...+..++|+.|+.+|||+.+|+++++|..++..+..++|||.+++++++.++.++++|+.
T Consensus       175 ~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~  244 (327)
T PRK05949        175 EKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG  244 (327)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC
Confidence            9999999999999999999999999999999999999999998899999999998887788899998764

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=1.4e-42  Score=351.65  Aligned_cols=227  Identities=41%  Similarity=0.661  Sum_probs=220.1

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHH
Q 012567          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  289 (460)
Q Consensus       211 ~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~  289 (460)
                      +|++. ||+++ +++|+||+|||++|+++|++++.+++++..|.+++|++|+..+||.++++++..|+..++.|..|++.
T Consensus         7 ~~~~~~yl~~i-~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~   85 (317)
T PRK07405          7 TDLVRTYLREI-GRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK   85 (317)
T ss_pred             CcHHHHHHHHc-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence            68899 99999 99999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHH
Q 012567          290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE  369 (460)
Q Consensus       290 LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e  369 (460)
                      ||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||++||||++|.++|.++++++|+|.++..
T Consensus        86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~  165 (317)
T PRK07405         86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITE  165 (317)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCC
Q 012567          370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNL  438 (460)
Q Consensus       370 ~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~  438 (460)
                      .+++++++...+...+|+.||.+|||+.+|+++++|..++......+|||.+++++.+.++.++++|+.
T Consensus       166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~  234 (317)
T PRK07405        166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG  234 (317)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC
Confidence            999999999999999999999999999999999999999988888999999998877788889988764

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=1.2e-40  Score=353.92  Aligned_cols=223  Identities=36%  Similarity=0.594  Sum_probs=198.4

Q ss_pred             CCCCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccH
Q 012567          206 QEVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI  284 (460)
Q Consensus       206 ~~~~~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~  284 (460)
                      ......|+++ ||+++ +++|+||++||++|+++|+.+..++.   .+.+       ..+|+.   .....|...++.|.
T Consensus       205 ~~~~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~---~~~~-------~~~~~~---~~~~~l~~~~~~g~  270 (509)
T PRK05901        205 KLTATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEE---LLAE-------GEKLDP---ELRRDLQWIGRDGK  270 (509)
T ss_pred             hccccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhh---hhhh-------cccchh---hhhhhhhhhccchH
Confidence            3344678999 99999 99999999999999999997633322   1111       112332   24567888899999


Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC
Q 012567          285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  364 (460)
Q Consensus       285 ~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP  364 (460)
                      .|+++||.+|+|||+++|++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|+++.+.+|+|
T Consensus       271 ~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP  350 (509)
T PRK05901        271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIP  350 (509)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCcch
Q 012567          365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSL  442 (460)
Q Consensus       365 ~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~ds~  442 (460)
                      .++.+.++++.++.+.|...+|+.||.+|||+.||+++++|..++.....++|||.+++++++.++.++|+|+...++
T Consensus       351 ~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p  428 (509)
T PRK05901        351 VHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSP  428 (509)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCH
Confidence            999999999999999999999999999999999999999999999988899999999988878889999998755433

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

Probab=100.00  E-value=2.1e-40  Score=335.33  Aligned_cols=234  Identities=38%  Similarity=0.609  Sum_probs=213.3

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhh-hcCCCCcHH---------------HHHHHhCCC
Q 012567          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVD  272 (460)
Q Consensus       210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~-~~g~~pt~~---------------ewA~a~g~d  272 (460)
                      ..|.+. |+.++ +..+++++++|..+.+.++....+..+...|.. ..|..|+..               +|+..+..+
T Consensus         7 ~~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   85 (342)
T COG0568           7 SADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPE   85 (342)
T ss_pred             chhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChH
Confidence            467888 99999 999999999999999999887767677777776 667888876               555555554


Q ss_pred             H-HHHHHHHhccH---HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHH
Q 012567          273 Q-RELRRRLNYGI---LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ  348 (460)
Q Consensus       273 e-~~L~~~l~~G~---~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~  348 (460)
                      + ..|..++..|.   .|+.+||.+|++||++||++|.|+|+++.||||||++|||+|++||||.+|++|||||+||||+
T Consensus        86 Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrq  165 (342)
T COG0568          86 EEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQ  165 (342)
T ss_pred             HHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHH
Confidence            4 66888888884   5999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCC
Q 012567          349 AVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL  428 (460)
Q Consensus       349 aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~  428 (460)
                      +|.++|.+++++||+|.|+.+.++++.++.+.|.+.+|++|+++|||+.||++.++|..++.++..++|||.|++++++.
T Consensus       166 aI~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~  245 (342)
T COG0568         166 AITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDS  245 (342)
T ss_pred             HHHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcccccccCCCcchhh
Q 012567          429 KPSVCFILNLADSLII  444 (460)
Q Consensus       429 tl~Eli~D~~~ds~~~  444 (460)
                      .+.|+++|+...++..
T Consensus       246 ~l~d~leD~~~~~p~~  261 (342)
T COG0568         246 ELGDFLEDDKSVSPED  261 (342)
T ss_pred             HHHHHhhcCCcCCHHH
Confidence            9999999997654443

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=1.9e-39  Score=329.65  Aligned_cols=217  Identities=38%  Similarity=0.629  Sum_probs=196.3

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHH
Q 012567          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (460)
Q Consensus       210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e  288 (460)
                      .+|++. ||+++ +++|+||+|||.+|+++|+.+..++..           |+..+|+...  ....|...++.|..|++
T Consensus        24 ~~~~~~~Yl~~i-~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~   89 (324)
T PRK07921         24 AADLVRVYLNGI-GKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARR   89 (324)
T ss_pred             CCChHHHHHHHh-cccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHH
Confidence            468999 99999 999999999999999999987655533           2223332111  45678889999999999


Q ss_pred             HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH
Q 012567          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (460)
Q Consensus       289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~  368 (460)
                      .||..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+++++.+++|.++.
T Consensus        90 ~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~  169 (324)
T PRK07921         90 HLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLV  169 (324)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCc
Q 012567          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLAD  440 (460)
Q Consensus       369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~d  440 (460)
                      +.++++.++...|...+|+.||.+|||+.||+++++|..++..+...+|||.+++++++.++.|+++|+...
T Consensus       170 ~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~  241 (324)
T PRK07921        170 EQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEAT  241 (324)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCC
Confidence            999999999999999999999999999999999999999998888899999999887777899999986543

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=3e-35  Score=303.63  Aligned_cols=191  Identities=41%  Similarity=0.687  Sum_probs=180.5

Q ss_pred             CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHH
Q 012567          209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK  287 (460)
Q Consensus       209 ~~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~  287 (460)
                      ...|+++ ||++| +++|+||+++|.+|+++++.+                                        +..|+
T Consensus        93 ~~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A~  131 (367)
T PRK09210         93 KINDPVRMYLKEI-GRVPLLTAEEEIELAKRIEEG----------------------------------------DEEAK  131 (367)
T ss_pred             ccCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHhh----------------------------------------HHHHH
Confidence            3478999 99999 999999999999999888752                                        26799


Q ss_pred             HHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcch
Q 012567          288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM  367 (460)
Q Consensus       288 e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~  367 (460)
                      +.||..|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+|||+||||++|.++|+++.+.+|+|.++
T Consensus       132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~  211 (367)
T PRK09210        132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM  211 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCc
Q 012567          368 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLAD  440 (460)
Q Consensus       368 ~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~d  440 (460)
                      .+.++++.++.+.|..++|+.||.+|||+.||+++++|..++..+..++|||.+++++++.++.|+++|+...
T Consensus       212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~  284 (367)
T PRK09210        212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDAT  284 (367)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCC
Confidence            9999999999999999999999999999999999999999999888899999999988788899999987644

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2e-33  Score=307.46  Aligned_cols=159  Identities=40%  Similarity=0.695  Sum_probs=152.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ..|+++||.+|++||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|+++.+++|+
T Consensus       379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~iri  458 (619)
T PRK05658        379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI  458 (619)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceec
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCcch
Q 012567          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSL  442 (460)
Q Consensus       364 P~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~ds~  442 (460)
                      |.++.+.++++.++...|.+++|+.||.+|||+.||+++++|..++..+..++|||.|++++++.++.|+++|+...++
T Consensus       459 p~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p  537 (619)
T PRK05658        459 PVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELP  537 (619)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCCh
Confidence            9999999999999999999999999999999999999999999999999999999999998888899999998765443

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=99.97  E-value=4.2e-30  Score=257.53  Aligned_cols=189  Identities=23%  Similarity=0.377  Sum_probs=161.8

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHH
Q 012567          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  289 (460)
Q Consensus       211 ~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~  289 (460)
                      .+.++ ||+++ +++|+||+++|.+|+.+++..                                       ++..|++.
T Consensus         5 ~~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~~---------------------------------------gd~~A~~~   44 (289)
T PRK07500          5 ASADRSMIRSA-MKAPYLEREEEHALAYRWKDH---------------------------------------RDEDALHR   44 (289)
T ss_pred             hhHHHHHHHHH-hcCCCCCHHHHHHHHHHHHHC---------------------------------------CCHHHHHH
Confidence            34667 99999 999999999999999876531                                       23789999


Q ss_pred             HHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHH
Q 012567          290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE  369 (460)
Q Consensus       290 LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e  369 (460)
                      ||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++.+.+|+|.+...
T Consensus        45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~  124 (289)
T PRK07500         45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQ  124 (289)
T ss_pred             HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999988654


Q ss_pred             --HHHHHHHHHHHHHH---HhCCCCCHHHHHHHhCCCHHHHHHHHh-CCCCCcccccccccCCCC--CcccccccCCC
Q 012567          370 --ATYRVKEARKQLYS---ENGRHPNNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQNL--KPSVCFILNLA  439 (460)
Q Consensus       370 --~i~kl~ka~~~L~~---~~gr~pS~eEIAe~LGIS~e~Vk~~l~-~ar~~lSLD~~v~~e~d~--tl~Eli~D~~~  439 (460)
                        ...++++....+..   .+|+.||.+|||+.||+++++|..+.. .....+|||.+++++++.  ++.|+++|+..
T Consensus       125 ~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~  202 (289)
T PRK07500        125 KALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP  202 (289)
T ss_pred             HHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC
Confidence              33455555554444   678999999999999999999988753 455799999999765543  68899987643

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=99.97  E-value=1.1e-29  Score=251.50  Aligned_cols=154  Identities=25%  Similarity=0.349  Sum_probs=142.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ..++++||..|++||+++|++|.++|++++||||+|+|||++|+++|||++|++|+|||+||||++|.++++++.+.+++
T Consensus        39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~  118 (264)
T PRK07122         39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKV  118 (264)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCcccc
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC--CCCCcccccccccCCC--CCcccccccC
Q 012567          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQN--LKPSVCFILN  437 (460)
Q Consensus       364 P~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~--ar~~lSLD~~v~~e~d--~tl~Eli~D~  437 (460)
                      |.++.+.+++++++...|..++|+.||.+|||+.||+++++|..++..  ...++|||.+++++++  ..+.+.++|+
T Consensus       119 Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~~~  196 (264)
T PRK07122        119 PRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDV  196 (264)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccCCc
Confidence            999999999999999999999999999999999999999999998863  4568999999875433  3566777665

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.97  E-value=2.6e-29  Score=251.19  Aligned_cols=187  Identities=25%  Similarity=0.397  Sum_probs=157.6

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHH
Q 012567          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (460)
Q Consensus       210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e  288 (460)
                      +.+++. |++++ ++.|+||.++|.+|+.+++..                                       ++..|++
T Consensus        12 ~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~~---------------------------------------Gd~~a~~   51 (284)
T PRK06596         12 PEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLREH---------------------------------------GDLEAAK   51 (284)
T ss_pred             CccHHHHHHHHH-hccCCCCHHHHHHHHHHHHHc---------------------------------------CCHHHHH
Confidence            457889 99999 999999999999998875420                                       2378999


Q ss_pred             HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH
Q 012567          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (460)
Q Consensus       289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~  368 (460)
                      .||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++++++.+++|.+..
T Consensus        52 ~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~~  131 (284)
T PRK06596         52 QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKA  131 (284)
T ss_pred             HHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999888889998753


Q ss_pred             --HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC-CCCCcccccccccCC--CCCcccccccCC
Q 012567          369 --EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS-PKAPRSLDQKIGINQ--NLKPSVCFILNL  438 (460)
Q Consensus       369 --e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~-ar~~lSLD~~v~~e~--d~tl~Eli~D~~  438 (460)
                        ....++.+....+.  .++.|+.+|||+.||+++++|..++.. ....+|||.++++++  +.++.++++|+.
T Consensus       132 ~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~  204 (284)
T PRK06596        132 QRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS  204 (284)
T ss_pred             HHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC
Confidence              23334444444443  348999999999999999999998753 346899999987553  346788888864

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

Probab=99.97  E-value=7.4e-30  Score=248.25  Aligned_cols=155  Identities=41%  Similarity=0.719  Sum_probs=147.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc
Q 012567          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (460)
Q Consensus       286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~  365 (460)
                      |+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||.+|++|+|||+||||++|.++++++.+.+++|.
T Consensus         1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~   80 (238)
T TIGR02393         1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV   80 (238)
T ss_pred             CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCc
Q 012567          366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLAD  440 (460)
Q Consensus       366 ~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~d  440 (460)
                      ++.+.++++.++...|...+|+.||.+|||+.||+++++|..++......+|||.+++++++.++.|+++|+...
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~  155 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIE  155 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCC
Confidence            999999999999999999999999999999999999999999998777899999999877777888999887543

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

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.96  E-value=6.7e-29  Score=246.17  Aligned_cols=184  Identities=25%  Similarity=0.467  Sum_probs=152.4

Q ss_pred             HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHH
Q 012567          213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI  291 (460)
Q Consensus       213 ~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI  291 (460)
                      ++. ||+++ +++|+|+.++|.+|+.++..                                       .++..|++.||
T Consensus         2 ~~~~yl~~~-~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~Lv   41 (270)
T TIGR02392         2 SLDAYIRAV-NRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKKLV   41 (270)
T ss_pred             hHHHHHHHH-hcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHH
Confidence            567 99999 99999999999999887432                                       02378999999


Q ss_pred             HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchH--H
Q 012567          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV--E  369 (460)
Q Consensus       292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~--e  369 (460)
                      ..|+++|+++|++|.+++.+++||+|+|++||++++++|||++|++|+|||.|||+++|.++++++++.+|+|.+..  +
T Consensus        42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~  121 (270)
T TIGR02392        42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK  121 (270)
T ss_pred             HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999887889997643  3


Q ss_pred             HHHHHHHHHHHHHHHhCCCC-CHHHHHHHhCCCHHHHHHHHhCC-CCCcccccccccCCC--CCcccccccCC
Q 012567          370 ATYRVKEARKQLYSENGRHP-NNEEVAEATGLSMKRLHAVLLSP-KAPRSLDQKIGINQN--LKPSVCFILNL  438 (460)
Q Consensus       370 ~i~kl~ka~~~L~~~~gr~p-S~eEIAe~LGIS~e~Vk~~l~~a-r~~lSLD~~v~~e~d--~tl~Eli~D~~  438 (460)
                      ...++.++...+.  ..+.| +.+|||+.||+++++|..++... ...+|||.+++++++  .++.++++|+.
T Consensus       122 ~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~  192 (270)
T TIGR02392       122 LFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT  192 (270)
T ss_pred             HHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC
Confidence            3444555544442  12445 69999999999999999986533 348999999976544  35778887764

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.

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=99.96  E-value=2.2e-28  Score=240.83  Aligned_cols=156  Identities=29%  Similarity=0.471  Sum_probs=142.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCC-CCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  362 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~-g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir  362 (460)
                      ..|+++||..|+++|+++|++|.+. +.+++||+|+|++|||+|+++|||++|++|+||++|||+|+|.+++|++...+|
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            7899999999999999999999875 667999999999999999999999999999999999999999999999999999


Q ss_pred             cCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh--CCCCCcccccccccCCC--CCcccccccCC
Q 012567          363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQN--LKPSVCFILNL  438 (460)
Q Consensus       363 iP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~--~ar~~lSLD~~v~~e~d--~tl~Eli~D~~  438 (460)
                      +|.++.+.++++.++...|...+|+.||.+|||+.||+++++|..++.  .....+|||.+++++++  .++.+.++|+.
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            999999999999999999999999999999999999999999999864  44568999999865443  36778888765


Q ss_pred             C
Q 012567          439 A  439 (460)
Q Consensus       439 ~  439 (460)
                      .
T Consensus       184 ~  184 (256)
T PRK07408        184 Y  184 (256)
T ss_pred             c
Confidence            4

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=99.96  E-value=5.3e-28  Score=246.14  Aligned_cols=188  Identities=35%  Similarity=0.557  Sum_probs=174.0

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHH
Q 012567          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  289 (460)
Q Consensus       211 ~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~  289 (460)
                      .|..+ ||++| +..|+||+++|..|..+++.                                        ++..|++.
T Consensus        52 ~~~~~~y~~~~-~~~~~l~~~ee~~li~~~~~----------------------------------------Gd~~A~~~   90 (325)
T PRK05657         52 LDATQLYLNEI-GYSPLLTAEEEVYFARRALR----------------------------------------GDFAARQR   90 (325)
T ss_pred             ccHHHHHHHHH-hcCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHH
Confidence            67888 99999 99999999999999887764                                        23789999


Q ss_pred             HHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHH
Q 012567          290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE  369 (460)
Q Consensus       290 LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e  369 (460)
                      ||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||+.|.++++++.+.+++|.++..
T Consensus        91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~  170 (325)
T PRK05657         91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK  170 (325)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCC
Q 012567          370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLA  439 (460)
Q Consensus       370 ~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~  439 (460)
                      .++.+.++...|...+|+.|+.+|||+.||+++++|..++.......|||.+++.+...++.+.++|+..
T Consensus       171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~  240 (325)
T PRK05657        171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQE  240 (325)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCC
Confidence            8888888989999999999999999999999999999999877778999999987777788888887653

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=99.96  E-value=1.3e-27  Score=234.82  Aligned_cols=178  Identities=28%  Similarity=0.397  Sum_probs=160.7

Q ss_pred             hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHH
Q 012567          221 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS  300 (460)
Q Consensus       221 ~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~  300 (460)
                      ++++|+||+++|.+|+.+++.                                        ++..|++.|+..|+++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence            377999999999988877663                                        1367999999999999999


Q ss_pred             HHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHH
Q 012567          301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQ  380 (460)
Q Consensus       301 IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~  380 (460)
                      +|++|.+++.+++||+||||+|||+++++|||.+|.+|+||+++||+|.|.+++|++. .+++|.++.+...++.++...
T Consensus        50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~  128 (254)
T TIGR02850        50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK  128 (254)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999976 789999999999999999999


Q ss_pred             HHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCC--CCcccccccCCC
Q 012567          381 LYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN--LKPSVCFILNLA  439 (460)
Q Consensus       381 L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d--~tl~Eli~D~~~  439 (460)
                      +..++|+.||.+|||+.||+++++|..++.....++|||.++.++++  .++.+.++|+..
T Consensus       129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~  189 (254)
T TIGR02850       129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN  189 (254)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc
Confidence            99999999999999999999999999999888888999999864443  357788877643

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

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=99.94  E-value=3.4e-26  Score=225.03  Aligned_cols=176  Identities=28%  Similarity=0.399  Sum_probs=158.8

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHH
Q 012567          222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  301 (460)
Q Consensus       222 ~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~I  301 (460)
                      .++|+|+++++..|+.+++.                                        ++..+++.|+..|+++|+++
T Consensus        14 ~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~~   53 (258)
T PRK08215         14 SKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLSV   53 (258)
T ss_pred             CCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHHH
Confidence            56789999999988877663                                        23679999999999999999


Q ss_pred             HHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHH
Q 012567          302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL  381 (460)
Q Consensus       302 Akry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L  381 (460)
                      |++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+|+|.++++++. .+++|.+......++.++...+
T Consensus        54 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l  132 (258)
T PRK08215         54 IQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKL  132 (258)
T ss_pred             HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999986 7899999999999999999999


Q ss_pred             HHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCC--CcccccccCC
Q 012567          382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSVCFILNL  438 (460)
Q Consensus       382 ~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~--tl~Eli~D~~  438 (460)
                      ..++|+.|+..|||+.||+++++|...+.....+.|||.++.++++.  ++.+.++|+.
T Consensus       133 ~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~  191 (258)
T PRK08215        133 INENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEK  191 (258)
T ss_pred             HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCcc
Confidence            99999999999999999999999999988777888999998655433  4667777664

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=99.93  E-value=9e-25  Score=218.17  Aligned_cols=191  Identities=37%  Similarity=0.569  Sum_probs=172.2

Q ss_pred             CCCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHH
Q 012567          207 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL  285 (460)
Q Consensus       207 ~~~~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~  285 (460)
                      +....|.++ ||.+| +.+|.||.++|.+|..+++.               |                         +..
T Consensus         8 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~   46 (285)
T TIGR02394         8 ETRVADVTQLYLREI-GFKPLLTAEEEIAYARRALA---------------G-------------------------DFE   46 (285)
T ss_pred             ccCcchHHHHHHHHH-hccCCCCHHHHHHHHHHHHc---------------C-------------------------CHH
Confidence            345678999 99999 99999999999999887764               1                         378


Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc
Q 012567          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (460)
Q Consensus       286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~  365 (460)
                      |++.|+..|.++|+.+|++|.+++.+++||+||||+|||+++++||+.+|++|+||+.|||+.++.++++++.+.+++|.
T Consensus        47 a~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~  126 (285)
T TIGR02394        47 ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPV  126 (285)
T ss_pred             HHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             chHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCC
Q 012567          366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNL  438 (460)
Q Consensus       366 ~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~  438 (460)
                      .+....+.+.+..+.+...+|+.|+..++|+.||++++.|..++..+...+|+|.++..+...++.+.++++.
T Consensus       127 ~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~  199 (285)
T TIGR02394       127 HVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQ  199 (285)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCC
Confidence            9998888888888778888899999999999999999999999988888999999887666556666666554

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

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=99.93  E-value=3.7e-25  Score=218.15  Aligned_cols=154  Identities=25%  Similarity=0.369  Sum_probs=137.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccC---CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~---~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~  360 (460)
                      ..|++.||..|+++|+++|++|.+   .+.+.+||+|+|++|||+|+++|||++|++|+||+.||||++|.+++|++.+ 
T Consensus        22 ~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~-  100 (257)
T PRK05911         22 IEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW-  100 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCC-
Confidence            789999999999999999999862   4568999999999999999999999999999999999999999999998764 


Q ss_pred             cccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCC--CCccccccccc--C--CCCCccccc
Q 012567          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK--APRSLDQKIGI--N--QNLKPSVCF  434 (460)
Q Consensus       361 iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar--~~lSLD~~v~~--e--~d~tl~Eli  434 (460)
                        +|.++.+..+++.++...|...+|+.|+.+|||+.||+++++|..++..++  ..+|||.++..  +  .+.++.+.+
T Consensus       101 --~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~~l  178 (257)
T PRK05911        101 --VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERI  178 (257)
T ss_pred             --CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhhhc
Confidence              899999999999999999999999999999999999999999999887554  36899988743  2  234678888


Q ss_pred             ccCCCc
Q 012567          435 ILNLAD  440 (460)
Q Consensus       435 ~D~~~d  440 (460)
                      +|+...
T Consensus       179 ~d~~~~  184 (257)
T PRK05911        179 ADERAE  184 (257)
T ss_pred             cCCCCC
Confidence            886544

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

Probab=99.93  E-value=5.4e-25  Score=215.48  Aligned_cols=158  Identities=30%  Similarity=0.446  Sum_probs=140.7

Q ss_pred             HHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCC-CcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHH
Q 012567          276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGM-NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  353 (460)
Q Consensus       276 L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~-d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~  353 (460)
                      +....+.| ..++ .||+.|+|||.++|++|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||..+|+++|+++
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            34444556 7888 9999999999999999998887 9999999999999999999999999999999999999999999


Q ss_pred             hhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCC--CCcccccccccCCCCCcc
Q 012567          354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK--APRSLDQKIGINQNLKPS  431 (460)
Q Consensus       354 Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar--~~lSLD~~v~~e~d~tl~  431 (460)
                      +|++. .+++|..+.+..+++..++..|..++|++||..|||+.|||+.++|...+....  ..+|+|..+..+++....
T Consensus        93 LR~~~-~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~~~  171 (247)
T COG1191          93 LRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVD  171 (247)
T ss_pred             HHhCC-CccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccchh
Confidence            99999 899999999999999999999999999999999999999999999999987553  688999877654444344


Q ss_pred             cccc
Q 012567          432 VCFI  435 (460)
Q Consensus       432 Eli~  435 (460)
                      +.+.
T Consensus       172 ~~~~  175 (247)
T COG1191         172 DQIE  175 (247)
T ss_pred             hccc
Confidence            4443

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=99.92  E-value=1.6e-24  Score=209.22  Aligned_cols=156  Identities=33%  Similarity=0.473  Sum_probs=143.7

Q ss_pred             hcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCc
Q 012567          281 NYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  359 (460)
Q Consensus       281 ~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r  359 (460)
                      +.| ..|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++||+..|.+|+||+++||+|.|.+++|++. 
T Consensus         6 ~~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-   84 (231)
T TIGR02885         6 QNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-   84 (231)
T ss_pred             HcCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-
Confidence            344 889999999999999999999999999999999999999999999999999999999999999999999999986 


Q ss_pred             ccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCC--CCcccccccC
Q 012567          360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN--LKPSVCFILN  437 (460)
Q Consensus       360 ~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d--~tl~Eli~D~  437 (460)
                      .+++|.++.....++.++...|..++|+.||.+|||+.||+++++|..++..+....|||.+++++++  .++.|.++|+
T Consensus        85 ~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~  164 (231)
T TIGR02885        85 IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADK  164 (231)
T ss_pred             CeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCC
Confidence            78999999999999999999999999999999999999999999999998877788999998875543  2566777776

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

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=99.92  E-value=2.2e-24  Score=213.47  Aligned_cols=179  Identities=22%  Similarity=0.269  Sum_probs=153.9

Q ss_pred             hhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHH
Q 012567          220 TTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI  299 (460)
Q Consensus       220 ~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~  299 (460)
                      |+|++|+||.++|.+|+..++..                                       ++..+++.++..|.++|+
T Consensus         5 ~~~~~~~~~~~~e~~l~~~~~~~---------------------------------------~d~~a~~~l~~~y~~lv~   45 (268)
T PRK06288          5 MSGKIPKYAQQDETELWREYKKT---------------------------------------GDPKIREYLILKYSPLVK   45 (268)
T ss_pred             ccCCCccccchHHHHHHHHHHHc---------------------------------------CCHHHHHHHHHHHHHHHH
Confidence            46899999999999999887641                                       237799999999999999


Q ss_pred             HHHHHcc-C--CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHH
Q 012567          300 SIAKNYQ-G--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKE  376 (460)
Q Consensus       300 ~IAkry~-~--~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~k  376 (460)
                      .+|++|. +  .+.+++||+||||+|||+++++||+.+|.+|+||+++||+|.|++++|+..   ++|.++.....++++
T Consensus        46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~  122 (268)
T PRK06288         46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIER  122 (268)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHH
Confidence            9999986 2  567899999999999999999999998999999999999999999999754   589999888999999


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCC--CCCcccccccccCC---CCCcccccccCCCc
Q 012567          377 ARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQ---NLKPSVCFILNLAD  440 (460)
Q Consensus       377 a~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a--r~~lSLD~~v~~e~---d~tl~Eli~D~~~d  440 (460)
                      +...|...+++.||.+|||+.+|++.+.|..++...  ...+|||.++..++   ..++.+.++++..+
T Consensus       123 ~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~  191 (268)
T PRK06288        123 AIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAAL  191 (268)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCC
Confidence            999999999999999999999999999999988643  45789998874222   23677778765444

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

Probab=99.91  E-value=1.4e-23  Score=202.00  Aligned_cols=154  Identities=29%  Similarity=0.420  Sum_probs=140.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ..|++.|+..|.++|+++|++|.+++.+.+||+|||++||++++++||+.+|.+|+||+++||+|.|.++++++.+.+++
T Consensus         2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri   81 (227)
T TIGR02980         2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV   81 (227)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCC--CcccccccccCC--CCCcccccccC
Q 012567          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKA--PRSLDQKIGINQ--NLKPSVCFILN  437 (460)
Q Consensus       364 P~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~--~lSLD~~v~~e~--d~tl~Eli~D~  437 (460)
                      |.++.+...+++++...+...+|+.|+..|+|+.||+++++|..++.....  ..|||.++.+++  +.++.+.++++
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~~~  159 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDE  159 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccCCc
Confidence            999999999999999999999999999999999999999999998875554  899999986332  23466666654

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

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=99.91  E-value=5.3e-23  Score=201.81  Aligned_cols=165  Identities=26%  Similarity=0.321  Sum_probs=149.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHH
Q 012567          225 RLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKN  304 (460)
Q Consensus       225 ~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkr  304 (460)
                      |.||+++|.+|..+++..                                       ++..|+++|+..|.++|+.+|++
T Consensus         8 ~~l~~~~~~~li~~~~~~---------------------------------------gd~~a~~~l~~~y~~~v~~~a~~   48 (255)
T TIGR02941         8 TNLTKEDVIQWIAEFQQN---------------------------------------QNGEAQEKLVDHYQNLVYSIAYK   48 (255)
T ss_pred             CCCCHHHHHHHHHHHHHC---------------------------------------CCHHHHHHHHHHhHHHHHHHHHH
Confidence            678999988888776641                                       12789999999999999999999


Q ss_pred             ccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHH
Q 012567          305 YQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSE  384 (460)
Q Consensus       305 y~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~  384 (460)
                      |.+++.+++||+||||+|||+++++|++..|.+|.||+++||+|.|.++++++...+++|.++.+...+++++...+...
T Consensus        49 ~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~~  128 (255)
T TIGR02941        49 YSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDH  128 (255)
T ss_pred             HhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999889999999999999999999999999


Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhC--CCCCcccccccccCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNL  428 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~--ar~~lSLD~~v~~e~d~  428 (460)
                      +|+.|+..|||+.||++.+.+..++..  .....|||.+++.+++.
T Consensus       129 ~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~  174 (255)
T TIGR02941       129 LQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDG  174 (255)
T ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCC
Confidence            999999999999999999999888753  34578999998765443

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

>PRK05572 sporulation sigma factor SigF; Validated

Probab=99.90  E-value=3.2e-22  Score=196.24  Aligned_cols=178  Identities=26%  Similarity=0.397  Sum_probs=156.3

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHH
Q 012567          222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  301 (460)
Q Consensus       222 ~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~I  301 (460)
                      ...|.||.+++.+|..+++.                                        ++..|++.|+..|.++|+.+
T Consensus         9 ~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v~~~   48 (252)
T PRK05572          9 KKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLVWSV   48 (252)
T ss_pred             cCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHHH
Confidence            45789999998888766543                                        23679999999999999999


Q ss_pred             HHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHH
Q 012567          302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL  381 (460)
Q Consensus       302 Akry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L  381 (460)
                      |++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||+|.|.+++|+.. .+++|..+.....++.++...+
T Consensus        49 a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~~~l  127 (252)
T PRK05572         49 VQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDEL  127 (252)
T ss_pred             HHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999988889999999999999999999885 7899999999999999999999


Q ss_pred             HHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCC--CcccccccCCCc
Q 012567          382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSVCFILNLAD  440 (460)
Q Consensus       382 ~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~--tl~Eli~D~~~d  440 (460)
                      ..++|+.|+..|||+.||++++.|..++.......||+.++.+++..  ++.|.++++...
T Consensus       128 ~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~~  188 (252)
T PRK05572        128 SKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSEE  188 (252)
T ss_pred             HHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCchh
Confidence            99999999999999999999999999888777889999988654432  355666665443

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=99.88  E-value=6.5e-22  Score=194.00  Aligned_cols=152  Identities=27%  Similarity=0.319  Sum_probs=135.5

Q ss_pred             HHHHHHH-Hhcc-HHHHHHHHHHhHHHHHHHHHHccC---CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHH
Q 012567          273 QRELRRR-LNYG-ILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK  347 (460)
Q Consensus       273 e~~L~~~-l~~G-~~A~e~LI~~nlrLV~~IAkry~~---~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr  347 (460)
                      +..|..+ ...| ..|++.|+..|.++|+++|++|.+   ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+
T Consensus         8 e~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~ir   87 (251)
T PRK07670          8 EQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIR   87 (251)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHH
Confidence            4455555 4444 899999999999999999999965   6889999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh--CCCCCcccccccccC
Q 012567          348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGIN  425 (460)
Q Consensus       348 ~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~--~ar~~lSLD~~v~~e  425 (460)
                      |.|++++|++.   ++|..+.+.+.+++++...+.+.+|+.|+.+|||+.||+++++|..++.  .....+|||.++.++
T Consensus        88 n~~~d~lR~~~---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~  164 (251)
T PRK07670         88 GAIIDGLRKED---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQ  164 (251)
T ss_pred             HHHHHHHHhcC---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCC
Confidence            99999999876   4899888999999999999999999999999999999999999999975  455689999998654


Q ss_pred             CC
Q 012567          426 QN  427 (460)
Q Consensus       426 ~d  427 (460)
                      ++
T Consensus       165 ~~  166 (251)
T PRK07670        165 DD  166 (251)
T ss_pred             CC
Confidence            44

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=99.88  E-value=1.9e-21  Score=191.08  Aligned_cols=166  Identities=25%  Similarity=0.323  Sum_probs=148.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHH
Q 012567          223 SSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA  302 (460)
Q Consensus       223 ~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IA  302 (460)
                      ..|.|++++|.+|..+++..                                       ++..|++.|+..|.++|+++|
T Consensus         6 ~~~~l~~~e~~~li~~~~~~---------------------------------------gd~~a~~~l~~~~~~~v~~~a   46 (257)
T PRK08583          6 QPTKLTKEEVNKWIAEYQEN---------------------------------------QDEEAQEKLVKHYKNLVESLA   46 (257)
T ss_pred             cCCcCChHHHHHHHHHHHHc---------------------------------------CCHHHHHHHHHHHHHHHHHHH
Confidence            34789999998887766531                                       237899999999999999999


Q ss_pred             HHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHH
Q 012567          303 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLY  382 (460)
Q Consensus       303 kry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~  382 (460)
                      ++|.+++.+++||+||||+|||+++++||+..|.+|+||+++||+|.|.+++|++...+++|.+..+..++++.+...+.
T Consensus        47 ~~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~  126 (257)
T PRK08583         47 YKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELT  126 (257)
T ss_pred             HHHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999998889999999999999999999999899999999999999999999999


Q ss_pred             HHhCCCCCHHHHHHHhCCCHHHHHHHHhCC--CCCcccccccccCCC
Q 012567          383 SENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQN  427 (460)
Q Consensus       383 ~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a--r~~lSLD~~v~~e~d  427 (460)
                      ..+++.|+.+|+|+.+|++.+.+...+...  ...+|+|.+++.+.+
T Consensus       127 ~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~  173 (257)
T PRK08583        127 TELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSD  173 (257)
T ss_pred             HHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCC
Confidence            999999999999999999999998877643  357899998865443

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=99.88  E-value=1.3e-21  Score=190.31  Aligned_cols=138  Identities=20%  Similarity=0.337  Sum_probs=123.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHccC---CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567          286 CKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  362 (460)
Q Consensus       286 A~e~LI~~nlrLV~~IAkry~~---~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir  362 (460)
                      -...|+..|+++|.+++++|.+   .+.+.+||+|||++|||+|+++||+.+| +|+||++|||+|+|.+++++...   
T Consensus        16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~---   91 (231)
T PRK12427         16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW---   91 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC---
Confidence            4567999999999999999874   4679999999999999999999998665 89999999999999999998653   


Q ss_pred             cCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh--CCCCCcccccccccCCC
Q 012567          363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQN  427 (460)
Q Consensus       363 iP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~--~ar~~lSLD~~v~~e~d  427 (460)
                      .|..+....++++++...|..++|+.||.+|||+.||+++++|..++.  .+....|||.+++++++
T Consensus        92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~  158 (231)
T PRK12427         92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAH  158 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCc
Confidence            688888889999999999999999999999999999999999999875  34568999999876544

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

Probab=99.87  E-value=2e-21  Score=187.07  Aligned_cols=146  Identities=27%  Similarity=0.375  Sum_probs=128.4

Q ss_pred             HHHHhHHHHHHHHHHccC---CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcc
Q 012567          290 MITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (460)
Q Consensus       290 LI~~nlrLV~~IAkry~~---~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~  366 (460)
                      |+..|.++|+++|++|.+   ++.+++||+|||++|||+++++|||.+|.+|+||+++||+|.|++++|+..   ++|..
T Consensus         1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~   77 (224)
T TIGR02479         1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS   77 (224)
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence            578999999999999986   789999999999999999999999999999999999999999999999865   48888


Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHh--CCCCCcccccccccC-CCCCcccccccCC
Q 012567          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGIN-QNLKPSVCFILNL  438 (460)
Q Consensus       367 ~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~--~ar~~lSLD~~v~~e-~d~tl~Eli~D~~  438 (460)
                      ....++++.++...|...+|+.|+.+|||+.||++++.|..++.  .....+|+|....++ ++.++.++++++.
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~  152 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDK  152 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccc
Confidence            88999999999999999999999999999999999999999985  344578898876543 3346666666433

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

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=99.83  E-value=1.1e-19  Score=176.44  Aligned_cols=143  Identities=31%  Similarity=0.451  Sum_probs=127.3

Q ss_pred             ccHHHHHHHHHHhHHHHHHHHHHcc---CCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567          282 YGILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (460)
Q Consensus       282 ~G~~A~e~LI~~nlrLV~~IAkry~---~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~  358 (460)
                      .|.-+++.|+..|.++|+++|++|.   +++.+++||+||||+|||+++++||+..|.+|+||+++||+|.|++++|++.
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            4677899999999999999999997   6789999999999999999999999998999999999999999999999976


Q ss_pred             cccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC--CCCCcccccccccCCC
Q 012567          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQN  427 (460)
Q Consensus       359 r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~--ar~~lSLD~~v~~e~d  427 (460)
                      +   +|..+.....++.++...+...++++|+.+|||+.||++.++|..++..  ....+|++..++++++
T Consensus        85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~  152 (236)
T PRK06986         85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGD  152 (236)
T ss_pred             C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCc
Confidence            4   6777777777888899999999999999999999999999999988863  3456789988765444

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.81  E-value=6.1e-19  Score=171.05  Aligned_cols=161  Identities=25%  Similarity=0.357  Sum_probs=129.3

Q ss_pred             HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHH
Q 012567          213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI  291 (460)
Q Consensus       213 ~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI  291 (460)
                      .+. |+.++ +..|+||+++|..|...++.                                        ++..|++.|+
T Consensus        17 ~~~~~~~~~-~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~   55 (233)
T PRK05803         17 FLVSYVKNN-SFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILI   55 (233)
T ss_pred             HHHHHHHHh-cccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHH
Confidence            345 99999 88999999999888776653                                        2378999999


Q ss_pred             HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc---cc-----
Q 012567          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI---RL-----  363 (460)
Q Consensus       292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i---ri-----  363 (460)
                      ..|.++|++++.+|.+++.+++|++|||++++|+++++|++.+|.+|.||+++|++|.+++++|+..+..   ..     
T Consensus        56 ~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~~~~~~~~~~  135 (233)
T PRK05803         56 ERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKKEVSLQDPIG  135 (233)
T ss_pred             HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccccCCCcccccc
Confidence            9999999999999999999999999999999999999999988889999999999999999998754311   00     


Q ss_pred             --------------Cc---ch------HHHHHHHHHHHHHHHHH--------h----CCCCCHHHHHHHhCCCHHHHHHH
Q 012567          364 --------------PF---HM------VEATYRVKEARKQLYSE--------N----GRHPNNEEVAEATGLSMKRLHAV  408 (460)
Q Consensus       364 --------------P~---~~------~e~i~kl~ka~~~L~~~--------~----gr~pS~eEIAe~LGIS~e~Vk~~  408 (460)
                                    +.   ..      ......+.+++..|+..        +    ..+.|++|||+.||+|.++|+..
T Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~  215 (233)
T PRK05803        136 VDKEGNEISLIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRI  215 (233)
T ss_pred             CCCCcCcccHHHHccCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHH
Confidence                          00   00      01223466666666553        2    35679999999999999999999


Q ss_pred             HhCCCC
Q 012567          409 LLSPKA  414 (460)
Q Consensus       409 l~~ar~  414 (460)
                      ++++..
T Consensus       216 ~~rA~~  221 (233)
T PRK05803        216 EKRALK  221 (233)
T ss_pred             HHHHHH
Confidence            876654

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.72  E-value=7.6e-17  Score=156.10  Aligned_cols=131  Identities=25%  Similarity=0.413  Sum_probs=107.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR-  362 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir-  362 (460)
                      ..|++.++..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.|++++|++.+... 
T Consensus        51 ~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~~~  130 (234)
T PRK08301         51 EAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKAE  130 (234)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccccc
Confidence            7899999999999999999999999999999999999999999999998877889999999999999999997543210 


Q ss_pred             --c--C-----------------c--ch-------HHHHHHHHHHHHHHHHH--------h----CCCCCHHHHHHHhCC
Q 012567          363 --L--P-----------------F--HM-------VEATYRVKEARKQLYSE--------N----GRHPNNEEVAEATGL  400 (460)
Q Consensus       363 --i--P-----------------~--~~-------~e~i~kl~ka~~~L~~~--------~----gr~pS~eEIAe~LGI  400 (460)
                        +  +                 .  ..       ......+.+++..|+.+        +    -.+.|++|||+.||+
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgi  210 (234)
T PRK08301        131 VSFDEPLNIDWDGNELLLSDVLGTDNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGI  210 (234)
T ss_pred             cccccccccccCCCcccHHHhccCcccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCC
Confidence              0  0                 0  00       01123467777777654        2    368899999999999


Q ss_pred             CHHHHHHHHhCCCC
Q 012567          401 SMKRLHAVLLSPKA  414 (460)
Q Consensus       401 S~e~Vk~~l~~ar~  414 (460)
                      |+++|+..+++++.
T Consensus       211 s~~tVk~~~~rA~~  224 (234)
T PRK08301        211 SQSYISRLEKRIIK  224 (234)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999887754

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.72  E-value=7.2e-17  Score=156.10  Aligned_cols=128  Identities=16%  Similarity=0.216  Sum_probs=109.8

Q ss_pred             HHhccHHHHHHHHHHhHHHHHHHHHHccCCC--CCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhh
Q 012567          279 RLNYGILCKDKMITSNIRLVISIAKNYQGAG--MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (460)
Q Consensus       279 ~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g--~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk  356 (460)
                      .++.|...++.||..|.|+|.++|++|.+++  .+.+|++|+|++|||+|+++||+++|.+|.||+.+||++.|++++|+
T Consensus         3 ~~~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk   82 (218)
T TIGR02895         3 PIQPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRK   82 (218)
T ss_pred             hhhcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            3556744499999999999999999998765  58999999999999999999999999999999999999999999998


Q ss_pred             cC---cccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHH------HhCCCHHHHH
Q 012567          357 QS---RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAE------ATGLSMKRLH  406 (460)
Q Consensus       357 ~~---r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe------~LGIS~e~Vk  406 (460)
                      ..   ..+++|....+....+..+..++..+.++.|+.+||+.      ..|||.+++-
T Consensus        83 ~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv  141 (218)
T TIGR02895        83 NQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELV  141 (218)
T ss_pred             cccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHh
Confidence            76   45678876666666788888888889999999999996      3578766653

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).

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.71  E-value=1.4e-16  Score=154.00  Aligned_cols=131  Identities=23%  Similarity=0.360  Sum_probs=106.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR-  362 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir-  362 (460)
                      ..|++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++++|++..+.+|.||++++++|.|++++|+..+..+ 
T Consensus        47 ~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~~  126 (227)
T TIGR02846        47 EEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKGE  126 (227)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhccccc
Confidence            7899999999999999999999999999999999999999999999999888889999999999999999987543210 


Q ss_pred             c---------------------Cc---c------hHHHHHHHHHHHHHHHHH--------h----CCCCCHHHHHHHhCC
Q 012567          363 L---------------------PF---H------MVEATYRVKEARKQLYSE--------N----GRHPNNEEVAEATGL  400 (460)
Q Consensus       363 i---------------------P~---~------~~e~i~kl~ka~~~L~~~--------~----gr~pS~eEIAe~LGI  400 (460)
                      .                     +.   .      ..+....+.+++..|+..        +    ..+.|++|||+.||+
T Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgi  206 (227)
T TIGR02846       127 VSLQDPIGVDKEGNEISLIDILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGI  206 (227)
T ss_pred             eeccccccCCcccCcccHHHHhcCCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCC
Confidence            0                     00   0      011223466666666553        2    256899999999999


Q ss_pred             CHHHHHHHHhCCCC
Q 012567          401 SMKRLHAVLLSPKA  414 (460)
Q Consensus       401 S~e~Vk~~l~~ar~  414 (460)
                      |+++|+..++++..
T Consensus       207 s~~tV~~~~~rAl~  220 (227)
T TIGR02846       207 SRSYVSRIEKRALM  220 (227)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999887654

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

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.68  E-value=6.8e-16  Score=149.97  Aligned_cols=131  Identities=25%  Similarity=0.379  Sum_probs=107.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR-  362 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir-  362 (460)
                      ..|++.++..|.+.|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++++++|.+++++|++.+... 
T Consensus        51 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~~  130 (234)
T TIGR02835        51 ESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRSE  130 (234)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccCc
Confidence            7899999999999999999999999999999999999999999999998877889999999999999999997654210 


Q ss_pred             cC----------------------c-----ch---HHHHHHHHHHHHHHHHH--------h----CCCCCHHHHHHHhCC
Q 012567          363 LP----------------------F-----HM---VEATYRVKEARKQLYSE--------N----GRHPNNEEVAEATGL  400 (460)
Q Consensus       363 iP----------------------~-----~~---~e~i~kl~ka~~~L~~~--------~----gr~pS~eEIAe~LGI  400 (460)
                      .+                      .     ..   ......+.+++..|+.+        +    ..+.|++|||+.||+
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgi  210 (234)
T TIGR02835       131 VSFDEPLNVDWDGNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGI  210 (234)
T ss_pred             ccccccccCCCCCCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCC
Confidence            00                      0     00   01223477777777653        2    257899999999999


Q ss_pred             CHHHHHHHHhCCCC
Q 012567          401 SMKRLHAVLLSPKA  414 (460)
Q Consensus       401 S~e~Vk~~l~~ar~  414 (460)
                      |+++|+..+++++.
T Consensus       211 s~~tV~~~l~ra~~  224 (234)
T TIGR02835       211 SQSYISRLEKRILK  224 (234)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999999887654

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.

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.66  E-value=8.2e-16  Score=143.96  Aligned_cols=145  Identities=19%  Similarity=0.258  Sum_probs=113.7

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      |++..|+..+..| ..|++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++..+..|.||++.+|++.
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            4567778888888 999999999999999999999999999999999999999999999999887779999999999999


Q ss_pred             HHHHhhhcCcccc--------------------------------cCcch---HHHHHHHHHHHHHHHHH--------hC
Q 012567          350 VRKSLSDQSRTIR--------------------------------LPFHM---VEATYRVKEARKQLYSE--------NG  386 (460)
Q Consensus       350 I~~~Lrk~~r~ir--------------------------------iP~~~---~e~i~kl~ka~~~L~~~--------~g  386 (460)
                      +++++++..+..+                                -|...   .+....+.+++..|+..        +-
T Consensus        84 ~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~~~  163 (198)
T TIGR02859        84 IITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQSYL  163 (198)
T ss_pred             HHHHHHHHHHhcccchhhhcCcccccccccccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence            9888864211000                                00000   11223355566654322        22


Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      .+.|++|||+.||+|+++|+..+++++..
T Consensus       164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~  192 (198)
T TIGR02859       164 DGKSYQEIACDLNRHVKSIDNALQRVKRK  192 (198)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            78899999999999999999999877653

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

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.66  E-value=8.6e-16  Score=143.17  Aligned_cols=144  Identities=17%  Similarity=0.207  Sum_probs=117.2

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      +++..|+..+..| ..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +..|.+|++.+++|.
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            4566777777777 99999999999999999999999999999999999999999999999975 458999999999999


Q ss_pred             HHHHhhhcCcccc--cCc---------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHH
Q 012567          350 VRKSLSDQSRTIR--LPF---------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHA  407 (460)
Q Consensus       350 I~~~Lrk~~r~ir--iP~---------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~  407 (460)
                      +.+++|++.....  ++.         .   ..+....+.+++..|+.+.+        .+.+++|||+.||+|..+|+.
T Consensus        84 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~  163 (186)
T PRK05602         84 CYDRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALES  163 (186)
T ss_pred             HHHHHHhcCCCCcccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHH
Confidence            9999997653211  110         0   01233456677776665433        788999999999999999999


Q ss_pred             HHhCCCCC
Q 012567          408 VLLSPKAP  415 (460)
Q Consensus       408 ~l~~ar~~  415 (460)
                      .+++++..
T Consensus       164 ~l~Rar~~  171 (186)
T PRK05602        164 LLARGRRA  171 (186)
T ss_pred             HHHHHHHH
Confidence            99988754

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.64  E-value=1.9e-15  Score=142.72  Aligned_cols=145  Identities=21%  Similarity=0.267  Sum_probs=111.9

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      ++...|+..++.| ..+++.|+..|.++|+.+|++|.++..+++|++||++++||+++.+|++.++.+|.||++.+++|.
T Consensus         9 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~   88 (208)
T PRK08295          9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQ   88 (208)
T ss_pred             CChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHH
Confidence            4566677777777 999999999999999999999999999999999999999999999999987789999999999999


Q ss_pred             HHHHhhhcCcccccC-----------------------------cch------HHHHHHHH-HHHHHHHHH-------hC
Q 012567          350 VRKSLSDQSRTIRLP-----------------------------FHM------VEATYRVK-EARKQLYSE-------NG  386 (460)
Q Consensus       350 I~~~Lrk~~r~iriP-----------------------------~~~------~e~i~kl~-ka~~~L~~~-------~g  386 (460)
                      +++++++..+..+.+                             ...      .+....+. .+...|+..       +-
T Consensus        89 ~~d~~r~~~r~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l~~  168 (208)
T PRK08295         89 IITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELYL  168 (208)
T ss_pred             HHHHHHHhhhhccccccceeecCCcccCCccchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            999987532211110                             000      00111221 222333322       34


Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      .+.+++|||+.||+|+++|+..+++++..
T Consensus       169 e~~s~~EIA~~lgis~~tV~~~l~rar~~  197 (208)
T PRK08295        169 DGKSYQEIAEELNRHVKSIDNALQRVKRK  197 (208)
T ss_pred             ccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            78999999999999999999999887654

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.64  E-value=1.4e-15  Score=143.15  Aligned_cols=143  Identities=14%  Similarity=0.102  Sum_probs=115.0

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567          272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (460)
Q Consensus       272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI  350 (460)
                      +...|+..+..| ..+++.|+..|.++|+++|.+|.++..+++|++||+|+++|+.+.+|++.+| .|.+|++.+++|.+
T Consensus        16 ~~~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~   94 (194)
T PRK09646         16 DLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRA   94 (194)
T ss_pred             cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHH
Confidence            455677777777 9999999999999999999999999999999999999999999999998655 79999999999999


Q ss_pred             HHHhhhcCccccc---------Cc---ch------HHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHH
Q 012567          351 RKSLSDQSRTIRL---------PF---HM------VEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKR  404 (460)
Q Consensus       351 ~~~Lrk~~r~iri---------P~---~~------~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~  404 (460)
                      ++++|++.+..+.         ..   ..      .+....+..++..|+...        -.+.+++|||+.||+|+++
T Consensus        95 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~t  174 (194)
T PRK09646         95 VDRVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGT  174 (194)
T ss_pred             HHHHHhhccccccccccccccccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHh
Confidence            9999976431111         00   00      112234666666665542        3789999999999999999


Q ss_pred             HHHHHhCCCCC
Q 012567          405 LHAVLLSPKAP  415 (460)
Q Consensus       405 Vk~~l~~ar~~  415 (460)
                      |+..+++++..
T Consensus       175 Vk~~l~ra~~~  185 (194)
T PRK09646        175 VKTRMRDGLIR  185 (194)
T ss_pred             HHHHHHHHHHH
Confidence            99999887653

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=2.8e-15  Score=140.61  Aligned_cols=143  Identities=14%  Similarity=0.152  Sum_probs=116.5

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      +++..|+..++.| ..|++.|+..|.+.|+++|+++.++..+.+|++||+|+++|+++.+|++.  ..|.+|++++++|.
T Consensus        11 ~~~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~   88 (194)
T PRK12513         11 ASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNL   88 (194)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHH
Confidence            4566777777777 99999999999999999999999999999999999999999999999964  47999999999999


Q ss_pred             HHHHhhhcCcccccCc-----------------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCC
Q 012567          350 VRKSLSDQSRTIRLPF-----------------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLS  401 (460)
Q Consensus       350 I~~~Lrk~~r~iriP~-----------------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS  401 (460)
                      +++++|+..+....+.                 .   ..+....+..++..|+...+        .+.|++|||+.||+|
T Consensus        89 ~~~~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis  168 (194)
T PRK12513         89 LIDHWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVP  168 (194)
T ss_pred             HHHHHHHhccccccccccchhhhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccCCCHHHHHHHHCCC
Confidence            9999997654322110                 0   01123446677777766533        678999999999999


Q ss_pred             HHHHHHHHhCCCCC
Q 012567          402 MKRLHAVLLSPKAP  415 (460)
Q Consensus       402 ~e~Vk~~l~~ar~~  415 (460)
                      +++|+..+++++..
T Consensus       169 ~~tV~~~l~ra~~~  182 (194)
T PRK12513        169 EETVKSRLRYALQK  182 (194)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999877654

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.62  E-value=3.6e-15  Score=139.75  Aligned_cols=144  Identities=15%  Similarity=0.154  Sum_probs=115.0

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCC---CCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAG---MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI  346 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g---~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wI  346 (460)
                      +++..|+..+..| ..|++.|+..|.+.|++++.++.+++   .+++|++||+++++|+++++|++..+ .|.+|++.++
T Consensus         3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~ia   81 (189)
T PRK06811          3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAIS   81 (189)
T ss_pred             CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHH
Confidence            5677788888888 89999999999999999999998753   47999999999999999999997544 7999999999


Q ss_pred             HHHHHHHhhhcCcccccC---c-------c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCH
Q 012567          347 KQAVRKSLSDQSRTIRLP---F-------H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSM  402 (460)
Q Consensus       347 r~aI~~~Lrk~~r~iriP---~-------~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~  402 (460)
                      +|.+++++|++.+.....   .       .      ..+....+.+++..|+.+.+        .+.+++|||+.||+|.
T Consensus        82 rn~~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~  161 (189)
T PRK06811         82 KYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTR  161 (189)
T ss_pred             HHHHHHHHHHhccccccccchhhhhcccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCH
Confidence            999999999765422111   0       0      11223346666666655422        7899999999999999


Q ss_pred             HHHHHHHhCCCCC
Q 012567          403 KRLHAVLLSPKAP  415 (460)
Q Consensus       403 e~Vk~~l~~ar~~  415 (460)
                      .+|+..+++++..
T Consensus       162 ~~V~~~l~Ra~~~  174 (189)
T PRK06811        162 SAIDNRLSRGRKK  174 (189)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999877653

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.61  E-value=5.8e-15  Score=137.95  Aligned_cols=140  Identities=19%  Similarity=0.209  Sum_probs=111.5

Q ss_pred             HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCC----CCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHH
Q 012567          274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ  348 (460)
Q Consensus       274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~----g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~  348 (460)
                      ..|+..+..| ..|++.|+..|.+.|+.+|.++.++    +.+++|++||+|+++|+++.+|++. +..|.+|++.+++|
T Consensus        12 ~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n   90 (189)
T PRK09648         12 DALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAH   90 (189)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHH
Confidence            4466777777 9999999999999999999998764    4689999999999999999999864 45899999999999


Q ss_pred             HHHHHhhhcCccccc-----Cc------c------hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHH
Q 012567          349 AVRKSLSDQSRTIRL-----PF------H------MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMK  403 (460)
Q Consensus       349 aI~~~Lrk~~r~iri-----P~------~------~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e  403 (460)
                      .+++++|++.+....     +.      .      ..+....+.+++..|+...        -.+.+++|||+.||+|+.
T Consensus        91 ~~~d~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~  170 (189)
T PRK09648         91 KVADAHRAAGRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPG  170 (189)
T ss_pred             HHHHHHHHhCCCccccccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHH
Confidence            999999986642211     10      0      1122334667777766643        378999999999999999


Q ss_pred             HHHHHHhCCCC
Q 012567          404 RLHAVLLSPKA  414 (460)
Q Consensus       404 ~Vk~~l~~ar~  414 (460)
                      +|+..+++++.
T Consensus       171 tV~~~l~Ra~~  181 (189)
T PRK09648        171 AVRVAQHRALA  181 (189)
T ss_pred             HHHHHHHHHHH
Confidence            99999987754

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.60  E-value=5.3e-15  Score=137.52  Aligned_cols=144  Identities=17%  Similarity=0.139  Sum_probs=114.9

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      +++..|...++.| ..+++.|+..|.+.|+.++++|.+++.+++|++||+++++|+++++|++.. ..|.+|++++++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~   86 (186)
T PRK13919          8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHA   86 (186)
T ss_pred             cCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHH
Confidence            3566777777777 999999999999999999999999999999999999999999999998654 36999999999999


Q ss_pred             HHHHhhhcCcccc-c------C------cc-----hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHH
Q 012567          350 VRKSLSDQSRTIR-L------P------FH-----MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMK  403 (460)
Q Consensus       350 I~~~Lrk~~r~ir-i------P------~~-----~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e  403 (460)
                      +++++|++.+... +      +      ..     .......+.+++..|+...+        .+.+++|||+.||+|++
T Consensus        87 ~~d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~  166 (186)
T PRK13919         87 AVDHVRRRAARPQPLEPDEREPEAFDLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLG  166 (186)
T ss_pred             HHHHHHhhhcccccccccccccccccCCCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHH
Confidence            9999997543210 1      0      00     01112346677777665433        78899999999999999


Q ss_pred             HHHHHHhCCCCC
Q 012567          404 RLHAVLLSPKAP  415 (460)
Q Consensus       404 ~Vk~~l~~ar~~  415 (460)
                      +|+..+++++..
T Consensus       167 ~V~~~l~ra~~~  178 (186)
T PRK13919        167 TLKTRARRALSR  178 (186)
T ss_pred             HHHHHHHHHHHH
Confidence            999999887653

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.60  E-value=4.8e-15  Score=133.38  Aligned_cols=129  Identities=16%  Similarity=0.155  Sum_probs=104.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc---
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT---  360 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~---  360 (460)
                      ..+++.|+..|.++|+.+++++ ++..+++|++||+++++|+++++|++..+ .|.+|++.+++|.+++++|++.+.   
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            3579999999999999999986 56679999999999999999999997666 799999999999999999986421   


Q ss_pred             ---cccCcc---hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          361 ---IRLPFH---MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       361 ---iriP~~---~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                         ...|..   ..+....+..++..|+..        +..+.|++|||+.||+|+++|+..+++++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~  148 (154)
T PRK06759         81 CVCVGEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALE  148 (154)
T ss_pred             ccccCCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence               111221   223345577777776554        347899999999999999999999987654

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

Probab=99.60  E-value=7.8e-15  Score=134.53  Aligned_cols=143  Identities=14%  Similarity=0.138  Sum_probs=115.0

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      |++..++..+..| ..|++.++..|.+.|++++.++.++..+++|++||+++.+|+.+++|++.  ..|.+|++.+++|.
T Consensus         1 ~~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~   78 (169)
T TIGR02954         1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINE   78 (169)
T ss_pred             CCHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHH
Confidence            4556677777777 99999999999999999999999999999999999999999999999964  37999999999999


Q ss_pred             HHHHhhhcCcccccCcc----------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567          350 VRKSLSDQSRTIRLPFH----------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLS  411 (460)
Q Consensus       350 I~~~Lrk~~r~iriP~~----------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~  411 (460)
                      +++++|+..+....+..          ..+....+..+...|+...+        .+.+++|||+.||+|+++|+..+++
T Consensus        79 ~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~R  158 (169)
T TIGR02954        79 CIDLLKKKKKVIPFDPNTSIEKGECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHR  158 (169)
T ss_pred             HHHHHHhcCCcCccccccccccchhhhchHHHHHHHHHHHhCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            99999986643222110          01112246666666655433        7889999999999999999999988


Q ss_pred             CCCC
Q 012567          412 PKAP  415 (460)
Q Consensus       412 ar~~  415 (460)
                      ++..
T Consensus       159 a~~~  162 (169)
T TIGR02954       159 ALKK  162 (169)
T ss_pred             HHHH
Confidence            7653

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.

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.60  E-value=9.1e-15  Score=136.81  Aligned_cols=144  Identities=14%  Similarity=0.149  Sum_probs=116.5

Q ss_pred             CCCHHHHHHHHhc----cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHH
Q 012567          270 GVDQRELRRRLNY----GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW  345 (460)
Q Consensus       270 g~de~~L~~~l~~----G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~w  345 (460)
                      .+++..|+..++.    +..|++.|+..|.+.|+.++.+|.++..+++|++||+|+++|+++++|++  ...|.+|++++
T Consensus         7 ~~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~--~~~~~~wl~~i   84 (188)
T PRK09640          7 ELNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEG--KSKFKTWLYSI   84 (188)
T ss_pred             CCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHH
Confidence            3566777777763    39999999999999999999999999999999999999999999999985  34799999999


Q ss_pred             HHHHHHHHhhhcCcccccC---------c---c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCH
Q 012567          346 IKQAVRKSLSDQSRTIRLP---------F---H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSM  402 (460)
Q Consensus       346 Ir~aI~~~Lrk~~r~iriP---------~---~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~  402 (460)
                      ++|.+++++|+..+.....         .   .   ..+....+.++...|+...+        .+.+++|||+.||+|.
T Consensus        85 a~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~  164 (188)
T PRK09640         85 TYNECITQYRKERRKRRLMDALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGL  164 (188)
T ss_pred             HHHHHHHHHHHhcccccCcchhhhcccccccccccccHHHHHHHHHHHHhcChhheeeeeeHHhcCCCHHHHHHHHCCCH
Confidence            9999999999754321110         0   0   11233557777777776543        6789999999999999


Q ss_pred             HHHHHHHhCCCCC
Q 012567          403 KRLHAVLLSPKAP  415 (460)
Q Consensus       403 e~Vk~~l~~ar~~  415 (460)
                      ++|+..+++++..
T Consensus       165 ~tV~~~l~Ra~~~  177 (188)
T PRK09640        165 SATKMRYKRALDK  177 (188)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999887653

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.60  E-value=6.7e-15  Score=136.21  Aligned_cols=143  Identities=13%  Similarity=0.122  Sum_probs=113.6

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567          272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (460)
Q Consensus       272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI  350 (460)
                      +...|+..+..| ..++..|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++.. ..|.||++..++|.+
T Consensus         5 ~~~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~-~~~~~wl~~ia~n~~   83 (179)
T PRK12514          5 DIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIARNHA   83 (179)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHH
Confidence            445566666666 899999999999999999999999999999999999999999999998654 469999999999999


Q ss_pred             HHHhhhcCccc-cc------------Ccch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHH
Q 012567          351 RKSLSDQSRTI-RL------------PFHM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLH  406 (460)
Q Consensus       351 ~~~Lrk~~r~i-ri------------P~~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk  406 (460)
                      ++++|++.+.. .+            |...   .+....+..++..|+...+        .+.|++|||+.||+|+++|+
T Consensus        84 ~d~~R~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~  163 (179)
T PRK12514         84 IDRLRARKAVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMR  163 (179)
T ss_pred             HHHHHhcCCcccccccchhccccCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHH
Confidence            99998765321 00            0000   1122346666666665433        68899999999999999999


Q ss_pred             HHHhCCCCC
Q 012567          407 AVLLSPKAP  415 (460)
Q Consensus       407 ~~l~~ar~~  415 (460)
                      ..+++++..
T Consensus       164 ~~l~Rar~~  172 (179)
T PRK12514        164 TWLRRSLLK  172 (179)
T ss_pred             HHHHHHHHH
Confidence            999987653

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=7.7e-15  Score=136.62  Aligned_cols=144  Identities=13%  Similarity=0.131  Sum_probs=115.9

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      ++...|+..+..| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+.+|+.+++|++.. ..|.+|++.+++|.
T Consensus         8 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~   86 (182)
T PRK12537          8 FDYEACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHL   86 (182)
T ss_pred             hhHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHH
Confidence            3445677777777 999999999999999999999999999999999999999999999998643 47999999999999


Q ss_pred             HHHHhhhcCcccccCc----------c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHH
Q 012567          350 VRKSLSDQSRTIRLPF----------H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRL  405 (460)
Q Consensus       350 I~~~Lrk~~r~iriP~----------~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~V  405 (460)
                      +++++|++.+......          .      ..+....+.+++..|+.+.+        .+.+++|||+.||+|+++|
T Consensus        87 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV  166 (182)
T PRK12537         87 ALNVLRDTRREVVLDDDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTV  166 (182)
T ss_pred             HHHHHHhccccCccccchhhhcccccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhH
Confidence            9999998764321110          0      01223456667776665433        7889999999999999999


Q ss_pred             HHHHhCCCCC
Q 012567          406 HAVLLSPKAP  415 (460)
Q Consensus       406 k~~l~~ar~~  415 (460)
                      +..+++++..
T Consensus       167 ~~~l~ra~~~  176 (182)
T PRK12537        167 KAWIKRSLKA  176 (182)
T ss_pred             HHHHHHHHHH
Confidence            9999877643

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=7.2e-15  Score=138.53  Aligned_cols=145  Identities=17%  Similarity=0.151  Sum_probs=117.2

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      +++..|+..+..| ..|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++. ...|.+|++..++|.
T Consensus        11 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~-~~~~~~wl~~ia~n~   89 (196)
T PRK12524         11 VSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQG-EARVSTWLYRVVCNL   89 (196)
T ss_pred             cCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhccccc-cchHHHHHHHHHHHH
Confidence            4667788877877 99999999999999999999999999999999999999999999999853 347999999999999


Q ss_pred             HHHHhhhcCcc-ccc---C---------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHH
Q 012567          350 VRKSLSDQSRT-IRL---P---------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRL  405 (460)
Q Consensus       350 I~~~Lrk~~r~-iri---P---------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~V  405 (460)
                      +++++|++.+. ..+   +         ..   ..+....+.+++..|+.+.+        .+.+++|||+.||+|..+|
T Consensus        90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~tV  169 (196)
T PRK12524         90 CTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAV  169 (196)
T ss_pred             HHHHHHhhcCCCCCccccccccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHH
Confidence            99999975432 110   0         00   11223456667777665433        7899999999999999999


Q ss_pred             HHHHhCCCCCc
Q 012567          406 HAVLLSPKAPR  416 (460)
Q Consensus       406 k~~l~~ar~~l  416 (460)
                      +..+++++..+
T Consensus       170 ~~~l~Ra~~~L  180 (196)
T PRK12524        170 ESLTARGKRAL  180 (196)
T ss_pred             HHHHHHHHHHH
Confidence            99999887654

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=1.2e-14  Score=140.98  Aligned_cols=130  Identities=18%  Similarity=0.154  Sum_probs=107.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ..+++.|+..|.+.|+.+++++.+++.+++|++||+|+++|+.+++|++.  ..|.+|++..++|.+++++|+..+....
T Consensus        29 ~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~~~  106 (231)
T PRK11922         29 EAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLVNL  106 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            78999999999999999999999999999999999999999999999975  4799999999999999999976542221


Q ss_pred             Cc-----------------------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012567          364 PF-----------------------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVL  409 (460)
Q Consensus       364 P~-----------------------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l  409 (460)
                      +.                       .   ..+....+.+++..|+...+        .+.+++|||+.||+|.++|+..+
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~tVk~~l  186 (231)
T PRK11922        107 AEMVMASTIAGGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRL  186 (231)
T ss_pred             hhcccccccccccccccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeehhcCCCHHHHHHHHCcCHHHHHHHH
Confidence            10                       0   01223456777777766533        67899999999999999999999


Q ss_pred             hCCCCC
Q 012567          410 LSPKAP  415 (460)
Q Consensus       410 ~~ar~~  415 (460)
                      ++++..
T Consensus       187 ~Rar~k  192 (231)
T PRK11922        187 HRARRL  192 (231)
T ss_pred             HHHHHH
Confidence            987754

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.58  E-value=1e-14  Score=135.19  Aligned_cols=142  Identities=15%  Similarity=0.142  Sum_probs=113.1

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567          272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (460)
Q Consensus       272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI  350 (460)
                      +...|+..++.| ..+++.++..|.++|+++|+++.++..+++|++||++++||+++.+|++..  .|.+|++.+++|.+
T Consensus         4 ~~~~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~   81 (187)
T PRK09641          4 LIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLT   81 (187)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHH
Confidence            345666777777 999999999999999999999999999999999999999999999999753  79999999999999


Q ss_pred             HHHhhhcCccccc----------------Cc------c---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHH
Q 012567          351 RKSLSDQSRTIRL----------------PF------H---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEA  397 (460)
Q Consensus       351 ~~~Lrk~~r~iri----------------P~------~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~  397 (460)
                      ++++|++.+....                +.      .   ..+....+..+...|+...        -.+.+++|||+.
T Consensus        82 ~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~~s~~eIA~~  161 (187)
T PRK09641         82 IDRLRKRKPDYYLDAEVAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEI  161 (187)
T ss_pred             HHHHHhcCccccccccccCCcchhhhcccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhCCCHHHHHHH
Confidence            9999986532111                00      0   0111234666666665532        278899999999


Q ss_pred             hCCCHHHHHHHHhCCCCC
Q 012567          398 TGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       398 LGIS~e~Vk~~l~~ar~~  415 (460)
                      ||+|+++|+..+++++..
T Consensus       162 lgis~~~v~~~l~Rar~~  179 (187)
T PRK09641        162 LDLPVGTVKTRIHRGREA  179 (187)
T ss_pred             HCCCHHHHHHHHHHHHHH
Confidence            999999999999877653

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.58  E-value=1.9e-14  Score=132.54  Aligned_cols=143  Identities=16%  Similarity=0.097  Sum_probs=115.4

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      |++..+...+..| ..+++.|+..|.+.|+.++++|.++..+++|++||+|+++|+++++|++.  .+|.+|++..++|.
T Consensus         3 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~   80 (176)
T PRK09638          3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL   80 (176)
T ss_pred             ccHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence            4566677777777 99999999999999999999999999999999999999999999999864  48999999999999


Q ss_pred             HHHHhhhcCcccccCc------------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHH
Q 012567          350 VRKSLSDQSRTIRLPF------------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLH  406 (460)
Q Consensus       350 I~~~Lrk~~r~iriP~------------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk  406 (460)
                      +++++|+..+......            .   .......+.+++..|+...+        .+.+++|||+.||+|+.+|+
T Consensus        81 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V~  160 (176)
T PRK09638         81 YKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVK  160 (176)
T ss_pred             HHHHHHHhccccchhhhcccccCCccchHHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcCCCHHHHHHHHCCChhHHH
Confidence            9999997653221110            0   11233456666666666533        67899999999999999999


Q ss_pred             HHHhCCCCC
Q 012567          407 AVLLSPKAP  415 (460)
Q Consensus       407 ~~l~~ar~~  415 (460)
                      ..+++++..
T Consensus       161 ~~l~ra~~~  169 (176)
T PRK09638        161 SRVHHGIKQ  169 (176)
T ss_pred             HHHHHHHHH
Confidence            999877643

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.58  E-value=1.2e-14  Score=134.79  Aligned_cols=140  Identities=12%  Similarity=0.140  Sum_probs=111.0

Q ss_pred             HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHH
Q 012567          274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  352 (460)
Q Consensus       274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~  352 (460)
                      ..|+..+..| ..++..|+..|.++|+.+|++|.+++.+++|++||+++++|+++.+|++..  .|.+|++.+++|.+++
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            3455666666 899999999999999999999999999999999999999999999999764  6999999999999999


Q ss_pred             HhhhcCcccccC----------------------cc-h--HHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhC
Q 012567          353 SLSDQSRTIRLP----------------------FH-M--VEATYRVKEARKQLYSEN--------GRHPNNEEVAEATG  399 (460)
Q Consensus       353 ~Lrk~~r~iriP----------------------~~-~--~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LG  399 (460)
                      ++|+..+.....                      .. +  .+....+.+++..|+...        -.+.+++|||+.||
T Consensus        84 ~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lg  163 (187)
T TIGR02948        84 RLRKRKPDFYLDDEVQGTDGLTMESQLAADEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMEDLSLKEISEILD  163 (187)
T ss_pred             HHHhhcccccccccccCccccccccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHC
Confidence            998754321100                      00 0  011233556666665532        36789999999999


Q ss_pred             CCHHHHHHHHhCCCCC
Q 012567          400 LSMKRLHAVLLSPKAP  415 (460)
Q Consensus       400 IS~e~Vk~~l~~ar~~  415 (460)
                      +|+++|+..+++++..
T Consensus       164 is~~~v~~~l~Rar~~  179 (187)
T TIGR02948       164 LPVGTVKTRIHRGREA  179 (187)
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            9999999999887653

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

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

Probab=99.58  E-value=1.3e-14  Score=132.31  Aligned_cols=135  Identities=16%  Similarity=0.132  Sum_probs=108.1

Q ss_pred             HHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhc
Q 012567          279 RLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  357 (460)
Q Consensus       279 ~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~  357 (460)
                      .+++| ..|++.|+..|.+.+++++.++.++..+++|++||+++++|+.+++|+...+ .|.+|++.+++|.+++++|++
T Consensus         4 ~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~   82 (170)
T TIGR02952         4 RAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGS   82 (170)
T ss_pred             HHHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhc
Confidence            34455 8999999999999999999999998899999999999999999999996544 899999999999999999986


Q ss_pred             CcccccC--------------cch---HHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567          358 SRTIRLP--------------FHM---VEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSP  412 (460)
Q Consensus       358 ~r~iriP--------------~~~---~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~a  412 (460)
                      .+....+              ...   .+....+.++...|+..        +-.+.+++|||+.||+|+++|+..++++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra  162 (170)
T TIGR02952        83 KRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRA  162 (170)
T ss_pred             CCCCCCcHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            5332211              000   11233466666666553        2378999999999999999999999877


Q ss_pred             CC
Q 012567          413 KA  414 (460)
Q Consensus       413 r~  414 (460)
                      +.
T Consensus       163 ~~  164 (170)
T TIGR02952       163 IK  164 (170)
T ss_pred             HH
Confidence            54

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.

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.57  E-value=2e-14  Score=135.31  Aligned_cols=144  Identities=17%  Similarity=0.168  Sum_probs=117.9

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      +++..++..+..| ..+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+.+++|++.  ..|.+|++.+++|.
T Consensus        12 ~~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~   89 (192)
T PRK09643         12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNA   89 (192)
T ss_pred             cCHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHH
Confidence            4566777777777 99999999999999999999999999999999999999999999999964  36999999999999


Q ss_pred             HHHHhhhcCcccccC-----------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHH
Q 012567          350 VRKSLSDQSRTIRLP-----------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHA  407 (460)
Q Consensus       350 I~~~Lrk~~r~iriP-----------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~  407 (460)
                      +++++|+.++....+           ..   ..+....+..++..|+...+        .+.+++|||+.||+|..+|+.
T Consensus        90 ~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~  169 (192)
T PRK09643         90 CLDRLRRAKARPTVPLDDVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKS  169 (192)
T ss_pred             HHHHHHccccCCCCCccccccccCCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Confidence            999999765322111           01   12334557777777766433        788999999999999999999


Q ss_pred             HHhCCCCCc
Q 012567          408 VLLSPKAPR  416 (460)
Q Consensus       408 ~l~~ar~~l  416 (460)
                      .+++++..+
T Consensus       170 rl~rar~~L  178 (192)
T PRK09643        170 RCARGRARL  178 (192)
T ss_pred             HHHHHHHHH
Confidence            998877643

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.56  E-value=2.1e-14  Score=139.97  Aligned_cols=144  Identities=17%  Similarity=0.177  Sum_probs=115.4

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567          272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (460)
Q Consensus       272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI  350 (460)
                      ++..|+..+..| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+.+++|++..+ .|.+|++.+++|.+
T Consensus        49 ~d~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~  127 (233)
T PRK12538         49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC  127 (233)
T ss_pred             cHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence            456677777777 8999999999999999999999999999999999999999999999986444 79999999999999


Q ss_pred             HHHhhhcCccc--cc-------Ccc-----hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHH
Q 012567          351 RKSLSDQSRTI--RL-------PFH-----MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAV  408 (460)
Q Consensus       351 ~~~Lrk~~r~i--ri-------P~~-----~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~  408 (460)
                      ++++|++.+..  ..       +..     ..+....+..++..|+...+        .+.+++|||+.||+|+++|+..
T Consensus       128 id~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~~  207 (233)
T PRK12538        128 IDLRRKPRTENVDAVPEVADGKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESL  207 (233)
T ss_pred             HHHHHhhcccccccccccccCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHHH
Confidence            99998754211  00       110     01222346677777766433        7889999999999999999999


Q ss_pred             HhCCCCCc
Q 012567          409 LLSPKAPR  416 (460)
Q Consensus       409 l~~ar~~l  416 (460)
                      +++++..+
T Consensus       208 l~RAr~kL  215 (233)
T PRK12538        208 LKRGRQQL  215 (233)
T ss_pred             HHHHHHHH
Confidence            99887643

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.56  E-value=1.4e-14  Score=134.88  Aligned_cols=142  Identities=12%  Similarity=0.079  Sum_probs=112.7

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHH
Q 012567          273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  351 (460)
Q Consensus       273 e~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~  351 (460)
                      ...+...+..| ..+++.|+..|.+.|+.++++|.++..+.+|++||+|+++|+.+++|++.++ .|.+|++.+++|.++
T Consensus        12 ~~~l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~   90 (187)
T PRK12534         12 TGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAI   90 (187)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHH
Confidence            34445554556 8999999999999999999999999999999999999999999999997644 689999999999999


Q ss_pred             HHhhhcCcccc------cC---------cc---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHH
Q 012567          352 KSLSDQSRTIR------LP---------FH---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRL  405 (460)
Q Consensus       352 ~~Lrk~~r~ir------iP---------~~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~V  405 (460)
                      +++|++.+...      .+         ..   ..+....+..++..|+...        -.+.+++|||+.||+|+++|
T Consensus        91 d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v  170 (187)
T PRK12534         91 DHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTV  170 (187)
T ss_pred             HHHHhcccccccccccchhhhccccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHH
Confidence            99997643110      00         00   1223445666777765543        27899999999999999999


Q ss_pred             HHHHhCCCCC
Q 012567          406 HAVLLSPKAP  415 (460)
Q Consensus       406 k~~l~~ar~~  415 (460)
                      +..+++++..
T Consensus       171 ~~~l~Rar~~  180 (187)
T PRK12534        171 KSWIRRGLAK  180 (187)
T ss_pred             HHHHHHHHHH
Confidence            9999987653

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.56  E-value=1.8e-14  Score=135.57  Aligned_cols=141  Identities=16%  Similarity=0.101  Sum_probs=111.5

Q ss_pred             HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHH
Q 012567          274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  352 (460)
Q Consensus       274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~  352 (460)
                      ..++..+..| ..+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+.+|++..+ .|.+|++.+++|.+++
T Consensus        15 ~~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld   93 (194)
T PRK12531         15 LECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFD   93 (194)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHH
Confidence            3455666667 8999999999999999999999999889999999999999999999996443 7999999999999999


Q ss_pred             HhhhcCccc-cc------Cc---------c-h---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHH
Q 012567          353 SLSDQSRTI-RL------PF---------H-M---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKR  404 (460)
Q Consensus       353 ~Lrk~~r~i-ri------P~---------~-~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~  404 (460)
                      ++|+..+.. ..      +.         . .   ......+.+++..|+.+.+        .+.+++|||+.||+|+++
T Consensus        94 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~t  173 (194)
T PRK12531         94 LLRKQKGKDLHIHADDIWPSDYYPPDLVDHYSPEQDMLKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGT  173 (194)
T ss_pred             HHHHhcccccccchhhcccccccccccccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHH
Confidence            999854311 10      00         0 0   0112346666666665433        788999999999999999


Q ss_pred             HHHHHhCCCCC
Q 012567          405 LHAVLLSPKAP  415 (460)
Q Consensus       405 Vk~~l~~ar~~  415 (460)
                      |+..+++++..
T Consensus       174 Vk~rl~ra~~~  184 (194)
T PRK12531        174 VKSRLRLAVEK  184 (194)
T ss_pred             HHHHHHHHHHH
Confidence            99999877653

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.56  E-value=3.3e-14  Score=132.08  Aligned_cols=142  Identities=17%  Similarity=0.183  Sum_probs=113.1

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567          272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (460)
Q Consensus       272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI  350 (460)
                      ++..|+..+..| ..+++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+.+.+|++.  ..|.+|++.+.+|.+
T Consensus         6 ~d~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~   83 (190)
T TIGR02939         6 LDLELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTA   83 (190)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHH
Confidence            455677777777 89999999999999999999999999999999999999999999999964  479999999999999


Q ss_pred             HHHhhhcCccccc----------------------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHH
Q 012567          351 RKSLSDQSRTIRL----------------------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEA  397 (460)
Q Consensus       351 ~~~Lrk~~r~iri----------------------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~  397 (460)
                      +++++++.+....                      |..   ..+....+..+...|+....        .+.+++|||+.
T Consensus        84 ~~~~r~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~  163 (190)
T TIGR02939        84 KNHLVAQGRRPPTSDVEIEDAEHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEGLSYEDIARI  163 (190)
T ss_pred             HHHHHHhccCCCcccccccchhhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcCCCHHHHHHH
Confidence            9999764432110                      000   01122346666666665433        67899999999


Q ss_pred             hCCCHHHHHHHHhCCCCC
Q 012567          398 TGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       398 LGIS~e~Vk~~l~~ar~~  415 (460)
                      ||+|+.+|+..+++++..
T Consensus       164 lgis~~tv~~~l~rar~~  181 (190)
T TIGR02939       164 MDCPVGTVRSRIFRAREA  181 (190)
T ss_pred             HCcCHHHHHHHHHHHHHH
Confidence            999999999999987654

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.

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.56  E-value=2.5e-14  Score=134.03  Aligned_cols=142  Identities=22%  Similarity=0.242  Sum_probs=111.9

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567          272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (460)
Q Consensus       272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI  350 (460)
                      +...|+..+..| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+. ..|++..+ .|.||++.+++|.+
T Consensus        15 ~~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~   92 (194)
T PRK12519         15 SDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRA   92 (194)
T ss_pred             cHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHH
Confidence            455677766777 9999999999999999999999999999999999999999976 67886554 79999999999999


Q ss_pred             HHHhhhcCccccc------------Cc-c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHH
Q 012567          351 RKSLSDQSRTIRL------------PF-H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMK  403 (460)
Q Consensus       351 ~~~Lrk~~r~iri------------P~-~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e  403 (460)
                      ++++|++.+....            +. .      ..+....+..++..|+.+.+        .+.+++|||+.||+|+.
T Consensus        93 ~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~  172 (194)
T PRK12519         93 IDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLG  172 (194)
T ss_pred             HHHHHhcccccchhhhhhhhhcccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHH
Confidence            9999976532110            00 0      01123446666666665433        68899999999999999


Q ss_pred             HHHHHHhCCCCC
Q 012567          404 RLHAVLLSPKAP  415 (460)
Q Consensus       404 ~Vk~~l~~ar~~  415 (460)
                      +|+..+++++..
T Consensus       173 tV~~~l~Ra~~~  184 (194)
T PRK12519        173 TVKARARQGLLK  184 (194)
T ss_pred             HHHHHHHHHHHH
Confidence            999999877643

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.55  E-value=2.5e-14  Score=131.04  Aligned_cols=134  Identities=19%  Similarity=0.184  Sum_probs=106.5

Q ss_pred             Hhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567          280 LNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (460)
Q Consensus       280 l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~  358 (460)
                      ++.| ..|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++.+|+  .+.+|.+|++.++++.+.+.+|+..
T Consensus         4 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~   81 (182)
T PRK09652          4 VQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQG   81 (182)
T ss_pred             hhcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHccc
Confidence            3445 889999999999999999999999999999999999999999999999  4568999999999999999998754


Q ss_pred             cccccC----------------------cch---HHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHH
Q 012567          359 RTIRLP----------------------FHM---VEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRL  405 (460)
Q Consensus       359 r~iriP----------------------~~~---~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~V  405 (460)
                      +....+                      ...   ......+..+...|+..        +..+.+++|||+.||+|+.+|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV  161 (182)
T PRK09652         82 RRPPASDVDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTV  161 (182)
T ss_pred             CCCCccccccccccccccccccccccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHH
Confidence            432111                      000   11234455555555443        237889999999999999999


Q ss_pred             HHHHhCCCCC
Q 012567          406 HAVLLSPKAP  415 (460)
Q Consensus       406 k~~l~~ar~~  415 (460)
                      +..+++++..
T Consensus       162 ~~~l~ra~~~  171 (182)
T PRK09652        162 RSRIFRAREA  171 (182)
T ss_pred             HHHHHHHHHH
Confidence            9998876543

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.54  E-value=4.3e-14  Score=134.61  Aligned_cols=139  Identities=14%  Similarity=0.088  Sum_probs=109.3

Q ss_pred             HHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHh
Q 012567          276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  354 (460)
Q Consensus       276 L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~L  354 (460)
                      |...+..| ..+++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+.+.+|++.++ .|.+|++.+++|.+++++
T Consensus        28 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~  106 (206)
T PRK12526         28 LILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDML  106 (206)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHH
Confidence            44444555 8999999999999999999999999899999999999999999999997654 699999999999999999


Q ss_pred             hhcCccccc-------Cc---------chHH-----HHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHH
Q 012567          355 SDQSRTIRL-------PF---------HMVE-----ATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRL  405 (460)
Q Consensus       355 rk~~r~iri-------P~---------~~~e-----~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~V  405 (460)
                      |++.+....       |.         ....     ....+.+++..|+.+        +-.+.|++|||+.||+|+.+|
T Consensus       107 Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV  186 (206)
T PRK12526        107 RKIKAKKEQNLGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTV  186 (206)
T ss_pred             HHhccccccccccccchhhhhcccccCchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHH
Confidence            875432110       00         0000     112356666666554        337899999999999999999


Q ss_pred             HHHHhCCCCC
Q 012567          406 HAVLLSPKAP  415 (460)
Q Consensus       406 k~~l~~ar~~  415 (460)
                      +..+++++..
T Consensus       187 ~~~l~Ra~~~  196 (206)
T PRK12526        187 KSRLRLALAK  196 (206)
T ss_pred             HHHHHHHHHH
Confidence            9999877654

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.53  E-value=6.9e-14  Score=130.10  Aligned_cols=140  Identities=17%  Similarity=0.113  Sum_probs=109.6

Q ss_pred             HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccC-CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHH
Q 012567          274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQG-AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  351 (460)
Q Consensus       274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~-~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~  351 (460)
                      ..++..+..| ..|++.|+..|.+.|+.++.++.+ +..+.+|++||+|+.+|+.++.|++.  ..|.+|++.+++|.++
T Consensus         9 ~~~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~   86 (181)
T PRK12536          9 RALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLM   86 (181)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHH
Confidence            3455555555 899999999999999999988664 57899999999999999999999964  4799999999999999


Q ss_pred             HHhhhcCcccccC--------------cchHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012567          352 KSLSDQSRTIRLP--------------FHMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVL  409 (460)
Q Consensus       352 ~~Lrk~~r~iriP--------------~~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l  409 (460)
                      +++|++.+.....              ....+....+.+++..|+...+        .+.+++|||+.||+|+++|+..+
T Consensus        87 d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l  166 (181)
T PRK12536         87 DFLRSRARREALHDPLDDESELFATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGI  166 (181)
T ss_pred             HHHHHHhccccccCCccchhhhcCCCCcchHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            9999854321100              0112233456677776655322        78899999999999999999999


Q ss_pred             hCCCCC
Q 012567          410 LSPKAP  415 (460)
Q Consensus       410 ~~ar~~  415 (460)
                      ++++..
T Consensus       167 ~rar~~  172 (181)
T PRK12536        167 HRGLKA  172 (181)
T ss_pred             HHHHHH
Confidence            877653

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.53  E-value=7.4e-14  Score=130.73  Aligned_cols=141  Identities=15%  Similarity=0.172  Sum_probs=111.9

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHH
Q 012567          273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  351 (460)
Q Consensus       273 e~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~  351 (460)
                      ...|+..++.| ..+++.|+..|.+.|+.+++++.++..+.+|++||+|+++|+++.+|++..  .|.+|++.+++|.++
T Consensus         7 ~~~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~   84 (193)
T PRK11923          7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK   84 (193)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence            44566667777 899999999999999999999999999999999999999999999999763  599999999999999


Q ss_pred             HHhhhcCcccc-----c-----------------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHh
Q 012567          352 KSLSDQSRTIR-----L-----------------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEAT  398 (460)
Q Consensus       352 ~~Lrk~~r~ir-----i-----------------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~L  398 (460)
                      +++|++.+...     +                 |..   ..+....+..++..|+...+        .+.+++|||+.|
T Consensus        85 d~~rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l  164 (193)
T PRK11923         85 NHLVSRGRRPPDSDVSSEDAEFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVM  164 (193)
T ss_pred             HHHHHhcCCCccccccccchhhhcccccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcCCCHHHHHHHH
Confidence            99986443211     0                 000   01122345566666655433        678999999999


Q ss_pred             CCCHHHHHHHHhCCCCC
Q 012567          399 GLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       399 GIS~e~Vk~~l~~ar~~  415 (460)
                      |+|.++|+..+++++..
T Consensus       165 gis~~tv~~~l~Rar~~  181 (193)
T PRK11923        165 QCPVGTVRSRIFRAREA  181 (193)
T ss_pred             CCCHHHHHHHHHHHHHH
Confidence            99999999999887653

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.52  E-value=2.9e-14  Score=132.92  Aligned_cols=134  Identities=13%  Similarity=0.099  Sum_probs=108.6

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  362 (460)
Q Consensus       283 G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir  362 (460)
                      +..++..|+..|.+.++.+|.++.++..+++|++||.|+.+|+.+.+|+...+..|.||++.+++|.+++++|++.+...
T Consensus         7 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~~   86 (185)
T PRK12542          7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHET   86 (185)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence            38899999999999999999999999999999999999999999999986544589999999999999999998654221


Q ss_pred             cC------------cch------HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          363 LP------------FHM------VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       363 iP------------~~~------~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                      ..            ...      ......+.+++..|+...+        .+.+++|||+.||+|+++|++.+++++..+
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L  166 (185)
T PRK12542         87 FLEEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRV  166 (185)
T ss_pred             hhhhccccchhhhhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            10            000      1112346667777666433        789999999999999999999999877543

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.52  E-value=9.9e-14  Score=129.37  Aligned_cols=141  Identities=13%  Similarity=0.107  Sum_probs=111.8

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHH----HccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHH
Q 012567          273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAK----NYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK  347 (460)
Q Consensus       273 e~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAk----ry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr  347 (460)
                      ...|+..+..| ..|++.|+..|.+.|+.+++    ++.++..+.+|++||+++.+|+.+.+|++.  ..|.+|++.+++
T Consensus         8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~--~~f~~wl~~i~~   85 (184)
T PRK12539          8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPE--QPLTPWVYAIAR   85 (184)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCC--CChHHHHHHHHH
Confidence            44566666666 89999999999999999976    556788999999999999999999999974  369999999999


Q ss_pred             HHHHHHhhhcCcc-cccC---------c---chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHH
Q 012567          348 QAVRKSLSDQSRT-IRLP---------F---HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLH  406 (460)
Q Consensus       348 ~aI~~~Lrk~~r~-iriP---------~---~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk  406 (460)
                      |.+++++|+..+. ...+         .   ...+....+..++..|+...+        .+.+++|||+.||+|+++|+
T Consensus        86 n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~  165 (184)
T PRK12539         86 YKLIDHLRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK  165 (184)
T ss_pred             HHHHHHHHHHhccccccChhhhccccCCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHH
Confidence            9999999985431 1111         0   112334557777777766533        78899999999999999999


Q ss_pred             HHHhCCCCC
Q 012567          407 AVLLSPKAP  415 (460)
Q Consensus       407 ~~l~~ar~~  415 (460)
                      ..+++++..
T Consensus       166 ~~l~ra~~~  174 (184)
T PRK12539        166 VSVHRGLKA  174 (184)
T ss_pred             HHHHHHHHH
Confidence            999877653

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

Probab=99.51  E-value=1.8e-13  Score=127.59  Aligned_cols=134  Identities=18%  Similarity=0.169  Sum_probs=111.4

Q ss_pred             HhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCc
Q 012567          280 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  359 (460)
Q Consensus       280 l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r  359 (460)
                      ......++..++..|.+.++.+++++.++..+.+||+||+|+.+|+++..| .. +..|.||++.+++|.+++++|+.++
T Consensus        10 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~r   87 (182)
T COG1595          10 LRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRKR   87 (182)
T ss_pred             HhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhcc
Confidence            344488999999999999999999999998899999999999999999999 33 4589999999999999999997654


Q ss_pred             cccc-C-------------cch-----HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567          360 TIRL-P-------------FHM-----VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSP  412 (460)
Q Consensus       360 ~iri-P-------------~~~-----~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~a  412 (460)
                      .... +             ...     .+....+.+++..|+.+++        .+.|++|||+.||||+++|++.++++
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra  167 (182)
T COG1595          88 RRARVEEADLLPEEADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRA  167 (182)
T ss_pred             cccccccccccccccCcccccchHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3221 0             001     2344668888888887655        78999999999999999999999987


Q ss_pred             CCC
Q 012567          413 KAP  415 (460)
Q Consensus       413 r~~  415 (460)
                      +..
T Consensus       168 ~~~  170 (182)
T COG1595         168 RKK  170 (182)
T ss_pred             HHH
Confidence            653

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

Probab=99.51  E-value=1.2e-13  Score=135.80  Aligned_cols=145  Identities=6%  Similarity=-0.008  Sum_probs=117.0

Q ss_pred             hCCCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHH-------HHhhcCCCCCCchHh
Q 012567          269 AGVDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR-------GAEKFDASKGFKFST  340 (460)
Q Consensus       269 ~g~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLir-------AiekFDp~kG~rFST  340 (460)
                      ++.++..|+..++.| ..|+..|+..|.+.|+.++.++.++..+++|++||.|+.+|.       .+.+|++.  ..|.|
T Consensus        22 ~~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~t   99 (244)
T TIGR03001        22 LHAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLS   99 (244)
T ss_pred             ccccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHh
Confidence            445677788888888 899999999999999999999999999999999999999994       78889863  47999


Q ss_pred             HHHHHHHHHHHHHhhhcCcccccC---------------cch-H------HHHHHHHHHHHHHHHHhC--------CCCC
Q 012567          341 YAHWWIKQAVRKSLSDQSRTIRLP---------------FHM-V------EATYRVKEARKQLYSENG--------RHPN  390 (460)
Q Consensus       341 YA~~wIr~aI~~~Lrk~~r~iriP---------------~~~-~------e~i~kl~ka~~~L~~~~g--------r~pS  390 (460)
                      |++.+++|.+++++|++.+...+.               ... .      +....+.+++.+|+...+        .+.|
T Consensus       100 WL~~Ia~N~~id~lRk~~r~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg~S  179 (244)
T TIGR03001       100 WVRIVATRIALELQAQERRHSPVEEPTELAALPAPGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGLS  179 (244)
T ss_pred             HHHHHHHHHHHHHHHHhcccCccccccccccccCCCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCC
Confidence            999999999999999755321110               000 0      122346777777777543        7899


Q ss_pred             HHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          391 NEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       391 ~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      ++|||+.||||+++|+..+++++..
T Consensus       180 ~~EIA~~Lgis~~TVk~rl~RAr~~  204 (244)
T TIGR03001       180 MDRIGAMYQVHRSTVSRWVAQARER  204 (244)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            9999999999999999999887653

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.

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.51  E-value=1.3e-13  Score=128.86  Aligned_cols=144  Identities=14%  Similarity=0.110  Sum_probs=115.4

Q ss_pred             CCHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          271 VDQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       271 ~de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      +++..|...+..| ..+++.|+..|.+.++.++.++.++..+.+|++||+|+.+|+.+.+|++.  ..|.+|++..++|.
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            4667777777777 89999999999999999999999999999999999999999999999963  47999999999999


Q ss_pred             HHHHhhhcCccccc-------Cc------c---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHH
Q 012567          350 VRKSLSDQSRTIRL-------PF------H---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRL  405 (460)
Q Consensus       350 I~~~Lrk~~r~iri-------P~------~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~V  405 (460)
                      +++++++..+....       +.      .   ..+....+.++...|+.+.+        .+.+++|||+.||+|+++|
T Consensus        85 ~~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV  164 (189)
T PRK12515         85 ALSALRRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTV  164 (189)
T ss_pred             HHHHHHccCCCCCccccccccCCCCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHH
Confidence            99999975432110       00      0   01122345666666655433        7899999999999999999


Q ss_pred             HHHHhCCCCCc
Q 012567          406 HAVLLSPKAPR  416 (460)
Q Consensus       406 k~~l~~ar~~l  416 (460)
                      +..+++++..+
T Consensus       165 ~~~l~Rar~~L  175 (189)
T PRK12515        165 KTRMFYARKKL  175 (189)
T ss_pred             HHHHHHHHHHH
Confidence            99999887543

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

Probab=99.50  E-value=8.9e-14  Score=125.62  Aligned_cols=128  Identities=13%  Similarity=0.121  Sum_probs=103.9

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC-
Q 012567          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP-  364 (460)
Q Consensus       286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP-  364 (460)
                      +++.++..|.+.|+.+++++.++..+.+|++||+++.+|+++++|++..  .|.+|++..++|.+++++|++.+..... 
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~~~   79 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLVFD   79 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccccC
Confidence            7899999999999999999999999999999999999999999999753  6999999999999999999865432110 


Q ss_pred             cc----------------hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          365 FH----------------MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       365 ~~----------------~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      ..                ..+....+.+++..|+...        -.+.+++|||+.||||.++|+..+++++..
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~  154 (159)
T TIGR02989        80 DELLEALAAEAEATEADRSEDELQALEGCLEKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVR  154 (159)
T ss_pred             HHHHHHHHhhcccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            00                0112233566666665542        278899999999999999999999887654

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).

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.50  E-value=1.3e-13  Score=129.17  Aligned_cols=141  Identities=15%  Similarity=0.112  Sum_probs=112.7

Q ss_pred             HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHH
Q 012567          274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  352 (460)
Q Consensus       274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~  352 (460)
                      ..|+..+..| ..+++.|+..|.+.++.++. +.++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++
T Consensus        12 ~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d   88 (185)
T PRK09649         12 TALALSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVAD   88 (185)
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHH
Confidence            3456666666 89999999999999999995 67888899999999999999999999964  47999999999999999


Q ss_pred             HhhhcCccccc-----Ccc---------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567          353 SLSDQSRTIRL-----PFH---------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLL  410 (460)
Q Consensus       353 ~Lrk~~r~iri-----P~~---------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~  410 (460)
                      ++|++.+..+.     +..         ..+....+.+++..|+.+++        .+.|++|||+.||+|+++|+..++
T Consensus        89 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~  168 (185)
T PRK09649         89 HIRHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVA  168 (185)
T ss_pred             HHHHhccccccccccchhhccChhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            99975432111     110         01223457777777776544        788999999999999999999999


Q ss_pred             CCCCCcc
Q 012567          411 SPKAPRS  417 (460)
Q Consensus       411 ~ar~~lS  417 (460)
                      +++..+.
T Consensus       169 Rar~~Lr  175 (185)
T PRK09649        169 RARDALL  175 (185)
T ss_pred             HHHHHHH
Confidence            8877554

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

Probab=99.49  E-value=1.2e-13  Score=127.89  Aligned_cols=140  Identities=18%  Similarity=0.190  Sum_probs=106.9

Q ss_pred             HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCC-----CcccHHhHHHHHHHH-HHhhcCCCCCCchHhHHHHHH
Q 012567          274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGM-----NLQDLVQEGCRGLVR-GAEKFDASKGFKFSTYAHWWI  346 (460)
Q Consensus       274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~-----d~eDLiQEG~IGLir-AiekFDp~kG~rFSTYA~~wI  346 (460)
                      ..|+..+..| ..|++.|+..|.+.++.+|++|.++..     +++|++||+|+.+|+ ...+|++.  ..|.+|++.++
T Consensus         5 ~~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~   82 (183)
T TIGR02999         5 TELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAM   82 (183)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHH
Confidence            4456666667 899999999999999999999998877     899999999999998 78888753  37999999999


Q ss_pred             HHHHHHHhhhcCcccc------c------Cc---chHHHHHHHHHHHHH---HHHHhC--------CCCCHHHHHHHhCC
Q 012567          347 KQAVRKSLSDQSRTIR------L------PF---HMVEATYRVKEARKQ---LYSENG--------RHPNNEEVAEATGL  400 (460)
Q Consensus       347 r~aI~~~Lrk~~r~ir------i------P~---~~~e~i~kl~ka~~~---L~~~~g--------r~pS~eEIAe~LGI  400 (460)
                      +|.+++++|++.+..+      .      +.   ...+....+..+...   |+.+++        .+.|++|||+.|||
T Consensus        83 ~n~~~d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgi  162 (183)
T TIGR02999        83 RRILVDHARRRRAQKRGGGAVRVPLDEVLPDAEADLDEELLDLDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLGV  162 (183)
T ss_pred             HHHHHHHHHHHHHHhccCCccccccccccCCCCccHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence            9999999987432111      0      10   111222223333333   555433        78999999999999


Q ss_pred             CHHHHHHHHhCCCCC
Q 012567          401 SMKRLHAVLLSPKAP  415 (460)
Q Consensus       401 S~e~Vk~~l~~ar~~  415 (460)
                      |+++|+..+++++..
T Consensus       163 s~~tVk~~l~Rar~~  177 (183)
T TIGR02999       163 SVRTVERDWRFARAW  177 (183)
T ss_pred             CHHHHHHHHHHHHHH
Confidence            999999999987653

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.

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.48  E-value=1.6e-13  Score=126.54  Aligned_cols=129  Identities=9%  Similarity=0.047  Sum_probs=104.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc-
Q 012567          285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL-  363 (460)
Q Consensus       285 ~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri-  363 (460)
                      ..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+.+++|++.  .+|.+|++..++|.+++++|++.+.... 
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~Rk~~~~~~~~   80 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYV--ENYKKWITTICVRTFYDFYRKKKRWKDRI   80 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCc--cchHHHHHHHHHHHHHHHHHHhccccccc
Confidence            4589999999999999999999999999999999999999999999974  3799999999999999999876532110 


Q ss_pred             --------------------Ccc--hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567          364 --------------------PFH--MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPK  413 (460)
Q Consensus       364 --------------------P~~--~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar  413 (460)
                                          |..  ..+....+.+++..|+....        .+.+++|||+.||+|+++|+..+++++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~  160 (173)
T PRK12522         81 LDLFHKEDGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAK  160 (173)
T ss_pred             ccccchhhhhhhccccCCCChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence                                000  01223346666666666433        788999999999999999999999876


Q ss_pred             CC
Q 012567          414 AP  415 (460)
Q Consensus       414 ~~  415 (460)
                      ..
T Consensus       161 ~~  162 (173)
T PRK12522        161 KQ  162 (173)
T ss_pred             HH
Confidence            54

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.48  E-value=3.5e-13  Score=125.26  Aligned_cols=138  Identities=15%  Similarity=0.139  Sum_probs=108.7

Q ss_pred             HHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccC----CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567          276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQG----AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (460)
Q Consensus       276 L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~----~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI  350 (460)
                      ++..+..| ..|++.|+..|.+.|+.+++++.+    +..+++|++||+++.+|...++|+..  ..|.+|++.+++|.+
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            44455555 999999999999999999998875    34689999999999999999999863  479999999999999


Q ss_pred             HHHhhhcCccccc---------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHh
Q 012567          351 RKSLSDQSRTIRL---------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLL  410 (460)
Q Consensus       351 ~~~Lrk~~r~iri---------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~  410 (460)
                      .+++|++.+....         |..   .......+.++...|+...+        .+.+++|||+.||+|..+|+..++
T Consensus        90 ~d~~Rr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~  169 (184)
T PRK12512         90 IDALRRRGRRVFVDIDDFAETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALH  169 (184)
T ss_pred             HHHHHhhcccccCCchhccccccccchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            9999876543221         110   11223456667776666433        788999999999999999999998


Q ss_pred             CCCCC
Q 012567          411 SPKAP  415 (460)
Q Consensus       411 ~ar~~  415 (460)
                      +++..
T Consensus       170 ra~~~  174 (184)
T PRK12512        170 RGLAA  174 (184)
T ss_pred             HHHHH
Confidence            77653

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.48  E-value=1.4e-13  Score=129.03  Aligned_cols=129  Identities=14%  Similarity=0.161  Sum_probs=105.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc
Q 012567          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (460)
Q Consensus       286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~  365 (460)
                      +++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+.+.+|++.  .+|.+|++.+++|.+++++|++.+....+.
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            689999999999999999999999999999999999999999999854  379999999999999999998654321110


Q ss_pred             ------------------------------c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCC
Q 012567          366 ------------------------------H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLS  401 (460)
Q Consensus       366 ------------------------------~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS  401 (460)
                                                    .      ..+....+..++..|+...+        .+.|++|||+.||+|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis  160 (191)
T PRK12520         81 DDADEQSDDDLFDALFAADGHYREPPSDWGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQIT  160 (191)
T ss_pred             cccccchhhhhhhhhcccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCC
Confidence                                          0      01122346677777766543        688999999999999


Q ss_pred             HHHHHHHHhCCCCCc
Q 012567          402 MKRLHAVLLSPKAPR  416 (460)
Q Consensus       402 ~e~Vk~~l~~ar~~l  416 (460)
                      +++|+..+++++..+
T Consensus       161 ~~tV~~~l~Rar~~L  175 (191)
T PRK12520        161 ATNAWVLLYRARMRL  175 (191)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999999887643

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.47  E-value=2.4e-13  Score=124.94  Aligned_cols=132  Identities=14%  Similarity=0.062  Sum_probs=106.1

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  362 (460)
Q Consensus       283 G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir  362 (460)
                      +..+++.|+..|.+.|+.++.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++.+++|.+++++|++.+...
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            4789999999999999999999999989999999999999999999997532 479999999999999999997543211


Q ss_pred             --------cC-----cch--HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          363 --------LP-----FHM--VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       363 --------iP-----~~~--~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                              .+     ...  ......+..++..|+...+        .+.+++|||+.||+|+++|+..+++++..
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~  161 (173)
T PRK09645         86 EGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRA  161 (173)
T ss_pred             ccccccccCCCCCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence                    01     111  1112346677777766433        78999999999999999999999877653

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

Probab=99.47  E-value=1.9e-13  Score=119.73  Aligned_cols=127  Identities=21%  Similarity=0.291  Sum_probs=101.7

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCc------
Q 012567          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR------  359 (460)
Q Consensus       286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r------  359 (460)
                      |++.++..|.++|+++++++.+++.+.+|++|+|+++++++++.|++.  ..|.+|+.+++++.+.++++++.+      
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~~~~~~~   79 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRRLRRELD   79 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhccCCcchh
Confidence            689999999999999999999999999999999999999999999987  689999999999999999998763      


Q ss_pred             c-ccc------Ccc---hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          360 T-IRL------PFH---MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       360 ~-iri------P~~---~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      . ...      |..   .......+.++...|+..        +..+.+..|||+.+|+|..+|...+.+++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~  152 (158)
T TIGR02937        80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK  152 (158)
T ss_pred             hhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            0 000      000   112233455555555432        246789999999999999999999886543

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.

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.47  E-value=2.4e-13  Score=124.19  Aligned_cols=137  Identities=15%  Similarity=0.075  Sum_probs=108.1

Q ss_pred             HHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhh
Q 012567          277 RRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  355 (460)
Q Consensus       277 ~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lr  355 (460)
                      ...+..| ..|++.++..|.+.|+.+++++.++..+.+|++||++++||+.+.+|+  .+..|.+|++.++++.++++++
T Consensus         4 ~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r   81 (179)
T PRK11924          4 MPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLR   81 (179)
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHH
Confidence            3444555 899999999999999999999999999999999999999999999998  3458999999999999999998


Q ss_pred             hcCcccccCc-------------c------hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHH
Q 012567          356 DQSRTIRLPF-------------H------MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAV  408 (460)
Q Consensus       356 k~~r~iriP~-------------~------~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~  408 (460)
                      +..+......             .      ..+....+..++..|+..        +..+.+.+|||+.||+|..+|+..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~  161 (179)
T PRK11924         82 RRRREKAVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSR  161 (179)
T ss_pred             hcccccccCcccccccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence            7544222110             0      112233455555555443        236889999999999999999999


Q ss_pred             HhCCCCC
Q 012567          409 LLSPKAP  415 (460)
Q Consensus       409 l~~ar~~  415 (460)
                      +++++..
T Consensus       162 ~~ra~~~  168 (179)
T PRK11924        162 LRRARQL  168 (179)
T ss_pred             HHHHHHH
Confidence            9877643

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.46  E-value=2.5e-13  Score=126.16  Aligned_cols=130  Identities=13%  Similarity=0.127  Sum_probs=106.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR-  362 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir-  362 (460)
                      ..++..|+..|.+.|+.+++.|.++..+.+|++||+|+.+|+++.+|++..  .|.+|++.+++|.+.+++++..+..+ 
T Consensus         6 ~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~~~   83 (179)
T PRK12543          6 QEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRFRI   83 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccccc
Confidence            789999999999999999999999999999999999999999999999763  69999999999999999876432111 


Q ss_pred             --------------cCcch--HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          363 --------------LPFHM--VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       363 --------------iP~~~--~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                                    .|...  .+....+.++...|+...+        .+.+++|||+.||||+++|+..+++++..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~  160 (179)
T PRK12543         84 FEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK  160 (179)
T ss_pred             ccccccccccccccChHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                          11111  1234556677777766433        78899999999999999999999877654

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

Probab=99.46  E-value=2.5e-13  Score=127.44  Aligned_cols=131  Identities=15%  Similarity=0.098  Sum_probs=107.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ..+|+.|+..|.+.|+.+++++.++..+++|++||.|+.+|+.+.+|++.  ..|.+|++.+++|.+++++|++.+....
T Consensus        10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~   87 (193)
T TIGR02947        10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ   87 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence            78899999999999999999999999999999999999999999999863  4799999999999999999976532111


Q ss_pred             C--------------cc------h-------HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHH
Q 012567          364 P--------------FH------M-------VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAV  408 (460)
Q Consensus       364 P--------------~~------~-------~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~  408 (460)
                      .              ..      .       ......+..++..|+...+        .+.|++|||+.||+|+++|+..
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~  167 (193)
T TIGR02947        88 SDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSR  167 (193)
T ss_pred             ccchhhhhhhhccccccccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHH
Confidence            0              00      0       0112456777777777544        6789999999999999999999


Q ss_pred             HhCCCCCc
Q 012567          409 LLSPKAPR  416 (460)
Q Consensus       409 l~~ar~~l  416 (460)
                      +++++..+
T Consensus       168 l~Rar~~L  175 (193)
T TIGR02947       168 LHRGRKQL  175 (193)
T ss_pred             HHHHHHHH
Confidence            99887643

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.46  E-value=3.6e-13  Score=126.65  Aligned_cols=131  Identities=13%  Similarity=0.117  Sum_probs=107.8

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  362 (460)
Q Consensus       283 G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir  362 (460)
                      +..++..|+..|.+.++.+|+++.++..+++|++||.|+.+|+...+|+..  ..|.+|++++++|.+++++|++.+...
T Consensus         8 ~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~~   85 (187)
T PRK12516          8 GTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREVQ   85 (187)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCcc
Confidence            378999999999999999999999999999999999999999999999854  369999999999999999998654221


Q ss_pred             cCc-------------chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          363 LPF-------------HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       363 iP~-------------~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      ...             ........+..++..|+...+        .+.+++|||+.||+|+++|+..+++++..
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~  159 (187)
T PRK12516         86 DTDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQR  159 (187)
T ss_pred             ccccccccccCCCcchhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            100             011123457777777776533        78999999999999999999999987754

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.45  E-value=3.7e-13  Score=125.14  Aligned_cols=130  Identities=15%  Similarity=0.081  Sum_probs=105.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ..|++.|+..|.+.|+++++++.++..+++|++||+|+.+|+++.+|++.  ..|.+|++.+++|.+++++|+..+....
T Consensus        15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~~~   92 (179)
T PRK09415         15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKKVI   92 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccccc
Confidence            78999999999999999999999999999999999999999999999864  3799999999999999999874321110


Q ss_pred             C---------------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          364 P---------------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       364 P---------------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      +               ..   ..+....+.+++..|+...+        .+.|++|||+.||||+++|+..+++++..
T Consensus        93 ~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~  170 (179)
T PRK09415         93 VTEDIFTYMESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKEL  170 (179)
T ss_pred             ccccccccccccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            0               00   12233456666667766543        68899999999999999999999987654

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

Probab=99.44  E-value=5.8e-13  Score=121.02  Aligned_cols=131  Identities=17%  Similarity=0.095  Sum_probs=106.3

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc
Q 012567          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  362 (460)
Q Consensus       283 G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir  362 (460)
                      +..+++.++..|.+.|+.++..+.++..+.+|++||+|+.+|+.+++|+.  ...|.+|++..++|.+++++|++.+...
T Consensus         4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~~~   81 (162)
T TIGR02983         4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLLEL   81 (162)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccccc
Confidence            48899999999999999999999999999999999999999999999964  3489999999999999999997653110


Q ss_pred             ----cC-----c--chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          363 ----LP-----F--HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       363 ----iP-----~--~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                          .+     .  ........+..++..|+...+        .+.+++|||+.||+|+++|+..+.+++..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~  153 (162)
T TIGR02983        82 PTRELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALAR  153 (162)
T ss_pred             cccccCcccCCccchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence                00     0  012234456666666665433        67899999999999999999999877653

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.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.42  E-value=1e-12  Score=133.79  Aligned_cols=141  Identities=19%  Similarity=0.162  Sum_probs=112.1

Q ss_pred             HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHH
Q 012567          274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  352 (460)
Q Consensus       274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~  352 (460)
                      .+|+..+..| ..+++.|+..|.+.|+.+|+++.++..+.+|++||.|+.+|+.+.+|++.  ..|.+|++.+++|.+++
T Consensus         7 ~~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d   84 (339)
T PRK08241          7 AALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLD   84 (339)
T ss_pred             HHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHH
Confidence            3566666777 89999999999999999999999999999999999999999999999853  47999999999999999


Q ss_pred             HhhhcCcccc---c-----------------------Cc-----------ch---HHH-HHHHHHHHHHHHHHhC-----
Q 012567          353 SLSDQSRTIR---L-----------------------PF-----------HM---VEA-TYRVKEARKQLYSENG-----  386 (460)
Q Consensus       353 ~Lrk~~r~ir---i-----------------------P~-----------~~---~e~-i~kl~ka~~~L~~~~g-----  386 (460)
                      ++|++.+...   .                       +.           ..   .+. ...+..++..|+.+++     
T Consensus        85 ~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L  164 (339)
T PRK08241         85 ALEGRARRPLPTDLGAPAADPVDELVERPEVPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLIL  164 (339)
T ss_pred             HHHhhccccCccccCCCcCcccccccccccccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhh
Confidence            9997543210   0                       00           00   011 1236667777766544     


Q ss_pred             ---CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          387 ---RHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       387 ---r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                         .+.+++|||+.||+|+++|+..+++++..+
T Consensus       165 ~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~L  197 (339)
T PRK08241        165 RDVLGWSAAEVAELLDTSVAAVNSALQRARATL  197 (339)
T ss_pred             HHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence               678999999999999999999998776544

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.42  E-value=1e-12  Score=120.80  Aligned_cols=133  Identities=17%  Similarity=0.109  Sum_probs=103.7

Q ss_pred             Hhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567          280 LNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (460)
Q Consensus       280 l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~  358 (460)
                      ++.| ..+++.++..|.+.|+.+++++.+ ..+++|++||+|+.+|+.+++|++.  ..|.+|++.+++|.+++++|+..
T Consensus         5 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~   81 (175)
T PRK12518          5 CQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFA   81 (175)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhh
Confidence            4455 899999999999999999999875 4689999999999999999999964  47999999999999999998753


Q ss_pred             ccc----ccC-----------cch--HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567          359 RTI----RLP-----------FHM--VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPK  413 (460)
Q Consensus       359 r~i----riP-----------~~~--~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar  413 (460)
                      +..    ..+           ...  .+....+.++...|+...+        .+.+++|||+.||+|+++|+..+++++
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar  161 (175)
T PRK12518         82 QRPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYAR  161 (175)
T ss_pred             ccccchhcccccccccCCCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            211    000           000  1111235566666666433        678999999999999999999999876


Q ss_pred             CC
Q 012567          414 AP  415 (460)
Q Consensus       414 ~~  415 (460)
                      ..
T Consensus       162 ~~  163 (175)
T PRK12518        162 RQ  163 (175)
T ss_pred             HH
Confidence            54

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.42  E-value=1e-12  Score=120.30  Aligned_cols=130  Identities=11%  Similarity=0.106  Sum_probs=105.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ...+..++..|.+.|+.+|+++.++..+++|++||.|+.+|+...+|++.  ..|.+|++..++|.+++++|++++....
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~~~~~   82 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMG--TNLKAWLFTILRNEFYSQMRKRGREVQD   82 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            46789999999999999999999999999999999999999999999853  3699999999999999999975432111


Q ss_pred             C---------cc----hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          364 P---------FH----MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       364 P---------~~----~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      .         ..    .......+..++..|+...+        .+.+++|||+.||+|+++|+..+++++..
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~  155 (164)
T PRK12547         83 SDGVFTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNR  155 (164)
T ss_pred             ccccccccCCCCchhhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            0         00    11123456677777766433        78999999999999999999999987653

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

Probab=99.41  E-value=5.2e-13  Score=119.65  Aligned_cols=127  Identities=17%  Similarity=0.164  Sum_probs=100.4

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc--
Q 012567          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL--  363 (460)
Q Consensus       286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri--  363 (460)
                      |++.|+..|.+.|+.+++++.++..+.+|++||+++++|+.+.+|++.  .+|.+|++.++++.+.+++++..+....  
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~~~   79 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKYQE   79 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHHHH
Confidence            789999999999999999999998999999999999999999999863  4799999999999999999875432110  


Q ss_pred             --------------Ccc---hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          364 --------------PFH---MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       364 --------------P~~---~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                                    |..   ..+....+..+...|+..        +-.+.+..|||+.||+|..+|+..+++++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~  155 (161)
T TIGR02985        80 EILEIEVDELSENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALK  155 (161)
T ss_pred             HHHhhcccccCCCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                          000   012223355555544432        236889999999999999999999987654

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.

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.41  E-value=1.4e-12  Score=123.57  Aligned_cols=137  Identities=15%  Similarity=0.069  Sum_probs=108.4

Q ss_pred             HHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHH
Q 012567          275 ELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  353 (460)
Q Consensus       275 ~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~  353 (460)
                      +|+..+..| ..+++.++..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++.  ..|.+|++.+++|.++++
T Consensus        14 ~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~   90 (196)
T PRK12535         14 DLALAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDN   90 (196)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHH
Confidence            455555566 89999999999999999975 56888899999999999999999999863  379999999999999999


Q ss_pred             hhhcCccccc--------------Cc--chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012567          354 LSDQSRTIRL--------------PF--HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVL  409 (460)
Q Consensus       354 Lrk~~r~iri--------------P~--~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l  409 (460)
                      +|++.+..+.              |.  ...+....+.+++..|+...+        .+.+++|||+.||+|+++|+..+
T Consensus        91 ~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l  170 (196)
T PRK12535         91 IRHDMARPRKSATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRV  170 (196)
T ss_pred             HHhhccCCCcccccccccccccCCcchhHHHHHHHHHHHHHHcCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHH
Confidence            9975432110              00  011223456777777766543        77899999999999999999999


Q ss_pred             hCCCC
Q 012567          410 LSPKA  414 (460)
Q Consensus       410 ~~ar~  414 (460)
                      ++++.
T Consensus       171 ~Rar~  175 (196)
T PRK12535        171 ARARA  175 (196)
T ss_pred             HHHHH
Confidence            87765

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.41  E-value=8.7e-13  Score=122.67  Aligned_cols=131  Identities=9%  Similarity=0.004  Sum_probs=104.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccC--CCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQG--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~--~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i  361 (460)
                      ..++..|+..|.+.|+.++..+.+  +..+++|++||.|+.+|+...+|+......|.||++.+++|.+++++|++.+..
T Consensus        12 ~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~~~~   91 (178)
T PRK12529         12 RDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQSLEL   91 (178)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            889999999999999998765555  467899999999999999999997544457999999999999999998753211


Q ss_pred             -------cc-------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          362 -------RL-------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       362 -------ri-------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                             ..       |..   ..+....|.+++..|+.+++        .+.|++|||+.||+|+++|+..++++..
T Consensus        92 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl~  169 (178)
T PRK12529         92 AWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYV  169 (178)
T ss_pred             hhhhHhhhccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                   00       111   12234457778888877654        6899999999999999999999986643

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.41  E-value=1.2e-12  Score=126.37  Aligned_cols=132  Identities=14%  Similarity=0.124  Sum_probs=107.1

Q ss_pred             ccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc
Q 012567          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (460)
Q Consensus       282 ~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i  361 (460)
                      ....++..|+..|.+.++.+++++.++..+.+|++||+|+.+|+.+.+|++  + .|.+|++++++|.+++++|++++..
T Consensus        15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~--~-~~~aWL~~IarN~~~d~~Rk~~~~~   91 (216)
T PRK12533         15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRG--D-NARPWLLAIVRHTWYSEWRRRANAH   91 (216)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCc--c-chHhHHHHHHHHHHHHHHHhhcccc
Confidence            347899999999999999999999999999999999999999999999985  2 5999999999999999998764311


Q ss_pred             c------cCc------------c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHH
Q 012567          362 R------LPF------------H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVL  409 (460)
Q Consensus       362 r------iP~------------~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l  409 (460)
                      .      +..            .      ..+....+.+++..|+...+        .+.+++|||+.||||+++|+..+
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L  171 (216)
T PRK12533         92 EVAAPDTLDDADSLDDWQPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRL  171 (216)
T ss_pred             cccccccccccccccccccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence            0      000            0      11234557777777766533        78899999999999999999999


Q ss_pred             hCCCCCc
Q 012567          410 LSPKAPR  416 (460)
Q Consensus       410 ~~ar~~l  416 (460)
                      ++++..+
T Consensus       172 ~RAr~~L  178 (216)
T PRK12533        172 ARARRRL  178 (216)
T ss_pred             HHHHHHH
Confidence            9877643

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

Probab=99.40  E-value=1.3e-12  Score=121.09  Aligned_cols=131  Identities=19%  Similarity=0.161  Sum_probs=102.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcc----CCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC-
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQ----GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS-  358 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~----~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~-  358 (460)
                      ..|++.|+..|.+.|+.++++|.    ++..+++|++||+++.+|+++.+|+...+..|.+|++..++|.++++++++. 
T Consensus         6 ~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~~   85 (189)
T TIGR02984         6 QEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRHLG   85 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            88999999999999999999874    3567899999999999999999998765568999999999999999998641 


Q ss_pred             ---ccc----cc-----------------------Ccc---hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHH
Q 012567          359 ---RTI----RL-----------------------PFH---MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEA  397 (460)
Q Consensus       359 ---r~i----ri-----------------------P~~---~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~  397 (460)
                         +..    .+                       |..   ..+....+.+++..|+..        +-.+.+++|||+.
T Consensus        86 ~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g~s~~eIA~~  165 (189)
T TIGR02984        86 AQKRDIRREQSLDAGGRLDESSVRLAAQLAADGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEGLSFAEVAER  165 (189)
T ss_pred             HHhhhcccccCCCcccccCCcchhHHHHccCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCHHHHHHH
Confidence               100    00                       000   011223455666655543        3378899999999


Q ss_pred             hCCCHHHHHHHHhCCCC
Q 012567          398 TGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       398 LGIS~e~Vk~~l~~ar~  414 (460)
                      ||||+++|+..+++++.
T Consensus       166 lgis~~~v~~~l~Ra~~  182 (189)
T TIGR02984       166 MDRSEGAVSMLWVRGLA  182 (189)
T ss_pred             HCcCHHHHHHHHHHHHH
Confidence            99999999999987754

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).

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.40  E-value=1.4e-12  Score=118.77  Aligned_cols=129  Identities=13%  Similarity=0.126  Sum_probs=103.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ..+++.++..|.+.|+.++.++.++..+++|++||+++.+|+.+++|++.   .|.||++.+++|.+++++|++.+....
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            57899999999999999999999999999999999999999999999853   599999999999999999985532111


Q ss_pred             ----------Ccc-----hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          364 ----------PFH-----MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       364 ----------P~~-----~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                                +..     ..+....+..+...|+.+.+        .+.+++|||+.||+|+++|+..+++++..
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~  155 (161)
T PRK12541         81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKE  155 (161)
T ss_pred             chhhhhccCCCCcHHHHHHHhHHHHHHHHHHHCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                      000     01122334455556655433        78899999999999999999999887653

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.39  E-value=1.2e-12  Score=119.67  Aligned_cols=126  Identities=12%  Similarity=0.056  Sum_probs=101.5

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC--
Q 012567          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP--  364 (460)
Q Consensus       287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP--  364 (460)
                      ++.|+..|.+.|+.+|+++.++..+++|++||+++.+|+.+.+|++.   .|.+|++.+++|.+++++|+.++.....  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~~~   79 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVGTD   79 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccchh
Confidence            67899999999999999999999999999999999999999999863   6999999999999999999865421111  


Q ss_pred             ----------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          365 ----------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       365 ----------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                                ..   ..+....+.++...|+...+        .+.+++|||+.||+|+++|+..+++++..
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~  151 (165)
T PRK09644         80 EIEAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKR  151 (165)
T ss_pred             HHhhhcccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                      11   01222445566666655422        77899999999999999999999987653

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.38  E-value=1.3e-11  Score=120.99  Aligned_cols=89  Identities=15%  Similarity=0.280  Sum_probs=79.7

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCC--CcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHH
Q 012567          272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGM--NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ  348 (460)
Q Consensus       272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~--d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~  348 (460)
                      +...|+..++.| ..|++.|+..|.++|+++|.+|+++..  +.+|++|+|++++|+++++|++.+|..|.+|+.++|+|
T Consensus         4 ~~~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn   83 (237)
T PRK08311          4 SLEDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKR   83 (237)
T ss_pred             cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence            345566777777 889999999999999999999998775  58999999999999999999998888899999999999


Q ss_pred             HHHHHhhhcCcc
Q 012567          349 AVRKSLSDQSRT  360 (460)
Q Consensus       349 aI~~~Lrk~~r~  360 (460)
                      .+++++|++.+.
T Consensus        84 ~~iDylRk~~~~   95 (237)
T PRK08311         84 RLIDYFRKESKH   95 (237)
T ss_pred             HHHHHHHHhhcc
Confidence            999999986653

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

Probab=99.38  E-value=1.8e-12  Score=130.84  Aligned_cols=130  Identities=20%  Similarity=0.154  Sum_probs=105.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR-  362 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir-  362 (460)
                      ..+++.|+..|.+.|+.+|+++.++..+.+|++||.|+.+|+.+.+|++.  ..|.+|++.+++|.+++++|++.+... 
T Consensus         4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~   81 (324)
T TIGR02960         4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRP   81 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCc
Confidence            78999999999999999999999999999999999999999999999864  479999999999999999997543210 


Q ss_pred             -------------------------cCc--------------ch---HH-HHHHHHHHHHHHHHHhC--------CCCCH
Q 012567          363 -------------------------LPF--------------HM---VE-ATYRVKEARKQLYSENG--------RHPNN  391 (460)
Q Consensus       363 -------------------------iP~--------------~~---~e-~i~kl~ka~~~L~~~~g--------r~pS~  391 (460)
                                               ++.              ..   .+ ....+..++..|+.+.+        .+.++
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~  161 (324)
T TIGR02960        82 VGLGAPSADGTAAASEAAEVTWLEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRA  161 (324)
T ss_pred             cccCCCCCcccccccccccccccCCCCccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhCCCH
Confidence                                     000              00   11 11235667777766533        67899


Q ss_pred             HHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          392 EEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       392 eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      +|||+.||+|+++|++.+++++..
T Consensus       162 ~EIA~~lgis~~tV~~~l~Rar~~  185 (324)
T TIGR02960       162 AETAELLGTSTASVNSALQRARAT  185 (324)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHH
Confidence            999999999999999999877653

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.

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.37  E-value=1.7e-12  Score=119.70  Aligned_cols=131  Identities=12%  Similarity=0.089  Sum_probs=103.4

Q ss_pred             cc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc
Q 012567          282 YG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (460)
Q Consensus       282 ~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~  360 (460)
                      .| ..++..|+..|.+.|+.++.++.++..+.+|++||.|+.+|+. ..|...  ..|.+|++.+++|.+++++|++.+.
T Consensus         6 ~~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~   82 (172)
T PRK12523          6 SPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALE   82 (172)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45 8899999999999999999999999999999999999999986 456542  4799999999999999999975421


Q ss_pred             c----c---c-------Ccc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          361 I----R---L-------PFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       361 i----r---i-------P~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      .    .   .       |..   ..+....+.+++..|+.+.+        .+.+++|||+.||+|+++|+..++++...
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~  162 (172)
T PRK12523         83 QAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQ  162 (172)
T ss_pred             HHHHHHHhhcccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            1    0   0       011   01223456677777766433        78999999999999999999999877653

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.36  E-value=1.2e-12  Score=118.81  Aligned_cols=121  Identities=10%  Similarity=0.083  Sum_probs=96.8

Q ss_pred             HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc-c-------
Q 012567          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR-L-------  363 (460)
Q Consensus       292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir-i-------  363 (460)
                      +.|.+.|+.+|.++.++..+++|++||+|+.+|+++.+|++.   .|.+|++.+++|.+++++|++.+... .       
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            568899999999999999999999999999999999999852   59999999999999999997543211 0       


Q ss_pred             --------Ccch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          364 --------PFHM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       364 --------P~~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                              |...   .+....+..++..|+...+        .+.|++|||+.||+|+++|+..+++++..
T Consensus        79 ~~~~~~~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~  149 (160)
T PRK09642         79 ENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKW  149 (160)
T ss_pred             hhccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                    0000   1122346677777766533        78999999999999999999999987654

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.36  E-value=3.6e-12  Score=119.35  Aligned_cols=130  Identities=14%  Similarity=0.152  Sum_probs=105.7

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc-
Q 012567          285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL-  363 (460)
Q Consensus       285 ~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri-  363 (460)
                      .++..++..|.+.|+.+|.++.++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++++|++.+.... 
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~~   82 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPG--SNLPAWLFTILRNLFRSDYRKRRREVEDA   82 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCC--chHHHHHHHHHHHHHHHHHHhcccccccc
Confidence            5678899999999999999999999999999999999999999999865  3699999999999999999876542211 


Q ss_pred             -----------Ccc-hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          364 -----------PFH-MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       364 -----------P~~-~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                                 +.. .......+..++..|+..++        .+.|++|||+.||+|+++|+..+++++..+
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~L  155 (182)
T PRK12540         83 DGSYAKTLKSQPGQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL  155 (182)
T ss_pred             cccccccccCCCchHHHHHHHHHHHHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence                       000 11123456777777766533        788999999999999999999999887643

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.36  E-value=4.4e-12  Score=115.44  Aligned_cols=128  Identities=13%  Similarity=0.109  Sum_probs=101.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc--
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI--  361 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i--  361 (460)
                      ..+++.|+..|.+.|+.++.++.++..+.+|++||.|+.+|+....|++   ..|.+|++++++|.+++++|++.+..  
T Consensus         3 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~~~~   79 (161)
T PRK12528          3 SATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLERAY   79 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3689999999999999999999999999999999999999999888764   26999999999999999999753211  


Q ss_pred             -----ccCc----c------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          362 -----RLPF----H------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       362 -----riP~----~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                           ..+.    .      ..+....+.+++..|+...+        .+.+++|||+.||+|+++|+..++++..
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~  155 (161)
T PRK12528         80 LEALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM  155 (161)
T ss_pred             HHHhhccccccCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                 0110    0      01223456666666666433        7899999999999999999999987643

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.35  E-value=3.2e-12  Score=120.15  Aligned_cols=126  Identities=14%  Similarity=0.178  Sum_probs=99.6

Q ss_pred             HHHHHHhHHHHHHHHHHccCCCCC-cccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC--
Q 012567          288 DKMITSNIRLVISIAKNYQGAGMN-LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP--  364 (460)
Q Consensus       288 e~LI~~nlrLV~~IAkry~~~g~d-~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP--  364 (460)
                      +..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++.+|++.  ..|.+|++.+++|.+++++|++++.....  
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            457788999999999999999888 9999999999999999999863  47999999999999999999865321110  


Q ss_pred             --------------------------------cc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCC
Q 012567          365 --------------------------------FH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLS  401 (460)
Q Consensus       365 --------------------------------~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS  401 (460)
                                                      ..   ..+....+.+++..|+...+        .+.|++|||+.||+|
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g~s~~EIA~~lgis  165 (195)
T PRK12532         86 LDDELLDEAFESHFSQNGHWTPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGIS  165 (195)
T ss_pred             ccccccchhhhhhhccccccccccCccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHHhCCCHHHHHHHHCCC
Confidence                                            00   01122346666666665432        688999999999999


Q ss_pred             HHHHHHHHhCCCCC
Q 012567          402 MKRLHAVLLSPKAP  415 (460)
Q Consensus       402 ~e~Vk~~l~~ar~~  415 (460)
                      +++|+..+++++..
T Consensus       166 ~~tVk~~l~Rar~~  179 (195)
T PRK12532        166 TSNYHTIMHRARES  179 (195)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999987653

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.35  E-value=4.7e-12  Score=120.83  Aligned_cols=130  Identities=16%  Similarity=0.216  Sum_probs=105.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc--c
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT--I  361 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~--i  361 (460)
                      ..++..|+..|.+.++.++.++.++..+.+|++||+|+.+|+...+|++  + .|.+|++.+++|.+++++|+..+.  .
T Consensus        27 ~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~~~~~  103 (203)
T PRK09647         27 MPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRARIRME  103 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhcccCccc
Confidence            8899999999999999999999999999999999999999999999985  3 699999999999999999986431  1


Q ss_pred             ccC-----------c--c---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          362 RLP-----------F--H---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       362 riP-----------~--~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                      ..+           .  .   ..+....+..++..|+...        -.+.+++|||+.||||+++|+..+++++..+
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~L  182 (203)
T PRK09647        104 ALPEDYDRVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL  182 (203)
T ss_pred             cccccccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            000           0  0   0122344566666665542        3788999999999999999999999887543

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.34  E-value=3.1e-12  Score=121.37  Aligned_cols=126  Identities=12%  Similarity=0.083  Sum_probs=100.0

Q ss_pred             HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC---c
Q 012567          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP---F  365 (460)
Q Consensus       289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP---~  365 (460)
                      .++..|.+.++.+|+++.++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.+++++|++.+....+   .
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~~   89 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSALDA   89 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            348889999999999999999999999999999999999999965  36999999999999999999865432110   0


Q ss_pred             -----------------------------ch------HHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCH
Q 012567          366 -----------------------------HM------VEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSM  402 (460)
Q Consensus       366 -----------------------------~~------~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~  402 (460)
                                                   ..      .+....+.+++..|+...        -.+.+++|||+.||+|+
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~  169 (201)
T PRK12545         90 ELDGEALLDRELFKDNGHWAAHAKPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTA  169 (201)
T ss_pred             ccchhhhhhhhhhcccccccccccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCH
Confidence                                         00      011124566666666543        37889999999999999


Q ss_pred             HHHHHHHhCCCCCc
Q 012567          403 KRLHAVLLSPKAPR  416 (460)
Q Consensus       403 e~Vk~~l~~ar~~l  416 (460)
                      ++|+..+++++..+
T Consensus       170 ~tVk~~l~RAr~~L  183 (201)
T PRK12545        170 NHCSVLLYRARTRL  183 (201)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999877643

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.33  E-value=4.3e-12  Score=115.56  Aligned_cols=127  Identities=16%  Similarity=0.054  Sum_probs=101.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ..+++.|+..|.+.|+.+|+++.++..+.+|++||+|+.+|++  .|+.  +..|.+|++.+++|.+++++|+..+....
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            3579999999999999999999999999999999999999999  6763  34799999999999999999886542211


Q ss_pred             C---------------cc---hHHHHHHHHHHHHHHHH--------HhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          364 P---------------FH---MVEATYRVKEARKQLYS--------ENGRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       364 P---------------~~---~~e~i~kl~ka~~~L~~--------~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      .               ..   ..+....+.++...|+.        .+ .+.+++|||+.||+|+.+|+..+++++..
T Consensus        78 ~~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~  154 (166)
T PRK09639         78 ILGEFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKK  154 (166)
T ss_pred             ccchhhhhhccCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            0               00   01223345666665554        35 88999999999999999999999877653

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.32  E-value=5.3e-12  Score=118.60  Aligned_cols=126  Identities=14%  Similarity=0.135  Sum_probs=99.9

Q ss_pred             HHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC---
Q 012567          288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP---  364 (460)
Q Consensus       288 e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP---  364 (460)
                      +..|..|.+.++.+|.++.++..+++|++||.|+.+|+.+.+|++.  .+|.+|++++++|.+++++|++.+.....   
T Consensus        10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~~   87 (189)
T PRK12530         10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNESELI   87 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCccccc
Confidence            3457788999999999999999999999999999999999999864  36999999999999999999765421110   


Q ss_pred             ----------------------cc---------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHH
Q 012567          365 ----------------------FH---------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRL  405 (460)
Q Consensus       365 ----------------------~~---------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~V  405 (460)
                                            ..         ..+....+..++..|+...+        .+.|++|||+.||+|+++|
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV  167 (189)
T PRK12530         88 EEDSPNSFFDEKGHWKPEYYEPSEWQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNL  167 (189)
T ss_pred             ccccchhhhcccccccccccCCccccCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHH
Confidence                                  00         00112235677777766533        6889999999999999999


Q ss_pred             HHHHhCCCCC
Q 012567          406 HAVLLSPKAP  415 (460)
Q Consensus       406 k~~l~~ar~~  415 (460)
                      +..+++++..
T Consensus       168 k~~l~RAr~~  177 (189)
T PRK12530        168 HVLLYRARLQ  177 (189)
T ss_pred             HHHHHHHHHH
Confidence            9999987653

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.32  E-value=8.8e-12  Score=117.25  Aligned_cols=133  Identities=11%  Similarity=0.028  Sum_probs=106.2

Q ss_pred             hccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc
Q 012567          281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (460)
Q Consensus       281 ~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~  360 (460)
                      .....+++.++..|.+.|+.+|+++.++..+++|++||.|+.+|+.+..|++.  ..|.+|++.+++|.+++..+++.+.
T Consensus        19 ~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~~   96 (188)
T PRK12517         19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQFD   96 (188)
T ss_pred             hccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhccC
Confidence            34588999999999999999999999999999999999999999999999864  3799999999999988877654321


Q ss_pred             c-c-----cC-----c-chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          361 I-R-----LP-----F-HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       361 i-r-----iP-----~-~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      . .     .+     . ........+..++..|+...+        .+.+++|||+.||||+++|+..+++++..
T Consensus        97 ~~~~~~~~~~~~~~~~~e~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~  171 (188)
T PRK12517         97 LVDIEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQ  171 (188)
T ss_pred             ccCcccccccCccccChhHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            1 0     00     0 011122346777777776533        78899999999999999999999987654

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

Probab=99.32  E-value=5.3e-12  Score=118.59  Aligned_cols=127  Identities=13%  Similarity=0.109  Sum_probs=100.6

Q ss_pred             HHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC---
Q 012567          288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP---  364 (460)
Q Consensus       288 e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP---  364 (460)
                      .+++..|.+.|+.+++++.++..+++|++||+|+.+|+...+|++.  .+|.+|++.+++|.+++++|++.+....+   
T Consensus         5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~   82 (188)
T TIGR02943         5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLD   82 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCccccc
Confidence            3578889999999999999999999999999999999999999864  48999999999999999999765422111   


Q ss_pred             ------------------------c------c---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHH
Q 012567          365 ------------------------F------H---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMK  403 (460)
Q Consensus       365 ------------------------~------~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e  403 (460)
                                              .      .   ..+....+.+++..|+...        -.+.+++|||+.||+|++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~  162 (188)
T TIGR02943        83 DELDDEAFNALFTQNGHWAQHGQPQHWNTPEKQLENKEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTS  162 (188)
T ss_pred             cccccchhhhhhccccchhccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHH
Confidence                                    0      0   0111234566666665532        378899999999999999


Q ss_pred             HHHHHHhCCCCCc
Q 012567          404 RLHAVLLSPKAPR  416 (460)
Q Consensus       404 ~Vk~~l~~ar~~l  416 (460)
                      +|+..+.+++..+
T Consensus       163 tvk~rl~Rar~~L  175 (188)
T TIGR02943       163 NCHVLLYRARLSL  175 (188)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999876543

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.31  E-value=6.7e-12  Score=120.05  Aligned_cols=127  Identities=17%  Similarity=0.170  Sum_probs=100.8

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC--
Q 012567          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP--  364 (460)
Q Consensus       287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP--  364 (460)
                      -..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|+..  .+|.+|++++++|.+++++|++.+....+  
T Consensus        20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~   97 (206)
T PRK12544         20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL   97 (206)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence            35688899999999999999999999999999999999999999854  47999999999999999999765422111  


Q ss_pred             --------------------------------cch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCC
Q 012567          365 --------------------------------FHM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLS  401 (460)
Q Consensus       365 --------------------------------~~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS  401 (460)
                                                      ...   .+....+..++..|+.+.+        .+.+++|||+.||+|
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g~s~~EIAe~lgis  177 (206)
T PRK12544         98 LRDEEEEEDFEELFDESGHWQKDERPQAWGNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLS  177 (206)
T ss_pred             ccccchhhHHHHhhcccccccccccccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcC
Confidence                                            000   1111235556666655433        788999999999999


Q ss_pred             HHHHHHHHhCCCCC
Q 012567          402 MKRLHAVLLSPKAP  415 (460)
Q Consensus       402 ~e~Vk~~l~~ar~~  415 (460)
                      +++|+..+++++..
T Consensus       178 ~~tV~~~l~RAr~~  191 (206)
T PRK12544        178 VSNLNVLLYRARLR  191 (206)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999999988764

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.31  E-value=1e-11  Score=116.04  Aligned_cols=126  Identities=13%  Similarity=0.105  Sum_probs=100.8

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc-
Q 012567          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF-  365 (460)
Q Consensus       287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~-  365 (460)
                      ++.|+..|.+.|+.++.++.++..+++|++||.++.+|+.+..|++  +..|.+|++.+++|.+++++|++.+....+. 
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~--~~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~~~   80 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKD--GSSIKSWLYQIANNTIIDFYRKKNRSEELPDD   80 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhcc--ccchHHHHHHHHHHHHHHHHHhccccCCcchh
Confidence            6789999999999999999999999999999999999999999985  3479999999999999999997654322211 


Q ss_pred             -------c----hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          366 -------H----MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       366 -------~----~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                             .    ..+....+..+...|+...        -.+.+.+|||+.||+|.++|+..+.+++.
T Consensus        81 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~  148 (181)
T PRK09637         81 LLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRV  148 (181)
T ss_pred             hhccCCChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                   0    1122233555555555432        27889999999999999999999987765

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.31  E-value=4.6e-12  Score=113.82  Aligned_cols=120  Identities=13%  Similarity=0.116  Sum_probs=96.3

Q ss_pred             HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc--------
Q 012567          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL--------  363 (460)
Q Consensus       292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri--------  363 (460)
                      ..|.+.|+.++.++.++..+++|++||+++.+|+.+++|++   .+|.+|++..+++.++++++++.+....        
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~~~~~~~~   78 (154)
T TIGR02950         2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAIGDL   78 (154)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccccHhhhhhc
Confidence            57889999999999999899999999999999999999996   4799999999999999999875432111        


Q ss_pred             -------Ccch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          364 -------PFHM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       364 -------P~~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                             |...   .+....+.+++..|+....        .+.+++|||+.||+|+++|+..+++++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~  147 (154)
T TIGR02950        79 EQHPVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARK  147 (154)
T ss_pred             cccccCChhHHHHHHHHHHHHHHHHHhCCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                   0100   1122456777777766432        6789999999999999999999987754

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.

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.30  E-value=7.3e-12  Score=115.61  Aligned_cols=122  Identities=18%  Similarity=0.200  Sum_probs=97.2

Q ss_pred             HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcc-----
Q 012567          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH-----  366 (460)
Q Consensus       292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~-----  366 (460)
                      ..|.+.++.+++++.++..+++|++||+|+.+|+++.+|+.  +.+|.+|++.+++|.+++++|+..+...++..     
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~--~~~f~~wl~~iarn~~~d~~Rk~~~~~~~~~~~~~~~   79 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKD--GQKIQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD   79 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCC--cccHHHHHHHHHHHHHHHHHHhccCccccchhhcccC
Confidence            46788999999999999999999999999999999999996  35899999999999999999987653332211     


Q ss_pred             -------hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          367 -------MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       367 -------~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                             ..+....+.+++..|+..        .-.+.+.+|||+.||+|+.+|+..+++++..
T Consensus        80 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~  143 (170)
T TIGR02959        80 SAREETFVKELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKK  143 (170)
T ss_pred             CccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                   111223355555555543        2378899999999999999999999887754

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).

>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.30  E-value=7.7e-12  Score=97.93  Aligned_cols=70  Identities=23%  Similarity=0.377  Sum_probs=67.0

Q ss_pred             HHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCc
Q 012567          290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  359 (460)
Q Consensus       290 LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r  359 (460)
                      |++.|.++|++++++|.+++.+.+|++||++++||+++.+||++.+..|.+|++.+++|.++++++++++
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r   70 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR   70 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence            6889999999999999999999999999999999999999999999899999999999999999998764

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.29  E-value=1.4e-11  Score=116.10  Aligned_cols=129  Identities=17%  Similarity=0.151  Sum_probs=102.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      .++++.|.. |.+.|+.+|+.+.++..+.+|++||.|+.+|+.+..|+..  ..|.+|++.+++|.+++++|++.+....
T Consensus         7 ~~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~   83 (188)
T PRK12546          7 RDPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPD   83 (188)
T ss_pred             hhHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccC
Confidence            456666665 7799999999999999999999999999999999999853  4799999999999999999986542111


Q ss_pred             C------------cc-hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          364 P------------FH-MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       364 P------------~~-~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      .            .. .......+..++..|+....        .+.+.+|||+.||||+.+|+..+++++..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~  156 (188)
T PRK12546         84 PEGVHAASLAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARAR  156 (188)
T ss_pred             cccccccccccCCcchhHHHHHHHHHHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            0            00 01122456677777766533        78899999999999999999999987753

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.27  E-value=1.7e-11  Score=114.85  Aligned_cols=127  Identities=14%  Similarity=0.129  Sum_probs=101.2

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC--
Q 012567          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP--  364 (460)
Q Consensus       287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP--  364 (460)
                      ++..+..+++.|+.++.++.++..+.+|++||.|+.+|+.+..|+..  ..|.+|++.+++|.+++++|++.+.....  
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~~~   83 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRADE   83 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccccc
Confidence            44557889999999999999999999999999999999999999853  47999999999999999999865321110  


Q ss_pred             ----------cc--hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          365 ----------FH--MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       365 ----------~~--~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                                ..  .......+.+++..|+...+        .+.+++|||+.||||+++|+..+++++..
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~  154 (182)
T PRK12511         84 LAVLADASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAA  154 (182)
T ss_pred             hhhccccCCCcchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence                      00  11223446677777766533        78899999999999999999999887754

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.24  E-value=4.9e-11  Score=110.23  Aligned_cols=128  Identities=10%  Similarity=0.089  Sum_probs=101.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc--
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI--  361 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i--  361 (460)
                      ..++..++..|.+.++.++.++.++..+++|++||.|+.+|+. ..|++-  ..|.+|++.+++|.+++++|++.+..  
T Consensus         9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~--~~~~~wL~~iarn~~~d~~R~~~~~~~~   85 (172)
T PRK09651          9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTI--RDPRSFLCTIAKRVMVDLFRRNALEKAY   85 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-cccccc--cCHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            6789999999999999999999999999999999999999997 456533  26899999999999999998653211  


Q ss_pred             -----cc-----Cc--ch---HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          362 -----RL-----PF--HM---VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       362 -----ri-----P~--~~---~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                           .+     +.  ..   .+....+..++..|+.+.+        .+.+++|||+.||+|+++|+..++++..
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~  161 (172)
T PRK09651         86 LEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATE  161 (172)
T ss_pred             hhHHhhccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence                 00     11  01   1233456677777766533        7889999999999999999999987654

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.20  E-value=5.1e-11  Score=116.21  Aligned_cols=133  Identities=10%  Similarity=0.041  Sum_probs=101.5

Q ss_pred             HHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhc
Q 012567          278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  357 (460)
Q Consensus       278 ~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~  357 (460)
                      +.+.....+++.+++.| +.++.++.++.++..+.+|++||.|+.+|+.   |+..  ..|.+|++.+++|.+++++|++
T Consensus        11 ~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~Rk~   84 (228)
T PRK06704         11 NHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQIKSK   84 (228)
T ss_pred             cccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHHhcc
Confidence            33444477888777766 7899999999999999999999999999976   5533  3599999999999999999986


Q ss_pred             CcccccCc---------chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          358 SRTIRLPF---------HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       358 ~r~iriP~---------~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                      .+...+..         ...+....+..+...|+.+.+        .+.|++|||+.||+|+++|+..+++++..+
T Consensus        85 k~~~~~~~~~~~~~~~~~~~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~L  160 (228)
T PRK06704         85 SVHEKIRDQITFEEPHEKIADLHEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL  160 (228)
T ss_pred             ccccccccccccCChHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            54221111         011223345666666666433        678999999999999999999999888754

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.20  E-value=5.4e-11  Score=108.19  Aligned_cols=123  Identities=15%  Similarity=0.193  Sum_probs=95.4

Q ss_pred             HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccc------
Q 012567          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR------  362 (460)
Q Consensus       289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~ir------  362 (460)
                      .++..|.+.++.+|.++.++..+++|++||+++++|+....|++.   .|.+|++.+++|.+++++|++.+...      
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~~~~~~   78 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKYHGDEE   78 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccccccccc
Confidence            367789999999999999999999999999999999988877653   58999999999999999987543111      


Q ss_pred             ----cCc---c------hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          363 ----LPF---H------MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       363 ----iP~---~------~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                          .+.   .      ..+....+..+...|+.+.        -.+.+++|||+.||+|.++|+..+.+++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~  151 (163)
T PRK07037         79 DGLDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV  151 (163)
T ss_pred             cccccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                110   0      1122344566666665542        27889999999999999999999887654

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.18  E-value=5.4e-11  Score=108.03  Aligned_cols=121  Identities=9%  Similarity=0.042  Sum_probs=94.8

Q ss_pred             HHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc--------
Q 012567          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL--------  363 (460)
Q Consensus       292 ~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri--------  363 (460)
                      ..|.+.++.++.++.++..+++|++||.|+.+|+....|++   .+|.+|++.+++|.+++++|++......        
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~~~~~~~~~~   78 (159)
T PRK12527          2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEE   78 (159)
T ss_pred             hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcccccchhhhhcc
Confidence            56888899999999999899999999999999999999874   2799999999999999999865321100        


Q ss_pred             -----C--cc---hHHHHHHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          364 -----P--FH---MVEATYRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       364 -----P--~~---~~e~i~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                           |  ..   ..+....+..++..|+.+.        ..+.+++|||+.||+|+++|+..+.+++..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~  148 (159)
T PRK12527         79 ERLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKH  148 (159)
T ss_pred             ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence                 0  00   1122335667777776643        378899999999999999999999877653

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.18  E-value=1.6e-10  Score=106.19  Aligned_cols=128  Identities=11%  Similarity=0.094  Sum_probs=99.8

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc--
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI--  361 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i--  361 (460)
                      ..++..++..|.+.++.++.++.++..+.+|++||.|+.+|+....++.   ..|.+|++++++|.+++++|+.....  
T Consensus         8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~~~~   84 (168)
T PRK12525          8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLERAY   84 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999986555442   37999999999999999998643110  


Q ss_pred             -----c-------cCcc---hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          362 -----R-------LPFH---MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       362 -----r-------iP~~---~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                           .       .|..   ..+....+.+++..|+...+        .+.|++|||+.||+|+++|+..+.++..
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~  160 (168)
T PRK12525         85 LQSLAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK  160 (168)
T ss_pred             HHHHhcccccccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                 0       1110   11223446666666665433        7889999999999999999999987653

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.09  E-value=4.2e-10  Score=112.91  Aligned_cols=127  Identities=14%  Similarity=0.061  Sum_probs=98.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc--c--
Q 012567          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT--I--  361 (460)
Q Consensus       286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~--i--  361 (460)
                      ....++..|.+.++.+|+++.++..+++|++||.++. |.....|+   ...|.+|++++++|.|++++|++.+.  .  
T Consensus         5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~~~   80 (293)
T PRK09636          5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRETYV   80 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccccccc
Confidence            4678999999999999999999999999999999999 55667775   34799999999999999999975421  0  


Q ss_pred             --ccCcc----------h---HHH-HHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          362 --RLPFH----------M---VEA-TYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       362 --riP~~----------~---~e~-i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                        .++..          .   .+. ...+..++..|+.+.+        .+.+++|||+.||+|+.+|++.+++++..+
T Consensus        81 ~~~~~e~~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~L  159 (293)
T PRK09636         81 GPWLPEPVVEELDDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHV  159 (293)
T ss_pred             CCcCCcCCCCCCCChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence              01110          0   111 1235666666665433        788999999999999999999999877644

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.04  E-value=5.6e-10  Score=112.47  Aligned_cols=128  Identities=10%  Similarity=-0.045  Sum_probs=98.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc-c--
Q 012567          285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT-I--  361 (460)
Q Consensus       285 ~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~-i--  361 (460)
                      ..+..++..|.+.++.+|+++.++..+.+|++||.|+.+|++...+    ...|.+|++.+.+|.|++++|+..+. .  
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~n~~id~lRk~~~rr~~~   80 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTSRLCLDHIKSASTRRERP   80 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence            5688899999999999999999999999999999999999986543    13699999999999999999874311 0  


Q ss_pred             -----ccC----------cch----HHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          362 -----RLP----------FHM----VEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       362 -----riP----------~~~----~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                           ..|          ...    .+....+..++..|+...+        .+.+++|||+.||+|+.+|++.+++++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~  160 (290)
T PRK09635         81 QDIAAWHDGDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR  160 (290)
T ss_pred             ccccccCccccCCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence                 001          000    1112345556666655433        6789999999999999999999988776


Q ss_pred             Cc
Q 012567          415 PR  416 (460)
Q Consensus       415 ~l  416 (460)
                      .+
T Consensus       161 ~L  162 (290)
T PRK09635        161 KI  162 (290)
T ss_pred             HH
Confidence            44

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.03  E-value=1e-09  Score=97.88  Aligned_cols=113  Identities=10%  Similarity=0.062  Sum_probs=85.3

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhh-----cCCCCCCchHhHHHHHHHHHHHHHhhhcCccc
Q 012567          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK-----FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (460)
Q Consensus       287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiek-----FDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i  361 (460)
                      ++.++..|.++++.+|++|...    +| +||.++.+|....+     |++  ...|.||++.+++|.+++++|++.+..
T Consensus         1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~--~~~~~~wL~~iarN~~id~~Rk~~~~~   73 (142)
T TIGR03209         1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNT--ENDLEKYISTSLKRYCLDICNKKNRDK   73 (142)
T ss_pred             ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCc--hhHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            3679999999999999999662    24 49999999999865     553  247999999999999999999764321


Q ss_pred             cc------------C-cc--hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHH
Q 012567          362 RL------------P-FH--MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLH  406 (460)
Q Consensus       362 ri------------P-~~--~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk  406 (460)
                      ..            + ..  ..+....+.+++..|+..++        .+.|++|||+.||||+++|+
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        74 KIIYNSEITDIKLSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             hhhhhhhhhccccchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence            11            0 00  11123457777777777544        78899999999999999986

Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.

>PRK09191 two-component response regulator; Provisional

Probab=99.02  E-value=7.1e-10  Score=107.23  Aligned_cols=121  Identities=14%  Similarity=0.078  Sum_probs=95.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCc
Q 012567          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (460)
Q Consensus       286 A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~  365 (460)
                      ++..|+..|.+.|+.+|.++.++..+.+|++||+|+.+|+...+|++.  ..|.+|+++++++........... ...+ 
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~~~~~~~-~~~~-   77 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSAGANDPE-PGSP-   77 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccccccCCC-CCCC-
Confidence            578899999999999999999999999999999999999999999864  469999999998876443222110 0011 


Q ss_pred             chHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          366 HMVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       366 ~~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                          ....+.+++..|+...+        .+.|++|||+.||+|+++|+..+++++.
T Consensus        78 ----~~~~l~~~l~~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~  130 (261)
T PRK09191         78 ----FEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARA  130 (261)
T ss_pred             ----chHHHHHHHHhCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                11256777777766544        6889999999999999999999886654

>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=98.99  E-value=7.3e-10  Score=89.71  Aligned_cols=76  Identities=29%  Similarity=0.389  Sum_probs=64.9

Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCCCCcccccccCCCcchhh
Q 012567          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSVCFILNLADSLII  444 (460)
Q Consensus       369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d~tl~Eli~D~~~ds~~~  444 (460)
                      +.+++|.++...|.+++|+.||.+|||+.|||++++|..++..++..+||+.+++.+++.++.++|+|+...++..
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e   76 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEE   76 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHH
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhh
Confidence            4578999999999999999999999999999999999999999999999999999888899999999997776643

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 ....

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

Probab=98.98  E-value=1.7e-09  Score=108.16  Aligned_cols=124  Identities=16%  Similarity=0.053  Sum_probs=92.6

Q ss_pred             HHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccc------c
Q 012567          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI------R  362 (460)
Q Consensus       289 ~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~i------r  362 (460)
                      +++..|.+.++.+|+++.++..+.+|++||+++.+++.  .|+.  ...|.+|++++++|.+++++|+..+..      .
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~~~~~~   76 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREVYVGPW   76 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccccCCCC
Confidence            36889999999999999999999999999999997765  5543  237999999999999999998753210      1


Q ss_pred             cCcc----------hH---HHH-HHHHHHHHHHHHHh--------CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          363 LPFH----------MV---EAT-YRVKEARKQLYSEN--------GRHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       363 iP~~----------~~---e~i-~kl~ka~~~L~~~~--------gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                      +|..          ..   +.+ ..+..++..|+...        -.+.+++|||+.||+|+.+|++.+++++..+
T Consensus        77 ~~e~~~~~~~~~~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~L  152 (281)
T TIGR02957        77 LPEPLLTTSADPAESVELAESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHL  152 (281)
T ss_pred             CCcccCCCCCChHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            1110          01   111 12344555555432        2788999999999999999999998877644

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=98.91  E-value=2.3e-09  Score=97.01  Aligned_cols=106  Identities=12%  Similarity=0.050  Sum_probs=79.0

Q ss_pred             CCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC----------------------
Q 012567          307 GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP----------------------  364 (460)
Q Consensus       307 ~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP----------------------  364 (460)
                      ++..+++|++||+|+.+|+.+..+ +  +..|.+|++.+++|.+++++|++.+..+..                      
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            345678999999999999998863 2  457999999999999999998754321110                      


Q ss_pred             ------cc------hHHHHHHHHHHHHHHHHHhC--------CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          365 ------FH------MVEATYRVKEARKQLYSENG--------RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       365 ------~~------~~e~i~kl~ka~~~L~~~~g--------r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                            ..      ..+....+.+++..|+..++        .+.+++|||+.||+|+++|+..+++++..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~  149 (161)
T PRK09047         79 SADEGAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHA  149 (161)
T ss_pred             cccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                  00      01123446667777766533        78899999999999999999999877653

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=98.40  E-value=3.7e-06  Score=79.11  Aligned_cols=141  Identities=21%  Similarity=0.200  Sum_probs=96.8

Q ss_pred             HHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCC---CCCccc--HHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHH
Q 012567          274 RELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGA---GMNLQD--LVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK  347 (460)
Q Consensus       274 ~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~---g~d~eD--LiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr  347 (460)
                      ..|+..++.| ..|.+.|+..|++-+..+|+++.+.   +.+.+|  |+++.|+.+++.-...+......|..|+...++
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            3566777888 9999999999999999999876532   345555  466777777763332233333469999999999


Q ss_pred             HHHHHHhhhcCcccc------cC---------cchHHHHHHHHHHHHHHHH-----------HhCCCCCHHHHHHHhCCC
Q 012567          348 QAVRKSLSDQSRTIR------LP---------FHMVEATYRVKEARKQLYS-----------ENGRHPNNEEVAEATGLS  401 (460)
Q Consensus       348 ~aI~~~Lrk~~r~ir------iP---------~~~~e~i~kl~ka~~~L~~-----------~~gr~pS~eEIAe~LGIS  401 (460)
                      +.+++..|++....|      .+         ....+..-.+.++...|..           ..-.+.|.+|||+.||||
T Consensus        85 r~lid~~R~~~a~KRg~~~~~~~l~~~~~~~~~~~~~~~~~l~e~l~~L~~l~~~~~~~v~l~~~~Gls~~EIA~~lgiS  164 (185)
T PF07638_consen   85 RKLIDHARRRQAQKRGGDQVRVELDERADSGDEPSPEELLELEEALERLLALDPRQRRVVELRFFEGLSVEEIAERLGIS  164 (185)
T ss_pred             HHHHHHHHHHHHHhcCCCCcccchhhhhccccCCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHCCCCHHHHHHHHCcC
Confidence            999999986443222      11         0112223334444443322           122678999999999999


Q ss_pred             HHHHHHHHhCCCC
Q 012567          402 MKRLHAVLLSPKA  414 (460)
Q Consensus       402 ~e~Vk~~l~~ar~  414 (460)
                      +.+|+..+..++.
T Consensus       165 ~~tV~r~l~~aR~  177 (185)
T PF07638_consen  165 ERTVRRRLRRARA  177 (185)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999887663

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.07  E-value=1.3e-06  Score=61.67  Aligned_cols=32  Identities=44%  Similarity=0.559  Sum_probs=28.5

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHH
Q 012567          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLL  243 (460)
Q Consensus       211 ~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~  243 (460)
                      +|+++ ||++| +++||||++||++|+++|+.+.
T Consensus         1 ~D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g~   33 (37)
T PF00140_consen    1 SDSLRLYLKEI-GRYPLLTAEEEIELARRIRKGD   33 (37)
T ss_dssp             HHHHHHHHHHH-HHS-EETTHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHhH
Confidence            37899 99999 9999999999999999999863

2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=97.77  E-value=0.00066  Score=75.47  Aligned_cols=32  Identities=34%  Similarity=0.583  Sum_probs=30.8

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 012567          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL  242 (460)
Q Consensus       210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~  242 (460)
                      ++||++ ||++| |++||||+|+|++|+++|+.+
T Consensus       102 t~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G  134 (619)
T PRK05658        102 TDDPVRMYLREM-GTVELLTREGEIEIAKRIEAG  134 (619)
T ss_pred             CCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHH
Confidence            589999 99999 999999999999999999986

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

Probab=96.30  E-value=0.05  Score=53.11  Aligned_cols=130  Identities=20%  Similarity=0.151  Sum_probs=69.9

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHH-HHH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEG-CRG  322 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG-~IG  322 (460)
                      ++.+....|....|++||..|.|+.+|++...+.....                   ..    ....++++.++++ -..
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~-------------------~~----~~~~SLd~~~~~~~~~~  144 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKK-------------------IA----QEPISLETPIGEEEDSF  144 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-------------------Hh----ccCCCcCCCCCCCCccc
Confidence            34455677778889999999999999999876542211                   00    1122223322211 112


Q ss_pred             HHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHh----CCCCCHHHHHHHh
Q 012567          323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT  398 (460)
Q Consensus       323 LirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~----gr~pS~eEIAe~L  398 (460)
                      +...+..  +..............+..+..++..      +|..-..          -|...+    ..+.|.+|||+.|
T Consensus       145 l~d~l~d--~~~~~p~~~~~~~~~~~~l~~~l~~------L~~~er~----------vl~l~ygl~~~~~~t~~EIA~~l  206 (238)
T TIGR02393       145 LGDFIED--TSIESPDDYAAKELLREQLDEVLET------LTERERK----------VLRMRYGLLDGRPHTLEEVGKEF  206 (238)
T ss_pred             HHHHhcC--CCCCChHHHHHHHHHHHHHHHHHHh------CCHHHHH----------HHHHHhCCCCCCCccHHHHHHHH
Confidence            2222221  1111122333333334444444431      3322111          112223    3678999999999


Q ss_pred             CCCHHHHHHHHhCCCC
Q 012567          399 GLSMKRLHAVLLSPKA  414 (460)
Q Consensus       399 GIS~e~Vk~~l~~ar~  414 (460)
                      |+|.++|+++...+..
T Consensus       207 gis~~~V~q~~~~al~  222 (238)
T TIGR02393       207 NVTRERIRQIESKALR  222 (238)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999876544

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.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=96.03  E-value=0.036  Score=54.56  Aligned_cols=30  Identities=13%  Similarity=0.107  Sum_probs=26.3

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      +..+.|++|||+.||+|+++|+..+++++.
T Consensus       214 ~~~~~s~~EIA~~lgis~~tV~~~~~ra~~  243 (251)
T PRK07670        214 YKEELTLTEIGQVLNLSTSRISQIHSKALF  243 (251)
T ss_pred             HhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            357889999999999999999999987654

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=95.86  E-value=0.12  Score=56.57  Aligned_cols=132  Identities=17%  Similarity=0.230  Sum_probs=72.0

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHh-HHHHH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ-EGCRG  322 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQ-EG~IG  322 (460)
                      ++.+.+.+|...+|++||..|.|+.+|++...+....+                       +....+++++.+. ++...
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~-----------------------~~~~~~SLD~~i~~d~~~~  415 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK-----------------------YNREPISLDKTIGKEGDSQ  415 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-----------------------hcCCCcccccccccCCccc
Confidence            45567788888899999999999999999876543211                       1122233333332 11112


Q ss_pred             HHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCH
Q 012567          323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM  402 (460)
Q Consensus       323 LirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~  402 (460)
                      +..-+..  +........+.....+..+...|..      ++..-    ..|-..+--|  ..+.+.|.+|||+.||||.
T Consensus       416 l~d~l~D--~~~~~p~~~~~~~~l~~~L~~aL~~------L~eRE----r~VI~lRyGL--~~~e~~TL~EIa~~lGVSr  481 (509)
T PRK05901        416 FGDFIED--SEAVSPVDAVSFTLLQDQLQEVLET------LSERE----AGVIRMRFGL--TDGQPKTLDEIGQVYGVTR  481 (509)
T ss_pred             HHHhccC--CCCCCHHHHHHHHHHHHHHHHHHhh------CCHHH----HHHHHHHhhc--cCCCCCCHHHHHHHHCCCH
Confidence            2222211  1111223333444445455554432      22221    1111111101  1136789999999999999


Q ss_pred             HHHHHHHhCC
Q 012567          403 KRLHAVLLSP  412 (460)
Q Consensus       403 e~Vk~~l~~a  412 (460)
                      ++|+++...+
T Consensus       482 ERVRQIe~kA  491 (509)
T PRK05901        482 ERIRQIESKT  491 (509)
T ss_pred             HHHHHHHHHH
Confidence            9999987644

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=95.44  E-value=0.13  Score=51.34  Aligned_cols=34  Identities=35%  Similarity=0.502  Sum_probs=27.7

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~  277 (460)
                      ++.+...+|...+|++||..|.|+.+|++...+.
T Consensus       128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~  161 (264)
T PRK07122        128 RLGRATAELSQRLGRAPTASELAAELGMDREEVV  161 (264)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            3445566777888999999999999999987654

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=95.37  E-value=0.15  Score=53.42  Aligned_cols=128  Identities=22%  Similarity=0.203  Sum_probs=72.6

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHh-HHHHH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ-EGCRG  322 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQ-EG~IG  322 (460)
                      ++.+...+|...+|++||..|.|+.+|++...+...+..                   +.    ...++++.+. ++-..
T Consensus       217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~-------------------~~----~~~SLd~~~~~~~~~~  273 (367)
T PRK09210        217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI-------------------AQ----EPVSLETPIGEEDDSH  273 (367)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH-------------------hc----CCCCcCCCCCCCCcch
Confidence            345667778888999999999999999998766433221                   11    1122222221 11111


Q ss_pred             HHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHh----CCCCCHHHHHHHh
Q 012567          323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT  398 (460)
Q Consensus       323 LirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~----gr~pS~eEIAe~L  398 (460)
                      +..-+.  |+.............++..+.++|..      +|..-..    |      |.-.+    |.+.|.+|||+.|
T Consensus       274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~------L~~rEr~----V------l~lrygl~~~~~~tl~EIa~~l  335 (367)
T PRK09210        274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLDT------LTDREEN----V------LRLRFGLDDGRTRTLEEVGKVF  335 (367)
T ss_pred             hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh------CCHHHHH----H------HHHHhccCCCCCccHHHHHHHH
Confidence            222221  11112234444555566666665532      3332111    1      11223    3678999999999


Q ss_pred             CCCHHHHHHHHhCC
Q 012567          399 GLSMKRLHAVLLSP  412 (460)
Q Consensus       399 GIS~e~Vk~~l~~a  412 (460)
                      |+|.++|+++...+
T Consensus       336 gvs~erVrQi~~~A  349 (367)
T PRK09210        336 GVTRERIRQIEAKA  349 (367)
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999999987644

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=95.33  E-value=0.25  Score=51.02  Aligned_cols=132  Identities=17%  Similarity=0.179  Sum_probs=69.9

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHh-HHHHH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ-EGCRG  322 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQ-EG~IG  322 (460)
                      ++.+.+..|...+|++||..|.|+.+|++...+.....                   .+    ....++++.+. ++-..
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~-------------------~~----~~~~SLd~~~~~~~~~~  230 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIADLLE-------------------HS----RDPVSLDMPVGSDEEAP  230 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH-------------------Hc----CCCceecCCCCCCCCch
Confidence            45566778888899999999999999999866543211                   01    11122222221 11112


Q ss_pred             HHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCH
Q 012567          323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM  402 (460)
Q Consensus       323 LirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~  402 (460)
                      |...+..-+  .......+...-.+..+...|..      +|..-    ..|-...--|  ..+.+.|.+|||+.||||.
T Consensus       231 l~d~l~d~~--~~~pe~~~~~~~~~~~l~~~L~~------L~eRE----r~Vl~~rygl--~~~~~~Tl~eIa~~lgvS~  296 (324)
T PRK07921        231 LGDFIEDSE--ATSAENAVIAGLLHTDIRSVLAT------LDERE----QQVIRLRFGL--DDGQPRTLDQIGKLFGLSR  296 (324)
T ss_pred             HHHHhcCCC--CCCHHHHHHHHHHHHHHHHHHHh------CCHHH----HHHHHHHHhc--CCCCCcCHHHHHHHHCCCH
Confidence            333332211  11123334444444445554431      23221    1111111000  1135679999999999999


Q ss_pred             HHHHHHHhCC
Q 012567          403 KRLHAVLLSP  412 (460)
Q Consensus       403 e~Vk~~l~~a  412 (460)
                      +.|+++...+
T Consensus       297 eRVrQIe~~A  306 (324)
T PRK07921        297 ERVRQIEREV  306 (324)
T ss_pred             HHHHHHHHHH
Confidence            9999987654

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=95.17  E-value=0.03  Score=55.51  Aligned_cols=34  Identities=24%  Similarity=0.320  Sum_probs=28.1

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~  277 (460)
                      ++.+.+.+|...+|++||..|.|+.+|++...+.
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~  147 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQ  147 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHH
Confidence            3455677788889999999999999999987654

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=95.12  E-value=0.29  Score=48.70  Aligned_cols=132  Identities=17%  Similarity=0.118  Sum_probs=70.1

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHh----HH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ----EG  319 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQ----EG  319 (460)
                      ++.+.+..|+..+|++||..+.|..+|++...+......                   +  ....-.+++|.+.    +.
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~-------------------~--~~~~~~sld~~~~~~~~~~  177 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSK-------------------L--SGTSVVSLNDLWFGGDEGD  177 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHH-------------------H--hcccccchhhhhccCCCcc
Confidence            455667778888999999999999999987654322110                   0  0111122223221    00


Q ss_pred             HHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC
Q 012567          320 CRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG  399 (460)
Q Consensus       320 ~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LG  399 (460)
                      .+.++..+..-  ........+...-....+..++.      .+|......          +...+..+.|++|||+.||
T Consensus       178 ~~~l~~~~~~~--~~~~pe~~~~~~e~~~~l~~~l~------~L~~~~r~v----------l~l~~~~~~s~~eIA~~lg  239 (268)
T PRK06288        178 EVSLMDTLESP--AALNPDEIAEREEIKRVIVEAIK------TLPEREKKV----------LILYYYEDLTLKEIGKVLG  239 (268)
T ss_pred             cchhhhhccCC--CCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHH----------HHHHHHcCCCHHHHHHHHC
Confidence            12222222221  11112333333333333433332      234332211          1122346889999999999


Q ss_pred             CCHHHHHHHHhCCCC
Q 012567          400 LSMKRLHAVLLSPKA  414 (460)
Q Consensus       400 IS~e~Vk~~l~~ar~  414 (460)
                      +|+++|+..++++..
T Consensus       240 is~~tV~~~~~ra~~  254 (268)
T PRK06288        240 VTESRISQLHTKAVL  254 (268)
T ss_pred             cCHHHHHHHHHHHHH
Confidence            999999988876543

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=95.03  E-value=0.16  Score=54.15  Aligned_cols=35  Identities=20%  Similarity=0.351  Sum_probs=29.9

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~  278 (460)
                      ++.+.+..|...+|+.||..|.|+++|++...+..
T Consensus       263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~  297 (415)
T PRK07598        263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVRE  297 (415)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            56677788888899999999999999999877654

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

Probab=94.96  E-value=0.33  Score=48.37  Aligned_cols=144  Identities=19%  Similarity=0.190  Sum_probs=79.6

Q ss_pred             HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhccHHHHHHHHHHhH
Q 012567          216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI  295 (460)
Q Consensus       216 YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~G~~A~e~LI~~nl  295 (460)
                      |||+- .  +.--+.-=.+++.      ++++...+|+..+|++||..|.|+..|++.+++...+..+          +-
T Consensus        92 ~LR~~-~--~v~vpR~~~~~~~------~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~----------~~  152 (247)
T COG1191          92 YLRKN-D--SVKVPRSLRELGR------RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI----------NG  152 (247)
T ss_pred             HHHhC-C--CccCcHHHHHHHH------HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh----------cc
Confidence            77776 4  2222333333333      3445677888899999999999999999987665333222          11


Q ss_pred             HHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHH
Q 012567          296 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK  375 (460)
Q Consensus       296 rLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~  375 (460)
                      .....+--.....    +|    |.         -+...+..+..+-.+...+.+...+..      +|..-.    .  
T Consensus       153 ~~~~sld~~~~~~----~d----~~---------~~~~~~~~~~~~~~~~~~~~l~~ai~~------L~EREk----~--  203 (247)
T COG1191         153 SQLLSLDEDVLKD----DD----DD---------VDDQIENPDDGVEKEELLEILKEAIEP------LPEREK----L--  203 (247)
T ss_pred             ccccchhhhhccc----cc----cc---------hhhccccchhHHHHHHHHHHHHHHHHc------cCHHHH----H--
Confidence            1111111111110    01    11         111123345556666666666666541      222110    1  


Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567          376 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS  411 (460)
Q Consensus       376 ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~  411 (460)
                          -+.-.+..+.|..|||+.||||...|..+...
T Consensus       204 ----Vl~l~y~eelt~kEI~~~LgISes~VSql~kk  235 (247)
T COG1191         204 ----VLVLRYKEELTQKEIAEVLGISESRVSRLHKK  235 (247)
T ss_pred             ----HHHHHHHhccCHHHHHHHhCccHHHHHHHHHH
Confidence                11122346789999999999999999877653

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=94.85  E-value=0.21  Score=49.51  Aligned_cols=30  Identities=13%  Similarity=0.073  Sum_probs=25.8

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      +..+.|.+|||+.||+|.++|+.+++++..
T Consensus       218 y~e~~t~~EIA~~lgis~~~V~~~~~ral~  247 (257)
T PRK05911        218 YYEELVLKEIGKILGVSESRVSQIHSKALL  247 (257)
T ss_pred             HhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            346889999999999999999999886643

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

Probab=94.84  E-value=0.21  Score=50.51  Aligned_cols=29  Identities=17%  Similarity=0.193  Sum_probs=25.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          386 GRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      +.+.|.+|||+.||+|.++|+++++++..
T Consensus       267 ~~~~Tl~EIa~~lgiS~erVrq~~~rAl~  295 (298)
T TIGR02997       267 GEPLTLAEIGRRLNLSRERVRQIEAKALR  295 (298)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            36789999999999999999999987643

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=94.81  E-value=0.24  Score=51.18  Aligned_cols=28  Identities=21%  Similarity=0.197  Sum_probs=25.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      .+.|++|||+.||+|.++|++++.++..
T Consensus       285 e~~Tl~EIa~~lgiS~erVrq~~~rAl~  312 (327)
T PRK05949        285 KELSLAKVGERLNLSRERVRQLEHQALA  312 (327)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            6789999999999999999999887654

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=94.78  E-value=0.26  Score=49.86  Aligned_cols=28  Identities=18%  Similarity=0.236  Sum_probs=25.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      .+.|.+|||+.||+|.++|+++++.+..
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~Al~  271 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEARALE  271 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            6789999999999999999999886654

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

Probab=94.58  E-value=0.28  Score=47.22  Aligned_cols=30  Identities=20%  Similarity=0.203  Sum_probs=25.7

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      +..+.|++|||+.||+|.++|+..++++..
T Consensus       188 y~~~~s~~eIA~~lgis~~tV~~~~~ra~~  217 (224)
T TIGR02479       188 YYEELNLKEIGEVLGLTESRVSQIHSQALK  217 (224)
T ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            356789999999999999999998876643

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.

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=94.50  E-value=0.48  Score=49.90  Aligned_cols=34  Identities=26%  Similarity=0.393  Sum_probs=27.9

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~  277 (460)
                      ++.+....|...+|++||..|.|+.+|++...+.
T Consensus       224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~  257 (373)
T PRK07406        224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLR  257 (373)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            4555677788888999999999999999986653

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=94.32  E-value=0.094  Score=42.09  Aligned_cols=37  Identities=30%  Similarity=0.390  Sum_probs=28.6

Q ss_pred             HHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHH
Q 012567          243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR  279 (460)
Q Consensus       243 ~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~  279 (460)
                      .++.+.+.+|...+||+||..|.|+.+|++...+...
T Consensus         4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~   40 (78)
T PF04539_consen    4 RKIERARRELEQELGREPTDEEIAEELGISVEEVREL   40 (78)
T ss_dssp             HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHH
Confidence            3567788899999999999999999999998776543

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 ....

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=94.31  E-value=0.37  Score=49.42  Aligned_cols=34  Identities=21%  Similarity=0.375  Sum_probs=27.4

Q ss_pred             HHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (460)
Q Consensus       244 ~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~  277 (460)
                      ++.+.+..+...+|+.||..+.|+++|++...+.
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~  202 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR  202 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            4555667777788999999999999999876543

>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=93.88  E-value=0.26  Score=39.17  Aligned_cols=56  Identities=16%  Similarity=0.173  Sum_probs=45.3

Q ss_pred             HHHHHhcc-HHHHHHHHHHhHHHHHHHHHHcc----C--CCCCcccHHhHHHHHHHHHHhhcC
Q 012567          276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQ----G--AGMNLQDLVQEGCRGLVRGAEKFD  331 (460)
Q Consensus       276 L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~----~--~g~d~eDLiQEG~IGLirAiekFD  331 (460)
                      ++..+..| ..|.+++++.|.+++.+.+.+-.    +  ++.--+|+-|+--..|++++-+|+
T Consensus         3 vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen    3 VIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            34445566 99999999999999999987622    1  244558999999999999999996

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

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=93.56  E-value=0.8  Score=45.15  Aligned_cols=34  Identities=24%  Similarity=0.197  Sum_probs=27.2

Q ss_pred             HHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHH
Q 012567          245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (460)
Q Consensus       245 le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~  278 (460)
                      +.+...+|...+|++||..|.|+.+|++.+.+..
T Consensus       122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~  155 (254)
T TIGR02850       122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVF  155 (254)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHH
Confidence            3445566777789999999999999999876654

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=93.22  E-value=0.4  Score=47.16  Aligned_cols=30  Identities=13%  Similarity=0.139  Sum_probs=25.6

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      +..+.|++|||+.||+|.++|+..++++..
T Consensus       218 ~~~g~s~~eIA~~lgis~~~V~~~~~ra~~  247 (255)
T TIGR02941       218 FEENLSQKETGERLGISQMHVSRLQRQAIS  247 (255)
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            356889999999999999999999876543

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

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=93.22  E-value=0.62  Score=45.24  Aligned_cols=30  Identities=17%  Similarity=0.180  Sum_probs=26.0

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      +..+.|++|||+.||+|+++|+..++++..
T Consensus       197 ~~~g~s~~EIA~~lgis~~tV~~~~~ra~~  226 (236)
T PRK06986        197 YQEELNLKEIGAVLGVSESRVSQIHSQAIK  226 (236)
T ss_pred             hccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            346789999999999999999999887654

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=92.70  E-value=0.061  Score=40.16  Aligned_cols=30  Identities=20%  Similarity=0.174  Sum_probs=22.5

Q ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567          384 ENGRHPNNEEVAEATGLSMKRLHAVLLSPK  413 (460)
Q Consensus       384 ~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar  413 (460)
                      .+..+.|+.|||+.+|+|+++|+..+++++
T Consensus        22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~   51 (54)
T PF08281_consen   22 RYFQGMSYAEIAEILGISESTVKRRLRRAR   51 (54)
T ss_dssp             HHTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred             HHHHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            356889999999999999999999988654

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.

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=92.49  E-value=0.95  Score=43.69  Aligned_cols=32  Identities=34%  Similarity=0.482  Sum_probs=25.6

Q ss_pred             HhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567          246 EGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (460)
Q Consensus       246 e~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~  277 (460)
                      .+....|...+|+.||..|.|+.+|++...+.
T Consensus       100 ~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~  131 (231)
T TIGR02885       100 RYMKEELSKELGREPTINELAEALGVSPEEIV  131 (231)
T ss_pred             HHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHH
Confidence            33456677778999999999999999987654

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=91.56  E-value=2.3  Score=41.96  Aligned_cols=33  Identities=24%  Similarity=0.231  Sum_probs=26.7

Q ss_pred             HHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567          245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (460)
Q Consensus       245 le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~  277 (460)
                      +.+...++....|++|+..|.|..+|++...+.
T Consensus       125 ~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~  157 (258)
T PRK08215        125 ALQVREKLINENSKEPTVEEIAKELEVPREEVV  157 (258)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHH
Confidence            334556677788999999999999999987764

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=91.20  E-value=2.3  Score=41.58  Aligned_cols=33  Identities=18%  Similarity=0.336  Sum_probs=26.9

Q ss_pred             HHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHH
Q 012567          245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (460)
Q Consensus       245 le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~  277 (460)
                      +.+....|...+|++||..|.|+.+|++...+.
T Consensus       103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~  135 (231)
T PRK12427        103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQ  135 (231)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHH
Confidence            344566777788999999999999999987654

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=91.18  E-value=1.9  Score=43.21  Aligned_cols=30  Identities=23%  Similarity=0.283  Sum_probs=26.6

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      -.+.|++|||+.||+|+++|+.+++++...
T Consensus       240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlkk  269 (285)
T TIGR02394       240 YEPATLEEVAAEVGLTRERVRQIQVEALKK  269 (285)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            467899999999999999999999877654

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).

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=90.86  E-value=2.6  Score=42.55  Aligned_cols=26  Identities=19%  Similarity=0.299  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSP  412 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~a  412 (460)
                      .+.|.+|||+.||+|.++|+++...+
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~~A  272 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEKNA  272 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            57899999999999999999988754

>PRK05572 sporulation sigma factor SigF; Validated

Probab=90.41  E-value=2  Score=42.28  Aligned_cols=28  Identities=18%  Similarity=0.134  Sum_probs=24.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567          386 GRHPNNEEVAEATGLSMKRLHAVLLSPK  413 (460)
Q Consensus       386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar  413 (460)
                      ..+.|..|||+.+|+|..+|..+.+++.
T Consensus       216 ~~~~s~~eIA~~lgis~~~V~~~~~ral  243 (252)
T PRK05572        216 FKDKTQSEVAKRLGISQVQVSRLEKKIL  243 (252)
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4678999999999999999999887654

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=90.36  E-value=0.92  Score=35.98  Aligned_cols=42  Identities=33%  Similarity=0.389  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCC-HHHHHHHHh
Q 012567          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLS-MKRLHAVLL  410 (460)
Q Consensus       369 e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS-~e~Vk~~l~  410 (460)
                      +...+|..++.....+.|..||..|||+.+|++ ..+|...+.
T Consensus         6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen    6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            344567777888888999999999999999997 899988775

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.

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

Probab=90.25  E-value=2.2  Score=40.99  Aligned_cols=29  Identities=21%  Similarity=0.222  Sum_probs=25.2

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          386 GRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      ..+.|++|||+.||+|..+|...++++..
T Consensus       192 ~~~~s~~eIA~~lgis~~~v~~~~~ra~~  220 (227)
T TIGR02980       192 FEDKTQSEIAERLGISQMHVSRLLRRALK  220 (227)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            46789999999999999999999886643

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.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=89.17  E-value=3.2  Score=42.79  Aligned_cols=31  Identities=19%  Similarity=0.236  Sum_probs=26.9

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                      ..+.|.+|||+.||+|.++|+++++++...+
T Consensus       280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL  310 (325)
T PRK05657        280 YEAATLEDVAREIGLTRERVRQIQVEALRRL  310 (325)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            3678999999999999999999998776543

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=88.68  E-value=1.2  Score=41.83  Aligned_cols=62  Identities=15%  Similarity=0.260  Sum_probs=49.1

Q ss_pred             HHHHHHHHccCCCCC---cccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567          297 LVISIAKNYQGAGMN---LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (460)
Q Consensus       297 LV~~IAkry~~~g~d---~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~  358 (460)
                      .+..+.++|--+|..   -+|+|.+|.-.+++.+..||+++...+-.|....+-++..+.|.+..
T Consensus        49 Ia~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kEk  113 (179)
T PHA02547         49 IAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKEK  113 (179)
T ss_pred             HHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHHH
Confidence            344455555434443   68999999999999999999999988999999999998888776543

>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=88.38  E-value=0.88  Score=33.47  Aligned_cols=30  Identities=23%  Similarity=0.191  Sum_probs=25.0

Q ss_pred             HHhCCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567          383 SENGRHPNNEEVAEATGLSMKRLHAVLLSP  412 (460)
Q Consensus       383 ~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a  412 (460)
                      ..+..+.|..|||+.||+|.++|+.+...+
T Consensus        15 ~~y~~~~t~~eIa~~lg~s~~~V~~~~~~a   44 (50)
T PF04545_consen   15 LRYFEGLTLEEIAERLGISRSTVRRILKRA   44 (50)
T ss_dssp             HHHTST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHhcCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence            345788999999999999999999988754

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 ....

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

Probab=82.15  E-value=19  Score=37.76  Aligned_cols=36  Identities=25%  Similarity=0.317  Sum_probs=29.6

Q ss_pred             HHHHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHH
Q 012567          241 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQREL  276 (460)
Q Consensus       241 ~~~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L  276 (460)
                      -.-+|.+++.+|....|++|+..+.|+.+|+++..+
T Consensus       187 ~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V  222 (342)
T COG0568         187 LINKLRRVKRELLQELGREPTPEEIAEELGVSPDKV  222 (342)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHH
Confidence            334667788888888999999999999999987543

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=80.27  E-value=17  Score=36.24  Aligned_cols=27  Identities=19%  Similarity=0.268  Sum_probs=23.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHhCC
Q 012567          386 GRHPNNEEVAEATGLSMKRLHAVLLSP  412 (460)
Q Consensus       386 gr~pS~eEIAe~LGIS~e~Vk~~l~~a  412 (460)
                      ..+.|.+|||+.||+|.++|+++...+
T Consensus       234 ~~~~t~~eIA~~lgvS~~~V~q~~~~A  260 (270)
T TIGR02392       234 DDKLTLQELAAEYGVSAERIRQIEKNA  260 (270)
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            347899999999999999999887654

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.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=80.23  E-value=2.2  Score=34.85  Aligned_cols=26  Identities=19%  Similarity=0.207  Sum_probs=23.5

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567          386 GRHPNNEEVAEATGLSMKRLHAVLLS  411 (460)
Q Consensus       386 gr~pS~eEIAe~LGIS~e~Vk~~l~~  411 (460)
                      -.+.|+.|||+.||+|+.+|+..+..
T Consensus        30 ~eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879        30 EAGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            36889999999999999999999874

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	460
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		2e-37
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		1e-36
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		5e-35
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		7e-35
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		4e-34
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		4e-34
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		5e-34
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		2e-33
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		2e-33
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		3e-21
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		1e-19
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		1e-13
1rp3_A	239	Cocrystal Structure Of The Flagellar SigmaANTI-Sigm		3e-06

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score =  153 bits (387), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 89/230 (38%), Positives = 131/230 (56%), Gaps = 17/230 (7%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 259 SPTFAQWAAAAGVDQRELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDL 315
           +    +         +EL+R L+    G   +  +I +N+RLV+SIAK Y G G++  DL
Sbjct: 62  TARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL 121
Query: 316 VQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK 375
           +QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++ 
Sbjct: 122 IQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLS 181
Query: 376 EARKQLYSENGRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSLDQKIG 423
              +QL  E GR P+ EE+AEA   G   KR+   L   + P SL+  IG
Sbjct: 182 RTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIG 231

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score =  150 bits (380), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 92/252 (36%), Positives = 138/252 (54%), Gaps = 32/252 (12%)
Query: 208 VDYSDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSER 255
           V  SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +
Sbjct: 90  VSTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAK 149
Query: 256 CGGS------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRL 297
             G+      P   +      V++         +EL+R L+    G   +  +I +N+RL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 298 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 357
           V+SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGLSMKRLHAVLLSPKAP 415
           +RTIR+P HMVE   ++    +QL  E GR P+ EE+AEA   G   KR+   L   + P
Sbjct: 270 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 329
Query: 416 RSLDQKIGINQN 427
            SL+  IG  ++
Sbjct: 330 VSLETPIGDEKD 341

>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 =  145 bits (365), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 89/240 (37%), Positives = 132/240 (55%), Gaps = 32/240 (13%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 259 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 300
           +      P   +      V++         +EL+R L+    G   +  +I +N+RLV+S
Sbjct: 62  TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 121
Query: 301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360
           IAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+RT
Sbjct: 122 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 181
Query: 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSL 418
           IR+P HMVE   ++    +QL  E GR P+ EE+AEA   G   KR+   L   + P SL
Sbjct: 182 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 241

>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2 Complexed With -10 Promoter Element Ssdna Oligo (Tacaat) Length = 245

Iteration: 1
 Score =  145 bits (365), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 89/240 (37%), Positives = 132/240 (55%), Gaps = 32/240 (13%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 6   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 65
Query: 259 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 300
           +      P   +      V++         +EL+R L+    G   +  +I +N+RLV+S
Sbjct: 66  TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 125
Query: 301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360
           IAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+RT
Sbjct: 126 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 185
Query: 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSL 418
           IR+P HMVE   ++    +QL  E GR P+ EE+AEA   G   KR+   L   + P SL
Sbjct: 186 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 245

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

Iteration: 1
 Score =  142 bits (358), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 67/143 (46%), Positives = 94/143 (65%), Gaps = 2/143 (1%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
           G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 343 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGL 400
            WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P  EE+AEA   G 
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 401 SMKRLHAVLLSPKAPRSLDQKIG 423
             KR+   L   + P SL+  IG
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIG 322

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

Iteration: 1
 Score =  142 bits (358), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 67/143 (46%), Positives = 94/143 (65%), Gaps = 2/143 (1%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
           G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 343 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGL 400
            WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P  EE+AEA   G 
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 401 SMKRLHAVLLSPKAPRSLDQKIG 423
             KR+   L   + P SL+  IG
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIG 322

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

Iteration: 1
 Score =  142 bits (357), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 67/143 (46%), Positives = 94/143 (65%), Gaps = 2/143 (1%)
Query: 283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 342
           G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 343 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGL 400
            WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P  EE+AEA   G 
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 401 SMKRLHAVLLSPKAPRSLDQKIG 423
             KR+   L   + P SL+  IG
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIG 342

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score =  140 bits (352), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 102/158 (64%), Gaps = 4/158 (2%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 329
           +++ RR++ G       K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +K
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418
Query: 330 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 389
           F+  +G+KFSTYA WWI+QA+ +S++DQ+RTIR+P HM+E   ++    +Q+  E GR P
Sbjct: 419 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 478
Query: 390 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN 427
             EE+AE   +   ++  VL   K P S++  IG +++
Sbjct: 479 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDED 516

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

Iteration: 1
 Score =  140 bits (352), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 102/158 (64%), Gaps = 4/158 (2%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 329
           +++ RR++ G       K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +K
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418
Query: 330 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 389
           F+  +G+KFSTYA WWI+QA+ +S++DQ+RTIR+P HM+E   ++    +Q+  E GR P
Sbjct: 419 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 478
Query: 390 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN 427
             EE+AE   +   ++  VL   K P S++  IG +++
Sbjct: 479 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDED 516

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 99.8 bits (247), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 65/89 (73%), Gaps = 3/89 (3%)
Query: 274 RELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 330
           +EL+R L+    G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF
Sbjct: 91  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 331 DASKGFKFSTYAHWWIKQAVRKSLSDQSR 359
           +  +GF FSTYA WWI+QA+ ++++DQ+R
Sbjct: 151 EYKRGFAFSTYATWWIRQAINRAIADQAR 179

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 41/90 (45%), Positives = 64/90 (71%), Gaps = 4/90 (4%)
Query: 274 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 329
           +++ RR++ G       K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +K
Sbjct: 250 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 309
Query: 330 FDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359
           F+  +G+KFSTYA WWI+QA+ +S++DQ+R
Sbjct: 310 FEYRRGYKFSTYATWWIRQAITRSIADQAR 339

>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti- Sigma Factor Spoiiab With The Sporulation Sigma Factor Sigmaf Length = 243

Iteration: 1
 Score = 74.7 bits (182), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 44/129 (34%), Positives = 71/129 (55%), Gaps = 2/129 (1%)
Query: 274 RELRRRLNYGIL-CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA 332
           +EL RR   G    +D++I  N+RLV S+ + +   G    DL Q GC GL++  +KFD 
Sbjct: 16  KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDL 75
Query: 333 SKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNE 392
           S   KFSTYA   I   +++ L D   T+++   + E   ++++A+ +L    GR P   
Sbjct: 76  SYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVT 134
Query: 393 EVAEATGLS 401
           E+A+  G+S
Sbjct: 135 EIADHLGIS 143

>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma Complex, Sigma-28FLGM Length = 239

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 36/129 (27%), Positives = 63/129 (48%), Gaps = 12/129 (9%)
Query: 287 KDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAH 343
           ++++I   + LV +IA N +      ++++DL+  G  GL++  +        +   Y  
Sbjct: 14  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73
Query: 344 WWIKQAVR---KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGL 400
             IK A+    +SL   SR +R      E   R+KE  ++L  + GR P +EEVA+  G+
Sbjct: 74  LRIKGAIYDYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGI 127
Query: 401 SMKRLHAVL 409
           S + L   L
Sbjct: 128 STEELFKTL 136

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	460
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	3e-48
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	1e-47
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	2e-47
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	4e-45
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	2e-41
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	7e-31
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	2e-26
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	5e-05

>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 =  170 bits (431), Expect = 3e-48
 Identities = 85/307 (27%), Positives = 133/307 (43%), Gaps = 22/307 (7%)

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVR-SRRQTERKARR 178
             D  + +     E        +   L+   EE  L   ++S S  VR    +  +    
Sbjct: 35  EPDPDLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLL 94

Query: 179 TRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAG 238
           T   E   A  +     +  +    +  + D                ++ A         
Sbjct: 95  TLEEEVELARKVEEGMEAIKKLSEITGLDPDLIR------------EVVRAKILGSARVR 142

Query: 239 IQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLV 298
               LK     + + E      +  +       + +        G   +  +I +N+RLV
Sbjct: 143 HIPGLKETLDPKTVEEIDQKLKSLPK-------EHKRYLHIAREGEAARQHLIEANLRLV 195

Query: 299 ISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 358
           +SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+
Sbjct: 196 VSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQA 255

Query: 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM--KRLHAVLLSPKAPR 416
           RTIR+P HMVE   ++    +QL  E GR P  EE+AEA G     KR+   L   + P 
Sbjct: 256 RTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPV 315

Query: 417 SLDQKIG 423
           SL+  IG
Sbjct: 316 SLETPIG 322

>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 =  163 bits (414), Expect = 1e-47
 Identities = 64/149 (42%), Positives = 93/149 (62%), Gaps = 2/149 (1%)

Query: 272 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 331
           + +        G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF+
Sbjct: 97  ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFE 156

Query: 332 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNN 391
             + FKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P+ 
Sbjct: 157 YKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSY 216

Query: 392 EEVAE--ATGLSMKRLHAVLLSPKAPRSL 418
           EE+AE    G   KR+   L   + P SL
Sbjct: 217 EEIAEAMGPGWDAKRVEETLKIAQEPVSL 245

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Length = 438

 Score =  168 bits (426), Expect = 2e-47
 Identities = 82/336 (24%), Positives = 140/336 (41%), Gaps = 6/336 (1%)

Query: 94  KPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEEL 153
           K + S                +    + +    E   +    + + L    +LE   + L
Sbjct: 2   KKSKSKKKAAKAQEVEVKEPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPL 61

Query: 154 KLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDP 213
            L     +  +      + E +         +      +             +       
Sbjct: 62  DLEGPLEADLLPEEGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTLEEEIDLARKV 121

Query: 214 LRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 273
              + A    S     ++E+        +L    ++++   +    P   +         
Sbjct: 122 EEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSL 181

Query: 274 RELRRRLNY----GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 329
            +  +R  +    G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EK
Sbjct: 182 PKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEK 241

Query: 330 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 389
           F+  + FKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P
Sbjct: 242 FEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREP 301

Query: 390 NNEEVAEATGLSM--KRLHAVLLSPKAPRSLDQKIG 423
           + EE+AEA G     KR+   L   + P SL+  IG
Sbjct: 302 SYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIG 337

>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 =  156 bits (397), Expect = 4e-45
 Identities = 46/153 (30%), Positives = 81/153 (52%), Gaps = 2/153 (1%)

Query: 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 330
           + +EL RR   G    +D++I  N+RLV S+ + +   G    DL Q GC GL++  +KF
Sbjct: 14  EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKF 73

Query: 331 DASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN 390
           D S   KFSTYA   I   +++ L D   T+++   + E   ++++A+ +L    GR P 
Sbjct: 74  DLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPT 132

Query: 391 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIG 423
             E+A+  G+S + +     + + P S+ + + 
Sbjct: 133 VTEIADHLGISPEDVVLAQEAVRLPTSIHETVY 165

>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 =  154 bits (391), Expect = 2e-41
 Identities = 64/156 (41%), Positives = 99/156 (63%), Gaps = 4/156 (2%)

Query: 272 DQRELRRRLNYG----ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGA 327
             +++ RR++ G       K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  
Sbjct: 357 QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 416

Query: 328 EKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGR 387
           +KF+  +G+KFSTYA WWI+QA+ +S++DQ+RTIR+P HM+E   ++    +Q+  E GR
Sbjct: 417 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 476

Query: 388 HPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIG 423
            P  EE+AE   +   ++  VL   K P S++  IG
Sbjct: 477 EPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG 512

>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 =  118 bits (297), Expect = 7e-31
 Identities = 35/143 (24%), Positives = 65/143 (45%), Gaps = 10/143 (6%)

Query: 287 KDKMITSNIRLVISIA---KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAH 343
           ++++I   + LV +IA   K +    ++++DL+  G  GL++  +        +   Y  
Sbjct: 14  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73

Query: 344 WWIKQAVRKSLSDQSRTI-RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM 402
             IK A+     D  R++      + E   R+KE  ++L  + GR P +EEVA+  G+S 
Sbjct: 74  LRIKGAIY----DYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGIST 129

Query: 403 KRLHAVLLSPKAPR--SLDQKIG 423
           + L   L         SL++   
Sbjct: 130 EELFKTLDKINFSYILSLEEVFR 152

>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 =  108 bits (271), Expect = 2e-26
 Identities = 38/73 (52%), Positives = 56/73 (76%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346
           K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +KF+  +G+KFSTYA WWI
Sbjct: 267 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 326

Query: 347 KQAVRKSLSDQSR 359
           +QA+ +S++DQ+R
Sbjct: 327 RQAITRSIADQAR 339

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 45.2 bits (106), Expect = 4e-05
 Identities = 54/374 (14%), Positives = 104/374 (27%), Gaps = 133/374 (35%)

Query: 137 QQPLNKSADLEPTHEELK--LLEEQVSQSIAVRSRRQTER------KARRTRAAEKAAAN 188
           +     + D +   +  K  L +E++   I  +              +++    +K    
Sbjct: 26  EDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEE 85

Query: 189 VMS-----VKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANE---EMQLSAGIQ 240
           V+      + S   + +++PS+    Y +            RL   N+   +  +S  +Q
Sbjct: 86  VLRINYKFLMSPIKTEQRQPSMMTRMYIE---------QRDRLYNDNQVFAKYNVSR-LQ 135

Query: 241 DLLKL-EGLREVLSER---------CGGSPTFAQWAAAAGVDQRELRRRLNYGIL----- 285
             LKL + L E+   +          G +     W A       +++ ++++ I      
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKT-----WVALDVCLSYKVQCKMDFKIFWLNLK 190

Query: 286 -CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHW 344
            C           V+            LQ L             + D +           
Sbjct: 191 NCNSP------ETVL----------EMLQKL----LY-------QIDPNW---------- 213

Query: 345 WIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN---------NEEVA 395
                   S SD S  I+L  H       ++   ++L      + N         N +  
Sbjct: 214 -------TSRSDHSSNIKLRIH------SIQAELRRLLKSK-PYENCLLVLLNVQNAKAW 259

Query: 396 EATGLSMKRL------------------HAVLLSPKAPRSLDQKIGI--------NQNLK 429
            A  LS K L                  H  L       + D+   +         Q+L 
Sbjct: 260 NAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLP 319

Query: 430 PSVCFILNLADSLI 443
             V        S+I
Sbjct: 320 REVLTTNPRRLSII 333

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Length = 164

 Score = 42.5 bits (100), Expect = 5e-05
 Identities = 21/90 (23%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

Query: 309 GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368
           G   +DLVQEG  GL++  + +D +K   FS++A   I++ +  ++   +    +  +  
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMVLNEA 59

Query: 369 EATYRVKEARKQLYSENGRHPNNEEVAEAT 398
             T  + E     + + G + NN + +E+ 
Sbjct: 60  LKTNAILE-DSAYFDDEGHNINNYKSSESN 88

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	460
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	99.91
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.76
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.7
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.64
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.61
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.58
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.39
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.26
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.2
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	99.04
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.95
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	97.14
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	96.59
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	92.55
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	92.2
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	91.74
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	90.75
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	89.66
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	87.82
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	86.47
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	86.0
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	85.85
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	84.66
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	84.17
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	84.03
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	82.61
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	81.83
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	81.68
3c57_A	95	Two component transcriptional regulatory protein;	80.04

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*

Probab=100.00  E-value=5.4e-38  Score=306.18  Aligned_cols=208  Identities=39%  Similarity=0.658  Sum_probs=131.4

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH-HHhHHHHHh-------h------------------hcCCCCcH
Q 012567          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK-LEGLREVLS-------E------------------RCGGSPTF  262 (460)
Q Consensus       210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~-le~~~~~L~-------~------------------~~g~~pt~  262 (460)
                      ++||++ ||++| |++||||++||++|+++|+.++. .+.+.....       +                  ..+.+|+.
T Consensus         5 ~~d~~~~yl~~i-~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~   83 (245)
T 3ugo_A            5 TSDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT   83 (245)
T ss_dssp             CCHHHHHHHHHH-TTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHH
T ss_pred             CCCcHHHHHHHc-ccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchh
Confidence            479999 99999 99999999999999999999864 333322110       0                  02578999


Q ss_pred             HHHHHHhCCC----HHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCch
Q 012567          263 AQWAAAAGVD----QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKF  338 (460)
Q Consensus       263 ~ewA~a~g~d----e~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rF  338 (460)
                      .+||.+.+++    ...|...+++|..|++.|+..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|
T Consensus        84 ~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F  163 (245)
T 3ugo_A           84 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  163 (245)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCH
T ss_pred             HHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcH
Confidence            9999998875    345667788889999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHHHHhCCCCCc
Q 012567          339 STYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       339 STYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LG--IS~e~Vk~~l~~ar~~l  416 (460)
                      +||++||||++|.++++++.+.+++|.++.+.+.++.++.+.|...+++.||++|||+.||  ||+++|++.+.+++..+
T Consensus       164 ~tya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~l  243 (245)
T 3ugo_A          164 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV  243 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTC-----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhcc
Confidence            9999999999999999999999999999999999999999999999999999999999999  99999999999999988


Q ss_pred             cc
Q 012567          417 SL  418 (460)
Q Consensus       417 SL  418 (460)
                      ||
T Consensus       244 sl  245 (245)
T 3ugo_A          244 SL  245 (245)
T ss_dssp             --
T ss_pred             CC
Confidence            86

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

Probab=100.00  E-value=8.2e-37  Score=319.75  Aligned_cols=228  Identities=36%  Similarity=0.573  Sum_probs=203.1

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHH------------------HHhhhcCCCCcHHHHHH---
Q 012567          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE------------------VLSERCGGSPTFAQWAA---  267 (460)
Q Consensus       210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~------------------~L~~~~g~~pt~~ewA~---  267 (460)
                      ..|+++ ||++| +++||||+|||++|+++|+.+..++....                  ......|+.|+..+|+.   
T Consensus        92 ~~d~~~~Yl~ei-~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (438)
T 1l9z_H           92 TSDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT  170 (438)
T ss_pred             CCChHHHHHHHh-ccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchh
Confidence            468999 99999 99999999999999999998754432211                  11223567888888743   


Q ss_pred             ---------HhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCch
Q 012567          268 ---------AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKF  338 (460)
Q Consensus       268 ---------a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rF  338 (460)
                               +.+++...|+..+++|..|+++||.+|+++|+++|++|.++|.+++|||||||+|||+++++|||.+|++|
T Consensus       171 ~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rF  250 (438)
T 1l9z_H          171 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  250 (438)
T ss_pred             hhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCh
Confidence                     23556678888888889999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHHHHhCCCCCc
Q 012567          339 STYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       339 STYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LG--IS~e~Vk~~l~~ar~~l  416 (460)
                      +||++|||||.|.++++++++.+++|.++.+.+++++++.+.+.+.+|+.|+.+|||+.+|  +++++|..++..+...+
T Consensus       251 sTYA~~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~~~~~  330 (438)
T 1l9z_H          251 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPV  330 (438)
T ss_pred             HHHHHHHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccccc
Confidence            9999999999999999999999999999999999999999999999999999999999999  99999999999888899


Q ss_pred             ccccccccCCCCCcccccccCC
Q 012567          417 SLDQKIGINQNLKPSVCFILNL  438 (460)
Q Consensus       417 SLD~~v~~e~d~tl~Eli~D~~  438 (460)
                      |||.+++++++.++.|+++|+.
T Consensus       331 SLd~~~~~d~d~~l~d~l~d~~  352 (438)
T 1l9z_H          331 SLETPIGDEKDSFYGDFIPDEN  352 (438)
T ss_pred             ccccccccccchhhhhhhcccc
Confidence            9999998777778888888754

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H

Probab=100.00  E-value=3.8e-37  Score=321.63  Aligned_cols=229  Identities=36%  Similarity=0.568  Sum_probs=200.7

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHH------------------HhhhcCCCCcHHHHH----
Q 012567          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREV------------------LSERCGGSPTFAQWA----  266 (460)
Q Consensus       210 ~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~------------------L~~~~g~~pt~~ewA----  266 (460)
                      ..||++ ||++| +++|+||+|||++|+++|+.+..+......                  .....|+.|+..+|+    
T Consensus        77 ~~d~~~~Yl~ei-~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (423)
T 2a6h_F           77 TSDPVRQYLHEI-GQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKT  155 (423)
T ss_dssp             THHHHHHHHHHH-HHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHH
T ss_pred             CCcHHHHHHHHh-cccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhh
Confidence            468999 99999 999999999999999999987543321111                  111224566655433    


Q ss_pred             -----H---HhCCCHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCch
Q 012567          267 -----A---AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKF  338 (460)
Q Consensus       267 -----~---a~g~de~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rF  338 (460)
                           .   +++++...|+..++.|..|+++||.+|+++|+++|++|.++|.+++||+||||+|||+++++|||.+|++|
T Consensus       156 ~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~F  235 (423)
T 2a6h_F          156 VEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  235 (423)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCH
T ss_pred             hhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCH
Confidence                 2   34667788888898889999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHHHHhCCCCCc
Q 012567          339 STYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       339 STYA~~wIr~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LG--IS~e~Vk~~l~~ar~~l  416 (460)
                      +||++||||+.|.++++++++.+++|.++.+.+++++++.+.+.+.+|+.|+.+|||+.||  +++++|..++..+...+
T Consensus       236 stYa~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~~~  315 (423)
T 2a6h_F          236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPV  315 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSCCE
T ss_pred             HHHHHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccCCc
Confidence            9999999999999999999999999999999999999999999999999999999999999  99999999998888899


Q ss_pred             ccccccccCCCCCcccccccCCC
Q 012567          417 SLDQKIGINQNLKPSVCFILNLA  439 (460)
Q Consensus       417 SLD~~v~~e~d~tl~Eli~D~~~  439 (460)
                      |||.+++++++.++.|+++|+..
T Consensus       316 Sld~~~~~~~~~~l~d~l~d~~~  338 (423)
T 2a6h_F          316 SLETPIGDEKDSFYGDFIPDEHL  338 (423)
T ss_dssp             ESSCBCSSSSSCBGGGSSCCSSS
T ss_pred             ccccccCCCCccchhhhhccccC
Confidence            99999988777788999887643

>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=99.91  E-value=5.1e-26  Score=247.46  Aligned_cols=169  Identities=38%  Similarity=0.695  Sum_probs=158.4

Q ss_pred             CHHHHHHHHhcc-HHH---HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHH
Q 012567          272 DQRELRRRLNYG-ILC---KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK  347 (460)
Q Consensus       272 de~~L~~~l~~G-~~A---~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr  347 (460)
                      +...|+.+++.| ..|   ++.|+..|+++|+++|++|.+++.+++||+||||+|||+++++|++.+|++|+||++||||
T Consensus       357 ~~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~ir  436 (613)
T 3iyd_F          357 QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR  436 (613)
T ss_dssp             THHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHH
Confidence            356677788888 566   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCcccccccccCCC
Q 012567          348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN  427 (460)
Q Consensus       348 ~aI~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~e~d  427 (460)
                      |.|.++++++.+.+++|.++.+.+++++++...+.+++|+.||.+|||+.||+++++|+.++..++.++||+.+++++++
T Consensus       437 n~i~~~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~~~~~~  516 (613)
T 3iyd_F          437 QAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDED  516 (613)
T ss_dssp             HHHHHHTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCCSSSSS
T ss_pred             HHHHHHHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCCCCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998888


Q ss_pred             CCcccccccCCCc
Q 012567          428 LKPSVCFILNLAD  440 (460)
Q Consensus       428 ~tl~Eli~D~~~d  440 (460)
                      ..+.++++|....
T Consensus       517 ~~l~d~i~d~~~~  529 (613)
T 3iyd_F          517 SHLGDFIEDTTLE  529 (613)
T ss_dssp             CCGGGSCCCSSSC
T ss_pred             ccHHHHhcCCCCC
Confidence            8889998876543

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

Probab=99.76  E-value=2.5e-19  Score=168.29  Aligned_cols=152  Identities=30%  Similarity=0.496  Sum_probs=51.6

Q ss_pred             CHHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567          272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (460)
Q Consensus       272 de~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI  350 (460)
                      +...|+..++.| ..|++.|+..|.++|+.+|++|.++..+++||+|||++++|+++++|++.+|..|.||+++|++|.+
T Consensus        14 ~~~~l~~~~~~gd~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~   93 (243)
T 1l0o_C           14 EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEI   93 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHH
Confidence            345567777777 8999999999999999999999999999999999999999999999999988899999999999999


Q ss_pred             HHHhhhcCcccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCccccccccc
Q 012567          351 RKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI  424 (460)
Q Consensus       351 ~~~Lrk~~r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~lSLD~~v~~  424 (460)
                      ++++|++. .+++|..+.....+++.+...+....++.++..++++.+|++.+.+...+.......|++.++.+
T Consensus        94 ~d~~r~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~  166 (243)
T 1l0o_C           94 QRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYE  166 (243)
T ss_dssp             ------CC-CCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC----------
T ss_pred             HHHHHhcC-CccCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccc
Confidence            99999987 78899999999999999999999999999999999999999999998887665567888877644

>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=99.70  E-value=2.1e-16  Score=148.52  Aligned_cols=137  Identities=25%  Similarity=0.353  Sum_probs=121.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcc---CCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~---~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~  360 (460)
                      ..+++.|+..|.++|+.+|++|.   +++.+++||+|||+++||+++++|++.+|.+|.||+++|++|.|++++|++.+ 
T Consensus        11 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~~-   89 (239)
T 1rp3_A           11 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLDF-   89 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSST-
T ss_pred             chHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcCc-
Confidence            45899999999999999999998   67899999999999999999999999998899999999999999999998764 


Q ss_pred             cccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCC--CCcccccccc
Q 012567          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK--APRSLDQKIG  423 (460)
Q Consensus       361 iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar--~~lSLD~~v~  423 (460)
                        .|........++.++...+...+++.|+..++|+.+|++++++..++....  ...|++.++.
T Consensus        90 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~  152 (239)
T 1rp3_A           90 --GSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFR  152 (239)
T ss_dssp             --TCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             --cchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCcccccccc
Confidence              677777788899999999999999999999999999999999988775331  2356776653

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.64  E-value=3.4e-16  Score=158.23  Aligned_cols=85  Identities=47%  Similarity=0.942  Sum_probs=79.3

Q ss_pred             HHHHHHHhcc-H---HHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHH
Q 012567          274 RELRRRLNYG-I---LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (460)
Q Consensus       274 ~~L~~~l~~G-~---~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~a  349 (460)
                      ..|...++.| .   .|++.|+..|+++|+++|++|.+++.+++||+||||+|||+++++|++.+|.+|+||++|||+|.
T Consensus       250 ~~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~  329 (339)
T 1sig_A          250 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA  329 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHH
Confidence            4567777788 6   89999999999999999999999999999999999999999999999998999999999999999


Q ss_pred             HHHHhhhcC
Q 012567          350 VRKSLSDQS  358 (460)
Q Consensus       350 I~~~Lrk~~  358 (460)
                      |++++|++.
T Consensus       330 ~~~~lr~~~  338 (339)
T 1sig_A          330 ITRSIADQA  338 (339)
T ss_dssp             HHHHHHHC-
T ss_pred             HHHHHHHhc
Confidence            999999865

>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=99.61  E-value=1.8e-15  Score=138.43  Aligned_cols=139  Identities=17%  Similarity=0.175  Sum_probs=113.2

Q ss_pred             HHHHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHH
Q 012567          273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  351 (460)
Q Consensus       273 e~~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~  351 (460)
                      +..|+..++.| ..|++.|+..|.+.|+.++++|.+ ..+++|++||+|+++|+++.+|++..  .|.+|++.+++|.++
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            45677777777 999999999999999999999999 99999999999999999999999864  599999999999999


Q ss_pred             HHhhhcCccccc----------------------Ccc---hHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHh
Q 012567          352 KSLSDQSRTIRL----------------------PFH---MVEATYRVKEARKQLYSE--------NGRHPNNEEVAEAT  398 (460)
Q Consensus       352 ~~Lrk~~r~iri----------------------P~~---~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~L  398 (460)
                      +++|++.+....                      |..   ..+....+..++..|+..        +..+.|++|||+.|
T Consensus        87 d~~R~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~l  166 (194)
T 1or7_A           87 NYLVAQGRRPPSSDVDAIEAENFESGGALKEISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIM  166 (194)
T ss_dssp             HHHHHHTTCCTHHHHHHHHHHSCCSSCC--------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHTTCCCHHHHHHHT
T ss_pred             HHHHHHhccCccccccccccccccccccccCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHHcCCCHHHHHHHH
Confidence            999876543210                      111   123334456666666553        34789999999999


Q ss_pred             CCCHHHHHHHHhCCCC
Q 012567          399 GLSMKRLHAVLLSPKA  414 (460)
Q Consensus       399 GIS~e~Vk~~l~~ar~  414 (460)
                      |+|+++|+..+++++.
T Consensus       167 gis~~tV~~~l~ra~~  182 (194)
T 1or7_A          167 DCPVGTVRSRIFRARE  182 (194)
T ss_dssp             TSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999999987754

>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=99.39  E-value=3.7e-13  Score=118.81  Aligned_cols=105  Identities=20%  Similarity=0.283  Sum_probs=77.5

Q ss_pred             CCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccC------------------------
Q 012567          309 GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP------------------------  364 (460)
Q Consensus       309 g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP------------------------  364 (460)
                      |.+++|++|||++++|+++.+|++.+ .+|.+|++++++|.+++++|++.+..+.+                        
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            57899999999999999999999887 78999999999999999999854321111                        


Q ss_pred             ----------cc---hHHHHHHHHHHHH-HHHH-------HhCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          365 ----------FH---MVEATYRVKEARK-QLYS-------ENGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       365 ----------~~---~~e~i~kl~ka~~-~L~~-------~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                                ..   ..+....+..++. .|+.       .+-.+.|++|||+.||+|.++|+..+++++.
T Consensus        80 ~~~~~~~~~~~~~~~~~e~~~~l~~~l~~~L~~~~r~v~~~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~  150 (164)
T 3mzy_A           80 NNYKSSESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLIRGYSYREIATILSKNLKSIDNTIQRIRK  150 (164)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hhhcccCCCHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                      10   1222334555555 4433       3458899999999999999999999987654

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

Probab=99.26  E-value=2.8e-14  Score=128.32  Aligned_cols=126  Identities=6%  Similarity=0.023  Sum_probs=97.1

Q ss_pred             HHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCcccccCcc
Q 012567          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (460)
Q Consensus       287 ~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iriP~~  366 (460)
                      ++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++.+|++.  ..|.+|++.+++|.+++++|+.......+. 
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~~~~~e-   79 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRD--VDPRLGLYRMFQGIWASANADGEAQTSQSD-   79 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCS--SCTTHHHHHHHHHHHHHHTTTTSCCCCCCS-
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCC--CcHHHHHHHHHHHHHHHHhhccCcccCCcc-
Confidence            56789999999999999999999999999999999999999999975  369999999999999999987542111111 


Q ss_pred             hHHHHHHHHHHHHHHHH--------HhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          367 MVEATYRVKEARKQLYS--------ENGRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       367 ~~e~i~kl~ka~~~L~~--------~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      ..+....+..++..|+.        .+-.+.|++|||+.||||+++|+..+++++..
T Consensus        80 ~~~~~~~l~~~l~~Lp~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~rar~~  136 (157)
T 2lfw_A           80 AEGTEAVARARLARMTPLSRQALLLTAMEGFSPEDAAYLIEVDTSEVETLVTEALAE  136 (157)
T ss_dssp             CSSSSSTTTTTTTTSCTTHHHHHTTTSSSCCCHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            01111122333333332        23478999999999999999999999877653

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

Probab=99.20  E-value=3.3e-12  Score=126.02  Aligned_cols=125  Identities=9%  Similarity=-0.006  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCccccc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r~iri  363 (460)
                      ..+|+.|+..|.+.++.+|++|.++..+++|++||.|+.+|+...+|++.  ..|.+|++++++|.+++++|+.......
T Consensus        20 ~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~~~~~~~   97 (286)
T 3n0r_A           20 EMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQLEVGHDQ   97 (286)
T ss_dssp             CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC----CCCC
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhccccccCCCc
Confidence            56899999999999999999999999999999999999999999999964  4799999999999999999864321111


Q ss_pred             CcchHHHHHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567          364 PFHMVEATYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPK  413 (460)
Q Consensus       364 P~~~~e~i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar  413 (460)
                      ..   +....+.+++..|+.+        .-.+.+++|||+.||+++++|+..+.+++
T Consensus        98 ~~---~~~~~l~~al~~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~rA~  152 (286)
T 3n0r_A           98 GL---HAGDDAAQRLMRIAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQ  152 (286)
T ss_dssp             CC---CTTSHHHHHHHHHSCHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cc---chHHHHHHHHHhCCHHHeeEEEEEeeCCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence            11   1123456666666554        33789999999999999999999887554

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

Probab=99.04  E-value=4.3e-10  Score=94.91  Aligned_cols=83  Identities=14%  Similarity=0.075  Sum_probs=71.5

Q ss_pred             HHHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHH
Q 012567          275 ELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  353 (460)
Q Consensus       275 ~L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~  353 (460)
                      .|+..+..| ..+++.|+..|.+.++.++.++ ++..+++|++||+|+.+|+.+.+|++.  ..|.+|++.+++|.++++
T Consensus        13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~   89 (112)
T 2o7g_A           13 ALALSAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADH   89 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHHH
Confidence            456666666 8999999999999999999999 888899999999999999999999964  479999999999999999


Q ss_pred             hhhcCcc
Q 012567          354 LSDQSRT  360 (460)
Q Consensus       354 Lrk~~r~  360 (460)
                      +|++.+.
T Consensus        90 ~R~~~~~   96 (112)
T 2o7g_A           90 IRHVRSR   96 (112)
T ss_dssp             TC-----
T ss_pred             HHHhhcc
Confidence            9987653

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

Probab=98.95  E-value=6.5e-10  Score=89.63  Aligned_cols=74  Identities=14%  Similarity=0.097  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcCc
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  359 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~r  359 (460)
                      ..+++.|+..|.+.++.++.++.++..+++|++||+++.+|+.+.+|++.  ..|.+|++.+++|.+++++|++.+
T Consensus        11 ~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~   84 (87)
T 1h3l_A           11 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQR   84 (87)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC----
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhcc
Confidence            88999999999999999999999999999999999999999999999974  479999999999999999987653

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

Probab=97.14  E-value=1.5e-07  Score=91.01  Aligned_cols=139  Identities=9%  Similarity=-0.023  Sum_probs=96.8

Q ss_pred             HHHHHhcc-HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHH----hHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHH
Q 012567          276 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLV----QEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (460)
Q Consensus       276 L~~~l~~G-~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLi----QEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI  350 (460)
                      |..+++.+ ..+.+.+...+.++++.+............|+.    |+.++.+|+.+..|++.  ..|.+|++.+++|.+
T Consensus        87 ll~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~--~~~~~WL~~ia~n~~  164 (258)
T 3clo_A           87 IYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNT--PAGNVWLIFCLYSLS  164 (258)
T ss_dssp             HHTTBCHHHHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEEC--TTSCEEEEEEEEEEC
T ss_pred             HHHhCChHHHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHH
Confidence            44455555 677899999999999999888777777888886    99999999999999864  379999999999988


Q ss_pred             HHHhhhcCccccc----------CcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          351 RKSLSDQSRTIRL----------PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       351 ~~~Lrk~~r~iri----------P~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                      .++.+.......+          +.........+..-.+++..-...+.|.+|||+.||+|+++|+..+++++..+
T Consensus       165 ~d~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~erevl~L~~~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL  240 (258)
T 3clo_A          165 ADQRPEQGIYATITQMERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKL  240 (258)
T ss_dssp             SCCCCCSSCCCEEEETTTTEEEECCCHHHHTTSSCHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             cchhhhhHHHHHHHhhcccccccchhhHHHHccCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            8776542211000          01111111112111122111123789999999999999999999998776543

>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=96.59  E-value=0.00054  Score=74.40  Aligned_cols=33  Identities=33%  Similarity=0.603  Sum_probs=13.4

Q ss_pred             CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 012567          209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL  242 (460)
Q Consensus       209 ~~~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~  242 (460)
                      .++||++ ||++| |++||||+|+|++|+++|+.+
T Consensus        93 ~~~dpvrmyl~em-g~~~ll~~~~e~~~ak~ie~g  126 (613)
T 3iyd_F           93 RTTDPVRMYMREM-GTVELLTREGEIDIAKRIEDG  126 (613)
T ss_dssp             ------------C---------CSSSTTTHHHHHH
T ss_pred             CCCCcHHHHHHHh-cccccCCchhHHHHHHHHHHh
Confidence            4689999 99999 999999999999999999986

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

Probab=92.55  E-value=0.82  Score=47.68  Aligned_cols=30  Identities=20%  Similarity=0.199  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                      .+.|.+|||+.||||.++|+++++++...+
T Consensus       394 e~~TleEIAe~LgIS~erVRqi~~RAlkKL  423 (438)
T 1l9z_H          394 REHTLEEVGAYFGVTRERIRQIENKALRKL  423 (438)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            689999999999999999999998775543

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

Probab=92.20  E-value=0.067  Score=43.08  Aligned_cols=30  Identities=13%  Similarity=0.077  Sum_probs=26.6

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      +-.+.|++|||+.||||..+|+..+++++.
T Consensus        50 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~   79 (92)
T 3hug_A           50 YYRGWSTAQIATDLGIAEGTVKSRLHYAVR   79 (92)
T ss_dssp             HTSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            467899999999999999999999987654

>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=91.74  E-value=3  Score=37.76  Aligned_cols=31  Identities=16%  Similarity=0.023  Sum_probs=26.7

Q ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          384 ENGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       384 ~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      .+..+.|.+|||+.||||.++|+..+++++.
T Consensus       199 ~~~~g~s~~EIA~~lgis~~~V~~~~~ra~~  229 (239)
T 1rp3_A          199 IFYEELPAKEVAKILETSVSRVSQLKAKALE  229 (239)
T ss_dssp             HHTSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3467899999999999999999999886654

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

Probab=90.75  E-value=0.11  Score=47.46  Aligned_cols=45  Identities=18%  Similarity=0.148  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          371 TYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       371 i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      ...+..++..|+..        +..+.|.+|||+.||||+.+|+..+++++..
T Consensus       189 ~~~l~~~l~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~  241 (243)
T 1l0o_C          189 KIALKKAIEELDERERLIVYLRYYKDQTQSEVASRLGISQVQMSRLEKKILQH  241 (243)
T ss_dssp             -----------------------------------------------------
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            34456666666654        3367899999999999999999999988754

>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=89.66  E-value=0.3  Score=40.58  Aligned_cols=29  Identities=14%  Similarity=0.134  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      .+.|++|||+.||+|.++|++.+.++...
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~rAlkk   66 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAKALRK   66 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            67899999999999999999998876543

>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=87.82  E-value=0.4  Score=36.13  Aligned_cols=30  Identities=13%  Similarity=0.134  Sum_probs=26.1

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      ..+.|.+|||+.||+|.++|+..++++...
T Consensus        23 ~~g~s~~eIA~~lgis~~tV~~~~~ra~~k   52 (68)
T 2p7v_B           23 NTDYTLEEVGKQFDVTRERIRQIEAKALRK   52 (68)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHHHHHHG
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            368999999999999999999998876543

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

Probab=86.47  E-value=0.99  Score=34.49  Aligned_cols=37  Identities=16%  Similarity=0.023  Sum_probs=28.8

Q ss_pred             HHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCCc
Q 012567          380 QLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR  416 (460)
Q Consensus       380 ~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~l  416 (460)
                      .+...+..+.+.+|||+.||+|..+|+..+.++...+
T Consensus        23 ~vl~l~~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl   59 (79)
T 1x3u_A           23 QVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMAKM   59 (79)
T ss_dssp             HHHHHHTTTCCHHHHHHHTTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            3333356789999999999999999999887665433

>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=86.00  E-value=0.91  Score=34.60  Aligned_cols=28  Identities=21%  Similarity=0.246  Sum_probs=24.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      .+.|.+|||+.||+|.++|+..+.++..
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~ra~~   56 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIENKALR   56 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7899999999999999999998876543

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

Probab=85.85  E-value=0.88  Score=36.10  Aligned_cols=28  Identities=14%  Similarity=0.214  Sum_probs=25.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      .+.|.+|||+.||+|.++|+..+.++..
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~ra~~   64 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEVKALR   64 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7899999999999999999999887654

>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=84.66  E-value=1.8  Score=29.11  Aligned_cols=27  Identities=15%  Similarity=0.113  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhCCC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLSPK  413 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~ar  413 (460)
                      .+.+..+||+.||++..+|...+....
T Consensus        20 ~g~s~~~IA~~lgis~~Tv~~~~~~~~   46 (51)
T 1tc3_C           20 LNVSLHEMSRKISRSRHCIRVYLKDPV   46 (51)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHCST
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHhhHH
Confidence            457899999999999999999987543

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

Probab=84.17  E-value=1.2  Score=33.07  Aligned_cols=30  Identities=7%  Similarity=0.070  Sum_probs=26.2

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      +..+.|++|||+.||+|..+|+..+++++.
T Consensus        28 ~~~g~s~~eIA~~lgis~~tv~~~~~ra~~   57 (70)
T 2o8x_A           28 QLLGLSYADAAAVCGCPVGTIRSRVARARD   57 (70)
T ss_dssp             HTSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            457899999999999999999999887654

>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=84.03  E-value=0.47  Score=40.03  Aligned_cols=31  Identities=10%  Similarity=-0.022  Sum_probs=26.9

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      +-.+.|+.|||+.||+|..+|+..+++++..
T Consensus        38 ~~~g~s~~EIA~~lgiS~~tV~~~l~ra~~k   68 (113)
T 1xsv_A           38 YLEDYSLSEIADTFNVSRQAVYDNIRRTGDL   68 (113)
T ss_dssp             HTSCCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            4578999999999999999999998877643

>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=82.61  E-value=0.23  Score=39.23  Aligned_cols=31  Identities=6%  Similarity=-0.015  Sum_probs=26.2

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      +..+.|++|||+.||+|..+|+..+++++..
T Consensus        33 ~~~g~s~~eIA~~l~is~~tV~~~l~r~~~k   63 (82)
T 1je8_A           33 IAQGLPNKMIARRLDITESTVKVHVKHMLKK   63 (82)
T ss_dssp             HTTTCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            3567899999999999999999998865543

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

Probab=81.83  E-value=2.3  Score=33.65  Aligned_cols=37  Identities=19%  Similarity=0.303  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHh-CCCCCHHHHHHHhCCCHHHHHHHHh
Q 012567          374 VKEARKQLYSEN-GRHPNNEEVAEATGLSMKRLHAVLL  410 (460)
Q Consensus       374 l~ka~~~L~~~~-gr~pS~eEIAe~LGIS~e~Vk~~l~  410 (460)
                      |...++.-..+. |..||..|||+.+|+|..+|+.-+.
T Consensus         9 IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~   46 (77)
T 2jt1_A            9 IISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLE   46 (77)
T ss_dssp             HHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            333333333333 7889999999999999999988775

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

Probab=81.68  E-value=2.2  Score=30.32  Aligned_cols=25  Identities=24%  Similarity=0.283  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567          387 RHPNNEEVAEATGLSMKRLHAVLLS  411 (460)
Q Consensus       387 r~pS~eEIAe~LGIS~e~Vk~~l~~  411 (460)
                      .+.|..|||+.||+|..+|...+..
T Consensus        30 ~g~s~~eIA~~lgis~~TV~~~l~~   54 (55)
T 2x48_A           30 MGYTVQQIANALGVSERKVRRYLES   54 (55)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            4579999999999999999988764

>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=80.04  E-value=0.73  Score=37.33  Aligned_cols=30  Identities=17%  Similarity=0.114  Sum_probs=25.6

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       386 gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      ..+.|++|||+.||+|..+|+..+.+++..
T Consensus        40 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~k   69 (95)
T 3c57_A           40 SEGLTNKQIADRMFLAEKTVKNYVSRLLAK   69 (95)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            467899999999999999999998766543

---

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	460
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	9e-29
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	5e-28
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	4e-18
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	1e-10
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	5e-09
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	1e-07

>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 =  113 bits (284), Expect = 9e-29
 Identities = 37/72 (51%), Positives = 54/72 (75%)

Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 345
            K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +KF+  +G+KFSTYA WW
Sbjct: 263 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 322

Query: 346 IKQAVRKSLSDQ 357
           I+QA+ +S++DQ
Sbjct: 323 IRQAITRSIADQ 334

>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 =  107 bits (268), Expect = 5e-28
 Identities = 55/181 (30%), Positives = 90/181 (49%), Gaps = 32/181 (17%)

Query: 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK------------------LEGLREV 251
           SDP+R YL        LLT  EE+ L+  +++ ++                  +   + +
Sbjct: 1   SDPVRQYLH-EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKIL 59

Query: 252 LSERCGGSPTFAQWAAAAGVDQ------------RELRRRLNYGILCKDKMITSNIRLVI 299
            + R    P   +      V++            +        G   +  +I +N+RLV+
Sbjct: 60  GTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVV 119

Query: 300 SIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 359
           SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+R
Sbjct: 120 SIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQAR 179

Query: 360 T 360
           T
Sbjct: 180 T 180

>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 = 76.9 bits (189), Expect = 4e-18
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 287 KDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAH 343
           ++++I   + LV +IA N +      ++++DL+  G  GL++  +        +   Y  
Sbjct: 12  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 71

Query: 344 WWIKQAVRKSLSDQS 358
             IK A+   L    
Sbjct: 72  LRIKGAIYDYLRSLD 86

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 60

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score = 54.3 bits (131), Expect = 1e-10
 Identities = 25/60 (41%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM--KRLHAVLLSPKAPRSL 418
           IR+P HMVE   ++    +QL  E GR P+ EE+AEA G     KR+   L   + P SL
Sbjct: 1   IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 60

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Length = 57

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 50.1 bits (120), Expect = 5e-09
 Identities = 11/51 (21%), Positives = 26/51 (50%)

Query: 359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 409
            T+++   + E   ++++A+ +L    GR P   E+A+  G+S + +    
Sbjct: 2   GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQ 52

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 46.7 bits (111), Expect = 1e-07
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 8/68 (11%)

Query: 358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL--LSPKAP 415
           SR +R      E   R+KE  ++L  + GR P +EEVA+  G+S + L   L  ++    
Sbjct: 2   SRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI 55

Query: 416 RSLDQKIG 423
            SL++   
Sbjct: 56  LSLEEVFR 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	460
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	100.0
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.81
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.75
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.27
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	98.82
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.75
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.58
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.49
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	96.14
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	94.95
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.77
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	93.99
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	92.73
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	91.76
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	85.04
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	84.6

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=100.00  E-value=3.1e-33  Score=257.37  Aligned_cols=149  Identities=36%  Similarity=0.621  Sum_probs=121.8

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHh------------------hhcCCCCcHHHHHHH---
Q 012567          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLS------------------ERCGGSPTFAQWAAA---  268 (460)
Q Consensus       211 ~d~l~-YL~~~~~~~~lLT~EEE~eL~~~Iq~~~~le~~~~~L~------------------~~~g~~pt~~ewA~a---  268 (460)
                      +||++ ||++| |++||||+|||++|+++|+.+..+.+...+..                  ...+..|...+|...   
T Consensus         1 tDpVr~YLrei-g~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~   79 (180)
T d1ku2a2           1 SDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTV   79 (180)
T ss_dssp             CHHHHHHHHHH-TTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTH
T ss_pred             CCcHHHHHHHh-cCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHH
Confidence            58999 99999 99999999999999999998765543332221                  112333443333322   


Q ss_pred             ------hCCC---HHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchH
Q 012567          269 ------AGVD---QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFS  339 (460)
Q Consensus       269 ------~g~d---e~~L~~~l~~G~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFS  339 (460)
                            ....   ...+......|..|+++||.+|++||+++|++|.+.|.+++||+|||++||++|+++|||++|++|+
T Consensus        80 ~~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f~  159 (180)
T d1ku2a2          80 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS  159 (180)
T ss_dssp             HHHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCHH
Confidence                  2221   2345667778899999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHhhhcCcc
Q 012567          340 TYAHWWIKQAVRKSLSDQSRT  360 (460)
Q Consensus       340 TYA~~wIr~aI~~~Lrk~~r~  360 (460)
                      |||+|||+++|.++|++++++
T Consensus       160 tya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         160 TYATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHHhCCC
Confidence            999999999999999998763

>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=99.81  E-value=2.1e-20  Score=185.00  Aligned_cols=90  Identities=46%  Similarity=0.899  Sum_probs=80.3

Q ss_pred             HhCCCHHHHH---HHHhcc----HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHh
Q 012567          268 AAGVDQRELR---RRLNYG----ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFST  340 (460)
Q Consensus       268 a~g~de~~L~---~~l~~G----~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFST  340 (460)
                      .+|++...+.   ..++.|    ..|+++||++|++||++||++|.++|++++||+|+|++|||+|+++|||.+|++|+|
T Consensus       238 ~~gl~~~elk~i~~~i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~  317 (334)
T d1siga_         238 ETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST  317 (334)
T ss_dssp             HHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHH
T ss_pred             HhhhhHHHHHHHHHHHHHHHhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHh
Confidence            3466665443   455555    679999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhc
Q 012567          341 YAHWWIKQAVRKSLSDQ  357 (460)
Q Consensus       341 YA~~wIr~aI~~~Lrk~  357 (460)
                      ||+||||++|.++|+++
T Consensus       318 ~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         318 YATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHHHHHHHC
T ss_pred             hhHHHHHHHHHHHHhCC
Confidence            99999999999999874

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.75  E-value=9.3e-19  Score=143.03  Aligned_cols=75  Identities=21%  Similarity=0.383  Sum_probs=69.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCC---CCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhhhcC
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGA---GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~---g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lrk~~  358 (460)
                      ...+++||..|++||.++|++|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|+++||+..
T Consensus         9 ~~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~d   86 (87)
T d1rp3a3           9 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD   86 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            3458999999999999999998654   78999999999999999999999999999999999999999999999864

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=98.82  E-value=3.4e-09  Score=79.85  Aligned_cols=58  Identities=43%  Similarity=0.651  Sum_probs=54.8

Q ss_pred             cccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCC--HHHHHHHHhCCCCCccc
Q 012567          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLS--MKRLHAVLLSPKAPRSL  418 (460)
Q Consensus       361 iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS--~e~Vk~~l~~ar~~lSL  418 (460)
                      ||+|.|+.+.+++++++.++|.+++|++||.+|||+.||++  +++|+.++..++.++||
T Consensus         1 IRlPvH~~e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~~~p~SL   60 (60)
T d1ku2a1           1 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL   60 (60)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGSSSCCCC
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHccCCCCC
Confidence            68999999999999999999999999999999999999854  88999999999999987

>d1h3la_ a.177.1.1 (A:) Sigma factor SigR {Streptomyces coelicolor a3(2) [TaxId: 100226]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigR
species: Streptomyces coelicolor a3(2) [TaxId: 100226]

Probab=98.75  E-value=5.4e-09  Score=81.08  Aligned_cols=70  Identities=13%  Similarity=0.070  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHccCCCCCcccHHhHHHHHHHHHHhhcCCCCCCchHhHHHHHHHHHHHHHhh
Q 012567          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  355 (460)
Q Consensus       284 ~~A~e~LI~~nlrLV~~IAkry~~~g~d~eDLiQEG~IGLirAiekFDp~kG~rFSTYA~~wIr~aI~~~Lr  355 (460)
                      ...+++++..|.+.++.+|.++.++..+++|++||.++.+|+..++|++.  .+|.+|++.+++|.+++++|
T Consensus         6 ~~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   75 (75)
T d1h3la_           6 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYR   75 (75)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHhC
Confidence            56799999999999999999999999999999999999999999999964  47999999999999999875

>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=98.58  E-value=2e-08  Score=74.70  Aligned_cols=53  Identities=21%  Similarity=0.369  Sum_probs=50.4

Q ss_pred             cccccCcchHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhC
Q 012567          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS  411 (460)
Q Consensus       359 r~iriP~~~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~  411 (460)
                      +++|+|.++.+..+++.++...|.+++|+.||.+|||+.||+|+++|..++..
T Consensus         2 g~IrvPr~~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_           2 GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCEeCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999999999998864

>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=98.49  E-value=8.7e-09  Score=80.78  Aligned_cols=70  Identities=27%  Similarity=0.247  Sum_probs=60.0

Q ss_pred             hHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHhCC--CCCcccccccccCCCCCcccccccC
Q 012567          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSVCFILN  437 (460)
Q Consensus       367 ~~e~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGIS~e~Vk~~l~~a--r~~lSLD~~v~~e~d~tl~Eli~D~  437 (460)
                      +.+..++|.++...|.+++|+.||.+|||+.|||++++|..++...  ...+|||.++++ ++.++.|++++.
T Consensus         5 ~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~d-~~~~~~e~lpss   76 (77)
T d1rp3a1           5 VREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRD-FARDYSELIPSS   76 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHTTTGGGS
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCccC-CCCchhccCCCC
Confidence            4577889999999999999999999999999999999999998643  357899998764 445788888874

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.14  E-value=0.0049  Score=44.65  Aligned_cols=40  Identities=20%  Similarity=0.287  Sum_probs=34.7

Q ss_pred             HHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHHhc
Q 012567          243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY  282 (460)
Q Consensus       243 ~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l~~  282 (460)
                      .++.+...+|...+||+||..|.|+++|++.+.+...+..
T Consensus        15 ~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_          15 NKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             HHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3677788999999999999999999999999988766653

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=94.95  E-value=0.0069  Score=44.80  Aligned_cols=44  Identities=11%  Similarity=0.088  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHH--------hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          371 TYRVKEARKQLYSE--------NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       371 i~kl~ka~~~L~~~--------~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      ...+.+++..|+..        +-.+.|++|||+.||+|+++|+..+++++.
T Consensus         9 ~~~l~~~l~~Lp~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~   60 (68)
T d1or7a1           9 RQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRARE   60 (68)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34455555555443        448899999999999999999999987653

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.77  E-value=0.022  Score=43.07  Aligned_cols=38  Identities=29%  Similarity=0.414  Sum_probs=33.2

Q ss_pred             HHHHhHHHHHhhhcCCCCcHHHHHHHhCCCHHHHHHHH
Q 012567          243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL  280 (460)
Q Consensus       243 ~~le~~~~~L~~~~g~~pt~~ewA~a~g~de~~L~~~l  280 (460)
                      .++++....|...+||+||..|.|..+||+...+...+
T Consensus        10 ~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l   47 (77)
T d1rp3a1          10 RRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTL   47 (77)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence            36778899999999999999999999999998876544

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=93.99  E-value=0.013  Score=43.29  Aligned_cols=30  Identities=17%  Similarity=0.054  Sum_probs=26.3

Q ss_pred             hCCCCCHHHHHHHhCCCHHHHHHHHhCCCC
Q 012567          385 NGRHPNNEEVAEATGLSMKRLHAVLLSPKA  414 (460)
Q Consensus       385 ~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~  414 (460)
                      +..+.|++|||+.||+|..+|+..+++++.
T Consensus        34 ~~~~~s~~eIA~~lgis~~tv~~~~~ra~~   63 (71)
T d1rp3a2          34 FYEELPAKEVAKILETSVSRVSQLKAKALE   63 (71)
T ss_dssp             HTSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HhHhCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            457899999999999999999999887643

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=92.73  E-value=0.12  Score=37.38  Aligned_cols=38  Identities=26%  Similarity=0.415  Sum_probs=30.1

Q ss_pred             HHHHhHHHHHhhhcCCCCcHHHHHHHhC--CCHHHHHHHH
Q 012567          243 LKLEGLREVLSERCGGSPTFAQWAAAAG--VDQRELRRRL  280 (460)
Q Consensus       243 ~~le~~~~~L~~~~g~~pt~~ewA~a~g--~de~~L~~~l  280 (460)
                      -++.+...+|...+||+||..|.|+++|  ++.+.+...+
T Consensus        12 ~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l   51 (60)
T d1ku2a1          12 NKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETL   51 (60)
T ss_dssp             HHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHG
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHH
Confidence            4567788999999999999999999997  4565554443

>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=91.76  E-value=0.2  Score=37.26  Aligned_cols=41  Identities=22%  Similarity=0.258  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC-CHHHHHHHHh
Q 012567          370 ATYRVKEARKQLYSENGRHPNNEEVAEATGL-SMKRLHAVLL  410 (460)
Q Consensus       370 ~i~kl~ka~~~L~~~~gr~pS~eEIAe~LGI-S~e~Vk~~l~  410 (460)
                      ...+|..++.....+.|..||+.|||+.+|+ |..+|...+.
T Consensus         6 rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~   47 (71)
T d1jhfa1           6 RQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   47 (71)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHH
Confidence            4466778888888899999999999999999 7999988876

>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=85.04  E-value=0.33  Score=38.98  Aligned_cols=32  Identities=13%  Similarity=0.071  Sum_probs=27.9

Q ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          384 ENGRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       384 ~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      .+-.+.|+.|||+.||||.++|+..+++++..
T Consensus        28 ~y~~~ls~~EIA~~lgiS~~aV~~~l~RA~~~   59 (106)
T d1s7oa_          28 YYADDYSLAEIADEFGVSRQAVYDNIKRTEKI   59 (106)
T ss_dssp             HHHTCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            34578999999999999999999999987654

>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=84.60  E-value=0.49  Score=37.91  Aligned_cols=32  Identities=9%  Similarity=-0.062  Sum_probs=28.2

Q ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHhCCCCC
Q 012567          384 ENGRHPNNEEVAEATGLSMKRLHAVLLSPKAP  415 (460)
Q Consensus       384 ~~gr~pS~eEIAe~LGIS~e~Vk~~l~~ar~~  415 (460)
                      .+-.+.|..|||+.||||.++|+..+++++..
T Consensus        30 ~~~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~   61 (106)
T d1xsva_          30 FYLEDYSLSEIADTFNVSRQAVYDNIRRTGDL   61 (106)
T ss_dssp             HHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            45689999999999999999999999987653