Citrus Sinensis ID: 009803

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-----
Protein Sequence
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
Secondary Structure (PSIPRED)
ccccccHHHHcccccccccccccccccccccccccccccccccccHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHcccHHHHHccccccHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccEEEEEcccccccccccHHHHHHcHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHccHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccEccHHHccccccccccccccccccccEEccccccccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHcccccHHHHccccHcccccccccHHcccccccHHHHHHHHcccccccEEccccccHHHHHHHHHHHHcccccccccccccccHHcccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcHccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHccccHHHHcccHHHHHHHHHHHcccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHcccHHHHHHHHHccc
Coil and Loop (DISEMBL)
mttvldveklrlpsleahSNAVAAnrqwtyfgavgpsteenlgtslatetltSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtnTSMWAQLTERERAsiigdsviveaapeeeyseqqplnksadleptHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSvksgstsrrkrpsvqevdysdplrylrattsssrlltANEEMQLSAGIQDLLKLEGLREVlsercggsptFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRgaekfdaskgfkfsTYAHWWIKQAVRKslsdqsrtirlpfhmVEATYRVKEARKQLYSengrhpnneeVAEATGLSMKRLHAVllspkaprsldqkiginqnlkpseviadpeaeTAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
Flexible Loop (DISEMBL)
mttvldveklrlpsleahsNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtNTSMWAQLTERERASIIGDSVIVEAAPeeeyseqqplnkSADLEPTHEELKLLEeqvsqsiavrsrrqterkARRTRaaekaaanvmsvksgstsrrkrpsvqevdysdplrylRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAaaagvdqrelRRRLNYGilckdkmitsNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKfdaskgfkfstYAHWWIKQAVrkslsdqsrtirlpfhmveatYRVKEARKQLysengrhpnneEVAEATGLSMKRLHAVLLSpkaprsldqkiginqnlkpseviadpeAETAEDLLIKKFMKEDLEKvldtlnprerqvvrwrfgledgrmktlqeigelmgvsrerIRQIESsafrklknkkrtkhlmqyaits
Low Complexity Region (SEG)
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTsdeaviaaasaeavalaraavkvakdaalMVNHHNsakpkskpaisssaDTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSrrqterkarrtraaekaaaNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
Disordered region (IsUnstruct)
*******************NAVAANRQWTYFGAVGP*********LATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMV************************************I******************************************************************************************************************LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK********************************************************************DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGV********************************
Disordered Region (DISOPRED)
*****D*EKLRL********************************************************************************************************************************************************************************************************PLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL******HPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI**
Disordered Region (DISEMBL)
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHH******************TSMWAQLTERERASIIGDSVIVEAAP***********KSADLEPTHEELKLLEEQVSQS********************************************VDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
Disordered Region (DISPRO)
*TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHH*******************SMWAQLTERERASII*****************************************************************************************YSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
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	525	2.2.26 [Sep-21-2011]
O22056	572	RNA polymerase sigma fact	yes	no	0.979	0.898	0.688	0.0
P26683	390	RNA polymerase sigma fact	yes	no	0.624	0.841	0.471	1e-79
P38023	399	RNA polymerase sigma fact	yes	no	0.588	0.774	0.487	3e-76
P52322	416	RNA polymerase sigma fact	yes	no	0.588	0.742	0.421	2e-70
Q9LD95	547	RNA polymerase sigma fact	no	no	0.678	0.650	0.386	3e-68
P74565	425	RNA polymerase sigma fact	N/A	no	0.447	0.552	0.512	2e-66
Q8CP24	368	RNA polymerase sigma fact	yes	no	0.470	0.671	0.463	4e-60
Q5HNY7	368	RNA polymerase sigma fact	yes	no	0.470	0.671	0.463	4e-60
Q99TT5	368	RNA polymerase sigma fact	yes	no	0.470	0.671	0.463	5e-60
P0A0I9	368	RNA polymerase sigma fact	yes	no	0.470	0.671	0.459	7e-60

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

 Score =  677 bits (1747), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/530 (68%), Positives = 427/530 (80%), Gaps = 16/530 (3%)

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 APRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWR 473
            PRSLDQKIG+NQNLKPSEVIADPEA T+ED+LIK+FM++DL+KVLD+L  RE+QV+RWR
Sbjct: 460 PPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWR 519

Query: 474 FGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523
           FG+EDGRMKTLQEIGE+MGVSRER+RQIESSAFRKLKNKKR  HL QY +
Sbjct: 520 FGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 569

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 =  297 bits (761), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 156/331 (47%), Positives = 220/331 (66%), Gaps = 3/331 (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 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP 430
             R+K+  K L  E GR P  EE+A    +++++L  +  S + P SL+  IG  ++ + 
Sbjct: 239 ISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRL 298

Query: 431 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGEL 490
            + I + + ET ED + K  ++EDLEKVLD+L+PRER V+R R+GL+DGRMKTL+EIG++
Sbjct: 299 GDFI-ESDGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQI 357

Query: 491 MGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
             V+RERIRQIE+ A RKL++  R   L +Y
Sbjct: 358 FNVTRERIRQIEAKALRKLRHPNRNSVLKEY 388

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

 Score =  286 bits (731), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 151/310 (48%), Positives = 207/310 (66%), Gaps = 1/310 (0%)

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 EEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM 451
           EE+A    +++++L  +  S + P SL+  IG  ++ +  + I + + ET ED + K  +
Sbjct: 269 EEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI-EADGETPEDEVAKNLL 327

Query: 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511
           +EDLE VL TL+PRER V+R R+GL+DGRMKTL+EIG+L  V+RERIRQIE+ A RKL++
Sbjct: 328 REDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRH 387

Query: 512 KKRTKHLMQY 521
             R   L +Y
Sbjct: 388 PNRNSILKEY 397

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

 Score =  267 bits (682), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 147/349 (42%), Positives = 205/349 (58%), Gaps = 40/349 (11%)

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 KAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRW 472
           + P SL+  IG  ++ +  + I + + ET ED + K  ++EDLE VLDTL+PRER V+R 
Sbjct: 307 QLPISLETPIGKEEDSRLGDFI-EADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRL 365

Query: 473 RFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
           R+GL+DGRMKTL+EIG++  V+RERIRQIE+ A RKL++  R   L +Y
Sbjct: 366 RYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEY 414

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

 Score =  259 bits (663), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 138/357 (38%), Positives = 214/357 (59%), Gaps = 1/357 (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 HAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPR 465
             +L + + P S+ Q I  +Q+    E+  D   ET    + K+ M+  +  +L+ L+P+
Sbjct: 427 DKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPK 486

Query: 466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA 522
           ER++++ RFG++ G+ ++L EIGE+ G+S+ER+RQ+ES A  +LK    +  L  YA
Sbjct: 487 ERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHAYA 543

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

 Score =  253 bits (647), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 121/236 (51%), Positives = 168/236 (71%), Gaps = 1/236 (0%)

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 HAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPR 465
             +  S + P SL+  IG  ++ +  + I + + ET ED + K  ++EDLE VLDTL+PR
Sbjct: 309 RFIAKSAQLPISLETPIGKEEDSRLGDFI-EADGETPEDEVSKNLLREDLENVLDTLSPR 367

Query: 466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
           ER V+R R+GL+DGRMKTL+EIG++  V+RERIRQIE+ A RKL++  R   L +Y
Sbjct: 368 ERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEY 423

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|Q8CP24|RPOD_STAES RNA polymerase sigma factor RpoD OS=Staphylococcus epidermidis (strain ATCC 12228) GN=rpoD PE=3 SV=1

 Score =  233 bits (593), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 115/248 (46%), Positives = 165/248 (66%), Gaps = 1/248 (0%)

Query: 275 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 333
           EL +R+  G  + K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD S
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFS 178

Query: 334 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 393
           KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P  EE
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEE 238

Query: 394 VAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKE 453
           + E   L  +++  +L   + P SL+  IG   +    + I D EA++  D    + +KE
Sbjct: 239 IGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKE 298

Query: 454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513
            LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  
Sbjct: 299 QLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPS 358

Query: 514 RTKHLMQY 521
           R+K L  +
Sbjct: 359 RSKRLKDF 366

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

Staphylococcus epidermidis (strain ATCC 12228) (taxid: 176280)

>sp|Q5HNY7|RPOD_STAEQ RNA polymerase sigma factor RpoD OS=Staphylococcus epidermidis (strain ATCC 35984 / RP62A) GN=rpoD PE=3 SV=1

 Score =  233 bits (593), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 115/248 (46%), Positives = 165/248 (66%), Gaps = 1/248 (0%)

Query: 275 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 333
           EL +R+  G  + K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD S
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFS 178

Query: 334 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 393
           KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P  EE
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEE 238

Query: 394 VAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKE 453
           + E   L  +++  +L   + P SL+  IG   +    + I D EA++  D    + +KE
Sbjct: 239 IGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKE 298

Query: 454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513
            LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  
Sbjct: 299 QLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPS 358

Query: 514 RTKHLMQY 521
           R+K L  +
Sbjct: 359 RSKRLKDF 366

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

Staphylococcus epidermidis (strain ATCC 35984 / RP62A) (taxid: 176279)

>sp|Q99TT5|RPOD_STAAN RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain N315) GN=rpoD PE=1 SV=1

 Score =  232 bits (592), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 115/248 (46%), Positives = 165/248 (66%), Gaps = 1/248 (0%)

Query: 275 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 333
           EL +R+  G  + K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178

Query: 334 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 393
           KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P  EE
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEE 238

Query: 394 VAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKE 453
           + E   L  +++  VL   + P SL+  IG   +    + I D EA++  D    + +KE
Sbjct: 239 IGEEMDLPAEKVREVLKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKE 298

Query: 454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513
            LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  
Sbjct: 299 QLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPS 358

Query: 514 RTKHLMQY 521
           R+K L  +
Sbjct: 359 RSKRLKDF 366

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

Staphylococcus aureus (strain N315) (taxid: 158879)

>sp|P0A0I9|RPOD_STAAW RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain MW2) GN=rpoD PE=3 SV=1

 Score =  231 bits (590), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 114/248 (45%), Positives = 165/248 (66%), Gaps = 1/248 (0%)

Query: 275 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 333
           EL +R+  G  + K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178

Query: 334 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 393
           KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P  EE
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEE 238

Query: 394 VAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKE 453
           + E   L  +++  +L   + P SL+  IG   +    + I D EA++  D    + +KE
Sbjct: 239 IGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKE 298

Query: 454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513
            LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  
Sbjct: 299 QLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPS 358

Query: 514 RTKHLMQY 521
           R+K L  +
Sbjct: 359 RSKRLKDF 366

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

Staphylococcus aureus (strain MW2) (taxid: 196620)

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	525
255565968	569	RNA polymerase sigma factor rpoD1, putat	0.969	0.894	0.773	0.0
449454538	580	PREDICTED: RNA polymerase sigma factor s	0.979	0.886	0.722	0.0
225436223	578	PREDICTED: RNA polymerase sigma factor r	0.996	0.904	0.786	0.0
296090195	575	unnamed protein product [Vitis vinifera]	0.996	0.909	0.786	0.0
224126061	567	predicted protein [Populus trichocarpa]	0.994	0.920	0.755	0.0
224144900	564	predicted protein [Populus trichocarpa]	0.992	0.923	0.737	0.0
297843640	572	hypothetical protein ARALYDRAFT_470915 [	0.984	0.903	0.698	0.0
7363218	575	sigma factor 2 [Sinapis alba]	0.979	0.893	0.681	0.0
15223259	572	RNApolymerase sigma subunit 2 [Arabidops	0.979	0.898	0.688	0.0
356509511	558	PREDICTED: RNA polymerase sigma factor r	0.973	0.915	0.687	0.0

>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 =  758 bits (1956), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 403/521 (77%), Positives = 454/521 (87%), Gaps = 12/521 (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 GINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMK 482
           G+N +LKPSEVIADPEAETAE+LL+K+FMK+DLEKVL+TLNPRE QVVRWRFGLEDGRMK
Sbjct: 468 GMNMDLKPSEVIADPEAETAEELLMKQFMKQDLEKVLNTLNPRETQVVRWRFGLEDGRMK 527

Query: 483 TLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523
           TLQEIGE+MGVSRERIRQIESSAFRKLKNKKRTK L QY +
Sbjct: 528 TLQEIGEIMGVSRERIRQIESSAFRKLKNKKRTKQLKQYLL 568

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  730 bits (1885), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/522 (72%), Positives = 440/522 (84%), Gaps = 8/522 (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 GINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMK 482
           GINQNLKPSEVI+DPEAET ED+LIK+FMK+DLEKVLD+LNPRE+QV+RWRFG+EDGRMK
Sbjct: 479 GINQNLKPSEVISDPEAETCEDMLIKQFMKQDLEKVLDSLNPREKQVIRWRFGMEDGRMK 538

Query: 483 TLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 524
           TLQEIGE+MGVSRERIRQIES AFRKLKNKKRTKHL QY ++
Sbjct: 539 TLQEIGEIMGVSRERIRQIESCAFRKLKNKKRTKHLQQYVMS 580

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 =  724 bits (1870), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/525 (78%), Positives = 455/525 (86%), Gaps = 2/525 (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 QKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDG 479
           QKIGINQNLKPSEVIADP+AETAE+LLIK+FM+EDLEKVL++LNPRE+QV+RWR+GLEDG
Sbjct: 474 QKIGINQNLKPSEVIADPDAETAEELLIKQFMREDLEKVLNSLNPREKQVIRWRYGLEDG 533

Query: 480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 524
           R KTLQEIGELMGVSRERIRQIES AFRKLKNK+RTKHL QY ++
Sbjct: 534 RTKTLQEIGELMGVSRERIRQIESCAFRKLKNKRRTKHLQQYLVS 578

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  724 bits (1870), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 413/525 (78%), Positives = 455/525 (86%), Gaps = 2/525 (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 QKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDG 479
           QKIGINQNLKPSEVIADP+AETAE+LLIK+FM+EDLEKVL++LNPRE+QV+RWR+GLEDG
Sbjct: 471 QKIGINQNLKPSEVIADPDAETAEELLIKQFMREDLEKVLNSLNPREKQVIRWRYGLEDG 530

Query: 480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 524
           R KTLQEIGELMGVSRERIRQIES AFRKLKNK+RTKHL QY ++
Sbjct: 531 RTKTLQEIGELMGVSRERIRQIESCAFRKLKNKRRTKHLQQYLVS 575

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 =  709 bits (1831), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 395/523 (75%), Positives = 450/523 (86%), Gaps = 1/523 (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 KIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGR 480
           K+G N +LK SEV ADPEAETAEDLL+K+FMK+DL KVL +L+PRE QVVRWRFG+EDGR
Sbjct: 464 KMGFNMDLKLSEVTADPEAETAEDLLMKEFMKKDLAKVLGSLSPRENQVVRWRFGMEDGR 523

Query: 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523
           MKTLQEIGELMGVSRER+RQIE SAFRKLKNK RTK L QY +
Sbjct: 524 MKTLQEIGELMGVSRERVRQIELSAFRKLKNKNRTKQLRQYMV 566

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 =  709 bits (1829), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 385/522 (73%), Positives = 443/522 (84%), Gaps = 1/522 (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 GINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMK 482
           G N +LK SEV ADPEAETAEDLL+K+FMK+DLE+VL++L+PRE QV+RWRFG+EDGRMK
Sbjct: 463 GFNMDLKLSEVTADPEAETAEDLLMKEFMKKDLERVLESLSPRENQVIRWRFGMEDGRMK 522

Query: 483 TLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 524
           TLQEIGELMGVSRERIRQIE SAFRKLKNK RTK L QY ++
Sbjct: 523 TLQEIGELMGVSRERIRQIELSAFRKLKNKNRTKQLRQYLVS 564

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 =  683 bits (1763), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/527 (69%), Positives = 427/527 (81%), Gaps = 10/527 (1%)

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 SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGL 476
           SLDQKIG+NQNLKPSEVIADPEA T+ED+LIK+FM++DL+KVLD+L  RE+QV+RWRFG+
Sbjct: 463 SLDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGM 522

Query: 477 EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523
           EDGRMKTLQEIGE+MGVSRER+RQIESSAFRKLKNKKR+ HL QY +
Sbjct: 523 EDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRSNHLQQYLV 569

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 =  681 bits (1757), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/530 (68%), Positives = 427/530 (80%), Gaps = 16/530 (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  ++     E++S S AVRS RQTER
Sbjct: 163 LGHLAVSDTGVVSDRITAPGSLECNKEASDDLTPAEKQEV---EKLSVSSAVRSTRQTER 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 APRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWR 473
            PRSLDQKIGIN NLKPSEVIADPEAET+ED+L+K+FM++DL+KVLD+L+ RE+QV+RWR
Sbjct: 460 PPRSLDQKIGINLNLKPSEVIADPEAETSEDILMKQFMRQDLDKVLDSLSTREKQVIRWR 519

Query: 474 FGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523
           FG+EDGRMKTLQEIGE MGVSRER+RQI++SAFRKLKNKKR  HL QY +
Sbjct: 520 FGMEDGRMKTLQEIGETMGVSRERVRQIDTSAFRKLKNKKRNSHLQQYLV 569

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 =  677 bits (1747), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/530 (68%), Positives = 427/530 (80%), Gaps = 16/530 (3%)

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 APRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWR 473
            PRSLDQKIG+NQNLKPSEVIADPEA T+ED+LIK+FM++DL+KVLD+L  RE+QV+RWR
Sbjct: 460 PPRSLDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWR 519

Query: 474 FGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523
           FG+EDGRMKTLQEIGE+MGVSRER+RQIESSAFRKLKNKKR  HL QY +
Sbjct: 520 FGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 569

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 =  675 bits (1742), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 360/524 (68%), Positives = 428/524 (81%), Gaps = 13/524 (2%)

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  ASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASII 120
           A++EA+ALA+AA KVAKDAAL+V     A+ + K  +SS +D     W +  E E    +
Sbjct: 96  AASEALALAKAAAKVAKDAALLVKKKPPAEAEYKSHVSSKSDDLLLKWFKQME-EVEDGV 154

Query: 121 GDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTR 180
            +  +   A   E  +  P  + +DLEP+HEEL+ L+EQ+S SIAVRSRRQTERKA+R R
Sbjct: 155 AEESMGAGAEIMEGVDVSPSEEESDLEPSHEELERLQEQLSDSIAVRSRRQTERKAKRVR 214

Query: 181 AAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQ 240
           A EKA  N  S K GS+SRRKR S+QEVDYSDPLRYLR TTS+SRLLT  EE++LSAGIQ
Sbjct: 215 ATEKATTNFTSFKPGSSSRRKRVSMQEVDYSDPLRYLRTTTSASRLLTPTEEIKLSAGIQ 274

Query: 241 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 300
           DLLKLE ++E L+ER G  PTFAQWAA AGVDQ+ LR+RLNYGI CKDKMI SNIRLVIS
Sbjct: 275 DLLKLEKIQEDLAERFGSQPTFAQWAAVAGVDQKTLRKRLNYGIFCKDKMIKSNIRLVIS 334

Query: 301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 360
           IAKNYQG+GMNLQDLVQEGCRGLV+GAEKFD +KGFKFSTYAHWWIKQAVRKSLSDQSRT
Sbjct: 335 IAKNYQGSGMNLQDLVQEGCRGLVKGAEKFDGTKGFKFSTYAHWWIKQAVRKSLSDQSRT 394

Query: 361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQ 420
           IRLPFHMVEATYRVKEARKQLYSENGR P++EEVAEATGLSMKRL+AVL++PKAPRSL+Q
Sbjct: 395 IRLPFHMVEATYRVKEARKQLYSENGRQPDDEEVAEATGLSMKRLNAVLMTPKAPRSLEQ 454

Query: 421 KIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGR 480
           KIGINQNLKPSEVI+DP+AETAE+ L+K+FMK+DLE+ LD+LNPRERQVVRWRFG++DGR
Sbjct: 455 KIGINQNLKPSEVISDPDAETAEEQLLKQFMKKDLEEALDSLNPRERQVVRWRFGMDDGR 514

Query: 481 MKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 524
            KTLQEIGE++GVSRERIRQIESSAF+KLKNKKRT HL QY ++
Sbjct: 515 TKTLQEIGEMLGVSRERIRQIESSAFKKLKNKKRTNHLQQYLVS 558

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	525
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.986	0.905	0.619	3.4e-164
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.619	0.594	0.392	3.4e-61
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.689	0.632	0.344	5.7e-59
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.476	0.675	0.434	1.4e-58
TIGR_CMR|BA_4515	373	BA_4515 "RNA polymerase sigma-	0.447	0.630	0.468	7.8e-58
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.596	0.592	0.401	1.6e-54
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.476	0.773	0.432	1.6e-54
TIGR_CMR|DET_0551	520	DET_0551 "RNA polymerase sigma	0.441	0.446	0.443	1.8e-54
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.451	0.410	0.417	9.9e-52
TIGR_CMR|ECH_0760	622	ECH_0760 "RNA polymerase sigma	0.441	0.372	0.416	2e-51

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

 Score = 1598 (567.6 bits), Expect = 3.4e-164, P = 3.4e-164
 Identities = 326/526 (61%), Positives = 382/526 (72%)

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 LDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLE 477
             LDQKIG+NQNLKPSEVIADPEA T+ED+LIK+FM++DL+KVLD+L  RE+QV+RWRFG+E
Sbjct:   464 LDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGME 523

Query:   478 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 523
             DGRMKTLQEIGE+MGVSRER+RQIESSAFRKLKNKKR  HL QY +
Sbjct:   524 DGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 569

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 = 626 (225.4 bits), Expect = 3.4e-61, P = 3.4e-61
 Identities = 128/326 (39%), Positives = 199/326 (61%)

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 ARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 436
             ARK    E    P+ EE+A   G+S ++L  +L + + P S+ Q I  +Q+    E+  D
Sbjct:   398 ARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPD 457

Query:   437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRE 496
                ET    + K+ M+  +  +L+ L+P+ER++++ RFG++ G+ ++L EIGE+ G+S+E
Sbjct:   458 SGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKE 517

Query:   497 RIRQIESSAFRKLKNKKRTKHLMQYA 522
             R+RQ+ES A  +LK    +  L  YA
Sbjct:   518 RVRQLESRALYRLKQNMNSHGLHAYA 543

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 = 605 (218.0 bits), Expect = 5.7e-59, P = 5.7e-59
 Identities = 127/369 (34%), Positives = 201/369 (54%)

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 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 441
               E G  P N  VA   G+++++L  +    + PRS+   +  ++ +   E+  DP  E 
Sbjct:   429 IME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEP 487

Query:   442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI 501
              +  + +  M++ +   L  L+PRE++++  RFG+ DG  KTL  IG++ G+S+ERIRQ+
Sbjct:   488 PDLSVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQL 547

Query:   502 ESSAFRKLK 510
             ++ A  KLK
Sbjct:   548 QNRALEKLK 556

GO:0009536 "plastid" evidence=RCA

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

 Score = 556 (200.8 bits), Expect = 1.4e-58, Sum P(3) = 1.4e-58
 Identities = 109/251 (43%), Positives = 166/251 (66%)

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 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF 450
              EE+A+  G+S  ++  ++   + P SL+  IG  ++    + + DP+A+   +      
Sbjct:   238 PEEIAKEMGISEDKVREIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTL 297

Query:   451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
             ++E L++VL TL  RE++V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL+
Sbjct:   298 LREQLDEVLKTLTEREQKVLRLRFGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLR 357

Query:   511 NKKRTKHLMQY 521
             +  R+K L  +
Sbjct:   358 HPSRSKKLKDF 368

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 = 566 (204.3 bits), Expect = 7.8e-58, Sum P(2) = 7.8e-58
 Identities = 110/235 (46%), Positives = 158/235 (67%)

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 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 466
              +L   + P SL+  IG   +    + I D EA +  D    + +KE LE VLDTL  RE
Sbjct:   257 EILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDRE 316

Query:   467 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
               V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  R+K L  +
Sbjct:   317 ENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDF 371

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 563 (203.2 bits), Expect = 1.6e-54, P = 1.6e-54
 Identities = 130/324 (40%), Positives = 195/324 (60%)

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 RKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP 437
             +++L  + GR P  EE+A+   ++ +++  +    + P SLDQ IG   + +  + I D 
Sbjct:   383 QRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDS 442

Query:   438 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRER 497
             EA  A D +    +++ L+ VLDTL+ RE  VVR RFGL DG+ +TL EIG++ GV+RER
Sbjct:   443 EAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRER 502

Query:   498 IRQIESSAFRKLKNKKRTKHLMQY 521
             IRQIES    KL++  R++ L  Y
Sbjct:   503 IRQIESKTMSKLRHPSRSQVLRDY 526

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

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

 Score = 563 (203.2 bits), Expect = 1.6e-54, P = 1.6e-54
 Identities = 108/250 (43%), Positives = 165/250 (66%)

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 EVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMK 452
             E+A  +G+ + +++ +L   + P SLD  +G  +     + I D EA +AE+ +I + + 
Sbjct:   193 ELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAELLH 252

Query:   453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
              D+  VL TL+ RE QV+R RFGL+DG+ +TL +IG+L G+SRER+RQIE     KL++ 
Sbjct:   253 TDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLRHG 312

Query:   513 KRTKHLMQYA 522
             +R   L  YA
Sbjct:   313 ERADRLRSYA 322

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

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

GO:0016987 "sigma factor activity" evidence=IGI

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

GO:0040007 "growth" evidence=IMP

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

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

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

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

 Score = 531 (192.0 bits), Expect = 1.8e-54, Sum P(2) = 1.8e-54
 Identities = 103/232 (44%), Positives = 154/232 (66%)

Query:   290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 349
             +I +N+RLV+S+AK + G GM L DL+QEG  GL+R  EKFD  +GFKFSTYA WWI+QA
Sbjct:   287 LIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWWIRQA 346

Query:   350 VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 409
             + ++++DQ+RTIR+P HMVE   ++    +QL  + GR P  +E+A    L  +++  + 
Sbjct:   347 ITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIAVEMDLPPEKVREIA 406

Query:   410 LSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQV 469
                + P SL+  IG  ++    + I D  A    D   ++ +KE ++ VL +L PRER+V
Sbjct:   407 KVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTVLGSLTPRERRV 466

Query:   470 VRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
             ++ RFGLEDGR +TL+E+G+   V+RERIRQIE+ A RKL++  R++ L  Y
Sbjct:   467 LQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSRKLKDY 518

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 505 (182.8 bits), Expect = 9.9e-52, Sum P(2) = 9.9e-52
 Identities = 99/237 (41%), Positives = 151/237 (63%)

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 LHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNP 464
             +  VL   K P SL+  IG  ++    + I D    +  + +IK  + E   +VL TL P
Sbjct:   459 VRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTARVLATLTP 518

Query:   465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
             RE +V+R RFG+ +    TL+E+G+   V+RERIRQIE+ A RKL++  R K L  +
Sbjct:   519 REEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRAKKLRSF 575

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|ECH_0760 ECH_0760 "RNA polymerase sigma factor RpoD" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 507 (183.5 bits), Expect = 2.0e-51, Sum P(2) = 2.0e-51
 Identities = 97/233 (41%), Positives = 151/233 (64%)

Query:   287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 346
             K +MI +N+RLV+SIAK Y   G+   DLVQEG  GL++  +KFD  +G+KFSTYA WW+
Sbjct:   386 KQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWWV 445

Query:   347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 406
             +QA+ ++++DQ+RTIR+P HM+E   ++    +Q+  E GR P  EE++    +++ ++ 
Sbjct:   446 RQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEMGREPTLEELSARLNINVDKIR 505

Query:   407 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 466
              V+   K P SL+  IG + +    + I D  A   ED  +   ++E   KVL TL P+E
Sbjct:   506 KVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPEDAAVLADLREITTKVLSTLTPKE 565

Query:   467 RQVVRWRFGL-EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 518
              +++R RFG+ + G+  TL+E+G+L  V+RERIRQIE+ A RKL++  R + L
Sbjct:   566 ERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPSRARKL 618

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

GO:0016987 "sigma factor activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O22056	SIGB_ARATH	No assigned EC number	0.6886	0.9790	0.8986	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	525
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	1e-101
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	1e-100
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	3e-91
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	5e-80
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	9e-79
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	1e-76
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	7e-76
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	6e-74
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	8e-71
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	3e-68
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	1e-61
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	1e-59
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	2e-48
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	2e-30
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	4e-30
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	1e-26
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	8e-25
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	1e-23
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	2e-23
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	3e-22
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	5e-21
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	2e-19
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	2e-18
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	3e-18
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	3e-18
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	2e-17
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	1e-16
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	2e-15
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	2e-15
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	8e-15
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	3e-14
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	1e-13
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	2e-13
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	3e-13
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	5e-13
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	2e-11
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	9e-11
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	4e-10
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	6e-10
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	2e-09
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	2e-09
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	5e-09
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	5e-08
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	1e-07
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	1e-07
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	1e-07
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	1e-05
COG1595	182	COG1595, RpoE, DNA-directed RNA polymerase special	8e-04
COG2771	65	COG2771, CsgD, DNA-binding HTH domain-containing p	0.003
smart00421	58	smart00421, HTH_LUXR, helix_turn_helix, Lux Regulo	0.003

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

 Score =  306 bits (785), Expect = e-101
 Identities = 131/299 (43%), Positives = 200/299 (66%), Gaps = 1/299 (0%)

Query: 212 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGV 271
           D +R          LLT  EE++L+  +Q ++ LE LRE L E+ G  P+  +WAAAAG+
Sbjct: 1   DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGL 60

Query: 272 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 331
            + ELR+RL  G   K+KMI +N+RLV+S+AK YQ  G+ L DL+QEG  GL R  EKFD
Sbjct: 61  SEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFD 120

Query: 332 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNN 391
            ++G+KFSTYA+WWI+Q + +++++QSRTIRLP H+ E   ++K+ +++L  + GR P+ 
Sbjct: 121 PTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSE 180

Query: 392 EEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM 451
            E+AEA  L  +++  +L   + P SLD  +G  ++ +  +++ D   E+ E+ + ++ +
Sbjct: 181 AEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERESL 239

Query: 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           ++DLE +L  L PRERQV+R RFGL+ G   TL EIG  + +SRER+RQIE+ A RKL+
Sbjct: 240 RQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298

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

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

 Score =  307 bits (788), Expect = e-100
 Identities = 153/383 (39%), Positives = 220/383 (57%), Gaps = 12/383 (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 KQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 438
           K L  E GR P  EE+AE+  +++++L  +  S + P SL+  IG  ++ +  + I + +
Sbjct: 230 KVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI-EAD 288

Query: 439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERI 498
            ET ED + K  ++EDLE VL TL+PRER V+R R+GL+DGRMKTL+EIG++  V+RERI
Sbjct: 289 GETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERI 348

Query: 499 RQIESSAFRKLKNKKRTKHLMQY 521
           RQIE+ A RKL++  R   L +Y
Sbjct: 349 RQIEAKALRKLRHPNRNSVLKEY 371

Length = 373

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

 Score =  278 bits (713), Expect = 3e-91
 Identities = 105/235 (44%), Positives = 160/235 (68%)

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 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 466
            +    + P SL+  IG  ++    + I D   E+ +D   K+ ++E L++VL+TL  RE
Sbjct: 122 EIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTERE 181

Query: 467 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
            +V+R R+GL DG+  TL+E+G+   V+RERIRQIES A RKL++  R+K L  +
Sbjct: 182 EKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSF 236

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

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

 Score =  252 bits (645), Expect = 5e-80
 Identities = 127/304 (41%), Positives = 198/304 (65%), Gaps = 3/304 (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 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 449
              E+AE   L+ K++   L   + P SLD ++G NQ+ +  E++ D    + ED   + 
Sbjct: 186 TIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT-GASPEDFATQS 244

Query: 450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509
            ++ DLE++++ L P++++V+  RFGLEDG+  TL +IGE + +SRER+RQIE  A  KL
Sbjct: 245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKL 304

Query: 510 KNKK 513
           + +K
Sbjct: 305 RKRK 308

Length = 317

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

 Score =  249 bits (639), Expect = 9e-79
 Identities = 125/320 (39%), Positives = 187/320 (58%), Gaps = 21/320 (6%)

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 NGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 444
            GR P  EE+AE  G+S  ++  +L     P SLD  IG +++ +  + + D ++ + ED
Sbjct: 202 LGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELGDFLEDDKSVSPED 261

Query: 445 LLIKKFMKEDLEKVLDT-LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503
            + ++ +KEDL +VL   L  RER+V+R RFGL+DG  KTL+E+GE  G+SRER+RQIE+
Sbjct: 262 AVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEA 321

Query: 504 SAFRKLKNKKRTKHLMQYAI 523
            A RKL+       L++  +
Sbjct: 322 KALRKLRRHPERSALLRSYL 341

Length = 342

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

 Score =  243 bits (623), Expect = 1e-76
 Identities = 122/301 (40%), Positives = 185/301 (61%), Gaps = 21/301 (6%)

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 MKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT 461
            +++  +L   + P SLD  +G ++     + I D EA +AE+ +I   +  D+  VL T
Sbjct: 203 EEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLAT 262

Query: 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
           L+ RE+QV+R RFGL+DG+ +TL +IG+L G+SRER+RQIE     KL+N +R   L  Y
Sbjct: 263 LDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322

Query: 522 A 522
           A
Sbjct: 323 A 323

Length = 324

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

 Score =  247 bits (634), Expect = 7e-76
 Identities = 144/491 (29%), Positives = 237/491 (48%), Gaps = 56/491 (11%)

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---APRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF 450
           +A+  G + ++   V    K    P SLD+ IG   + +  + I D EA +  D +    
Sbjct: 380 LAKEMGFTPEK---VREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTL 436

Query: 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           +++ L++VL+TL+ RE  V+R RFGL DG+ KTL EIG++ GV+RERIRQIES   RKL+
Sbjct: 437 LQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496

Query: 511 NKKRTKHLMQY 521
           +  R++ L  +
Sbjct: 497 HPSRSQVLRDF 507

Length = 509

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

 Score =  238 bits (609), Expect = 6e-74
 Identities = 110/235 (46%), Positives = 157/235 (66%)

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 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 466
            +L   + P SL+  IG   +    + I D +A +  D    + +KE LE VLDTL  RE
Sbjct: 251 EILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDRE 310

Query: 467 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
             V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  R+K L  +
Sbjct: 311 ENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365

Length = 367

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

 Score =  228 bits (584), Expect = 8e-71
 Identities = 110/288 (38%), Positives = 184/288 (63%), Gaps = 1/288 (0%)

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 HAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPR 465
              L   + P SLD ++G NQ+ + SE++ D E  + +  + ++ +++DL  +L  L P+
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELSELLED-EGPSPDQYITQELLRQDLNNLLAELTPQ 270

Query: 466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 513
           +R+V+  RFGLEDG+  +L ++GE + +SRER+RQ+E  A   L+ ++
Sbjct: 271 QREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRRR 318

Length = 327

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

 Score =  225 bits (574), Expect = 3e-68
 Identities = 119/331 (35%), Positives = 195/331 (58%), Gaps = 33/331 (9%)

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--SLDQKIGINQNLKP 430
           ++K+A++++  E GR P  E++A+   ++  ++  VLL  + PR  SL+ K+G +++ + 
Sbjct: 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL--RVPRSVSLETKVGKDKDTEL 320

Query: 431 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGEL 490
            +++ + +  + E++L+++ ++ DL+ +L  L  RER V+R RFGL DG   +L EIG  
Sbjct: 321 GDLL-ETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRA 379

Query: 491 MGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
           + +SRER+RQIES A +KL+  KR   +  Y
Sbjct: 380 LDLSRERVRQIESKALQKLRQPKRRNRIRDY 410

Length = 415

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

 Score =  213 bits (544), Expect = 1e-61
 Identities = 103/235 (43%), Positives = 153/235 (65%), Gaps = 6/235 (2%)

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 RLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLN 463
           ++  VL   K P SL+  IG +++    + I D  AE   D  I++ ++E    VL +L 
Sbjct: 499 KVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

Query: 464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 518
           PRE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ L
Sbjct: 559 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKL 613

Length = 619

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

 Score =  198 bits (505), Expect = 1e-59
 Identities = 88/225 (39%), Positives = 138/225 (61%)

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 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 466
            VL   +   SLD  +  + +    + IAD ++   E L+    +K+ +E  L  LN R+
Sbjct: 168 RVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQ 227

Query: 467 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511
           R+V+  RFGL      TL+E+   +G++RER+RQI+  A +KL+ 
Sbjct: 228 REVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272

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|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score =  169 bits (431), Expect = 2e-48
 Identities = 84/222 (37%), Positives = 133/222 (59%)

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 AVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAV 408
            + +++ +Q+RTIRLP H+V+       A ++L  +    P+ EE+AE     +  +  +
Sbjct: 150 TIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRM 209

Query: 409 LLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQ 468
           L   +   SLD  +G +      +++AD +    ED      MK+ + K L  LN ++R+
Sbjct: 210 LALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQRE 269

Query: 469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           V+  RFGL      TL+++   +G++RER+RQI+  A R+L+
Sbjct: 270 VLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311

Length = 325

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

 Score =  118 bits (298), Expect = 2e-30
 Identities = 75/253 (29%), Positives = 129/253 (50%), Gaps = 16/253 (6%)

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--PKAPRSLDQKIGINQNLKPSEVIADPEA 439
             E GR P +EE+AE  G+  +     LL+       SLD+ +     LK  +   D + 
Sbjct: 120 EQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDV-----LKDDDDDVDDQI 174

Query: 440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIR 499
           E  +D + K+ + E L++ ++ L  RE+ V+  R+  E     T +EI E++G+S  R+ 
Sbjct: 175 ENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVS 230

Query: 500 QIESSAFRKLKNK 512
           ++   A +KL+ +
Sbjct: 231 RLHKKAIKKLRKE 243

Length = 247

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

 Score =  117 bits (295), Expect = 4e-30
 Identities = 72/232 (31%), Positives = 120/232 (51%), Gaps = 19/232 (8%)

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--PRSLDQKIGINQNLKPSEVI-----ADPEAETAEDLLIKKFMKEDLEKVLD 460
            L +  A    SLD  I  + +  P  ++      D   ET ED       +  L+ +L 
Sbjct: 126 ALEAGNAYQALSLDASIE-DDDGDPIALLDTLGDEDDALETVED-------RLALKPLLA 177

Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
            L  RER+++  RF  ED   KT  EI E +G+S+  + ++   A +KL+ +
Sbjct: 178 ALPERERRILLLRF-FED---KTQSEIAERLGISQMHVSRLLRRALKKLREQ 225

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

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

 Score =  109 bits (274), Expect = 1e-26
 Identities = 75/242 (30%), Positives = 126/242 (52%), Gaps = 31/242 (12%)

Query: 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ 348
           ++I++++RLVIS+A  ++  G+ + DL+QEG  GL+  A +F+  +  +FSTYA WWI+ 
Sbjct: 44  RIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRA 103

Query: 349 A-----------VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA 397
           +           VR   S   +   L F++     R+ +A ++L     +   + E+A A
Sbjct: 104 SIQDYILRNWSIVRGGTSSAQKA--LFFNLRRLRARLAQADEEL----TKQEIHREIATA 157

Query: 398 TGLSMK-------RLHAVLLSPKAPRSLDQKIGINQ--NLKPSEVIADPEAETAEDLLIK 448
            G+S+        RL     S  AP+S + +    +   L     + D   E  E  +  
Sbjct: 158 LGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPD---EQVESSIDG 214

Query: 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 508
           +  +  L + L TLN RE +++R R   EDG   TL+ +GE +G+S+ER+RQIE+ A  K
Sbjct: 215 ERRRRWLTQALQTLNERELRIIRERRLREDGA--TLEALGEELGISKERVRQIEARALEK 272

Query: 509 LK 510
           L+
Sbjct: 273 LR 274

Length = 289

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

 Score =  102 bits (256), Expect = 8e-25
 Identities = 65/214 (30%), Positives = 111/214 (51%), Gaps = 22/214 (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 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR--SLDQK 421
               +E       A ++L +  GR P  EE+AE  G+ +K     L    A    SLD+ 
Sbjct: 81  KARKLE------RAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDEL 134

Query: 422 IGINQNL-KPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVV--RWRFGLED 478
           +    +     + I D ++E  E+ L ++ ++E L + +++L+ RE+ V+   +   L  
Sbjct: 135 LESGDDGGSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQLVLSLYYYEEL-- 192

Query: 479 GRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
                L+EIGE++G++  R+ QI S A +KL+ K
Sbjct: 193 ----NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222

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|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor

 Score =   99 bits (249), Expect = 1e-23
 Identities = 73/243 (30%), Positives = 127/243 (52%), Gaps = 15/243 (6%)

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 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV---IADPEAETAEDLLI 447
             E+A+   +  + +   L + + P SL + I  N    P  V   I+D E       L 
Sbjct: 139 VSEIAKELKVPQEEVVFALDAIQDPVSLFEPI-YNDGGDPIYVMDQISD-EKNKDSQWLE 196

Query: 448 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507
              +KE +++    LN RE+ ++  RF   +G  KT  E+ E +G+S+ ++ ++E +A +
Sbjct: 197 GIALKEAMKR----LNEREKMILNMRF--FEG--KTQMEVAEEIGISQAQVSRLEKAALK 248

Query: 508 KLK 510
            ++
Sbjct: 249 HMR 251

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

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

 Score = 98.2 bits (245), Expect = 2e-23
 Identities = 71/227 (31%), Positives = 123/227 (54%), Gaps = 12/227 (5%)

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 VLLSPKAPRSLDQKIGINQN--LKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPR 465
            L S ++P+SL   +  +    +   + IAD  +E  +   ++K     L++ +  L+ R
Sbjct: 133 ALESARSPQSLYDTVHQDDGDPIYLLDQIADKGSE--DSDWLEKIA---LKEAISKLDER 187

Query: 466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
           ERQ++  R+     + KT  E+  ++G+S+ ++ ++E    +K+K K
Sbjct: 188 ERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEK 230

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|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated

 Score = 95.5 bits (238), Expect = 3e-22
 Identities = 63/201 (31%), Positives = 100/201 (49%), Gaps = 10/201 (4%)

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

Query: 373 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR--SLDQKIGINQNLK- 429
           +V+ A ++L     R+   +EVA   G++ + + A +         S+D+K     + + 
Sbjct: 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGEN 169

Query: 430 PSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGE 489
            S  I D +  T E+ L+K+ + E+L + +  L+ +E+ V+   +  E     TL EIG+
Sbjct: 170 VSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEE----LTLTEIGQ 225

Query: 490 LMGVSRERIRQIESSAFRKLK 510
           ++ +S  RI QI S A  KLK
Sbjct: 226 VLNLSTSRISQIHSKALFKLK 246

Length = 251

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

 Score = 92.3 bits (230), Expect = 5e-21
 Identities = 75/243 (30%), Positives = 131/243 (53%), Gaps = 15/243 (6%)

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 EEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV---IADPEAETAEDLLIK 448
           EE+A+   +  + +   L + + P SL + I  +    P  V   I+D E    E+ L +
Sbjct: 143 EEIAKELEVPREEVVFALDAIQDPVSLFEPI-YHDGGDPIYVMDQISD-EKNKDENWLEE 200

Query: 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 508
             +KE ++K    LN RE+ ++  RF    G  KT  E+ E +G+S+ ++ ++E +A + 
Sbjct: 201 IALKEAMKK----LNDREKLILNLRF--FQG--KTQMEVAEEIGISQAQVSRLEKAALKH 252

Query: 509 LKN 511
           ++ 
Sbjct: 253 MRK 255

Length = 258

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

 Score = 87.7 bits (218), Expect = 2e-19
 Identities = 62/225 (27%), Positives = 121/225 (53%), Gaps = 10/225 (4%)

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 VLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRER 467
              + ++P+S+ +   +++N      + D  A+ +E+     F K  L++ +  L+ RER
Sbjct: 154 AQEASRSPQSIHET--VHENDGDPITLLDQIADQSEE---DWFDKIALKEAIRELDERER 208

Query: 468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
            +V  R+     + KT  E+ + +G+S+ ++ ++E    +++K K
Sbjct: 209 LIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249

Length = 252

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

 Score = 79.2 bits (196), Expect = 2e-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|235770 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed

 Score = 84.4 bits (209), Expect = 3e-18
 Identities = 62/208 (29%), Positives = 111/208 (53%), Gaps = 18/208 (8%)

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

Query: 370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL--LSPKAPRSLDQ-KIGINQ 426
               + EAR       GR P++EE+A+  G+S++  +++L  LS  +  SL+    G ++
Sbjct: 122 RAIAMLEARL------GRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDE 175

Query: 427 NLKPS--EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTL 484
             + S  + +  P A   +++  ++ +K  + + + TL  RE++V+   +  ED    TL
Sbjct: 176 GDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYY-YED---LTL 231

Query: 485 QEIGELMGVSRERIRQIESSAFRKLKNK 512
           +EIG+++GV+  RI Q+ + A  +L+ K
Sbjct: 232 KEIGKVLGVTESRISQLHTKAVLQLRAK 259

Length = 268

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

 Score = 84.2 bits (209), Expect = 3e-18
 Identities = 60/191 (31%), Positives = 103/191 (53%), Gaps = 17/191 (8%)

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--PKAPRSLDQKIGINQNL 428
             + K+ R++L  E GR P ++E+A+A  +S++    + L+   + P SLD  +  +++ 
Sbjct: 112 QRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDG 171

Query: 429 KPS--EVIADPEAETAEDLLIKKFMKED---LEKVLDTLNPRERQVVRWRFGLEDGRMKT 483
             S  +++ DP           +  +ED   L++ L  L  R R+V+ + F L D    T
Sbjct: 172 STSLGDLLPDPRYR------SFQLAQEDRIRLQQALAQLEERTREVLEFVF-LHD---LT 221

Query: 484 LQEIGELMGVS 494
            +E  E +G+S
Sbjct: 222 QKEAAERLGIS 232

Length = 256

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

 Score = 81.0 bits (201), Expect = 2e-17
 Identities = 64/217 (29%), Positives = 108/217 (49%), Gaps = 29/217 (13%)

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 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR--S 417
           ++R     V       +A +QL  E GR P + EVAE  GLS++    +LL     +  S
Sbjct: 89  SVRRNAREVA------QAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFS 142

Query: 418 LDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVR--WRFG 475
           +D+  G + +     V  D + E     L  + ++E L + +++L  RE+ V+   ++  
Sbjct: 143 IDELRGEHGD--SILVTEDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEE 200

Query: 476 LEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
           L       L+EIG ++GVS  R+ QI S A ++L+ +
Sbjct: 201 L------NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231

Length = 236

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

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 26/78 (33%), Positives = 48/78 (61%)

Query: 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL 428
           E   ++K A+++L  E GR P  EE+AE  G+S +++  VL + + P SLD  +G  ++ 
Sbjct: 1   ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDG 60

Query: 429 KPSEVIADPEAETAEDLL 446
           +  +++ D +AE+ ED +
Sbjct: 61  ELGDLLEDDDAESPEDAV 78

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

 Score = 76.2 bits (187), Expect = 2e-15
 Identities = 69/236 (29%), Positives = 108/236 (45%), Gaps = 22/236 (9%)

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 KRLH--------AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKED 454
           + L         A++LS                L+  E IAD  AET  D++ KK     
Sbjct: 141 QELSGWFSSARPALILSLNEEFPCQSDDEAGLALE--ERIADERAETGYDVVDKKEFSSI 198

Query: 455 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           L + +  L  +ER+V+   +  E      L+EIG+++GVS  R+ QI S A  KL+
Sbjct: 199 LAEAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKLR 250

Length = 257

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

 Score = 70.1 bits (173), Expect = 2e-15
 Identities = 29/54 (53%), Positives = 37/54 (68%), Gaps = 4/54 (7%)

Query: 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511
            L +L PRER+V+  RFG       TL+EIGE +G+SRER+RQIE  A RKL+ 
Sbjct: 1   ALASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50

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

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

 Score = 74.2 bits (182), Expect = 8e-15
 Identities = 62/230 (26%), Positives = 111/230 (48%), Gaps = 16/230 (6%)

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

Query: 347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 406
              +++ L D++ ++ +P  + E   ++K+A  +L     R P   E+A+  GLS + + 
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150

Query: 407 AVLLSPKAPR--SLDQKIGINQNLKPSEVIAD----PEAETAEDLLIKKFMKEDLEKVLD 460
            ++   ++ R  S+D  I   +       +A      E E   D   ++ +   LEK+L 
Sbjct: 151 EIMEMGQSYRALSVDDVI---EADSDGSTVARLDSVGEVEDGYDQTERRMV---LEKILP 204

Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
            L+ RE+ ++   F  E+   K   E GE +G+S+  + +++  A  KLK
Sbjct: 205 ILSEREKSIIHCTF-EENLSQK---ETGERLGISQMHVSRLQRQAISKLK 250

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

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

 Score = 72.7 bits (179), Expect = 3e-14
 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|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed

 Score = 71.4 bits (176), Expect = 1e-13
 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|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed

 Score = 69.2 bits (170), Expect = 2e-13
 Identities = 26/74 (35%), Positives = 44/74 (59%)

Query: 438 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRER 497
           E +   + +  K   E L K +D L+ RE++V+  R+GL +G+ KT +EI + +G+SR  
Sbjct: 152 EEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSY 211

Query: 498 IRQIESSAFRKLKN 511
           + +IE  A +KL  
Sbjct: 212 VSRIEKRALKKLFK 225

Length = 233

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

 Score = 69.4 bits (170), Expect = 3e-13
 Identities = 59/232 (25%), Positives = 103/232 (44%), Gaps = 17/232 (7%)

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--PRSLDQKIGINQNLKPSEVIA----DPEAETAEDLLIKKFMKEDLEKVLD 460
             L++  A    S+D   G   +   +        D   +  E+       +E L  +L 
Sbjct: 162 EGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDVDAGLDQIEN-------REALRPLLA 214

Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
            L  RER V+  RF      M T  +I E +G+S+  + ++ +    +L+++
Sbjct: 215 ALPERERTVLVLRFF---ESM-TQTQIAERVGISQMHVSRLLAKTLARLRDQ 262

Length = 264

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

 Score = 63.3 bits (155), Expect = 5e-13
 Identities = 24/59 (40%), Positives = 36/59 (61%), Gaps = 4/59 (6%)

Query: 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           +E LE+ LD L  RER+V+  RFG       + +EI E++G+SR  +RQ    A +KL+
Sbjct: 1   RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55

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

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

 Score = 63.9 bits (156), Expect = 2e-11
 Identities = 56/217 (25%), Positives = 111/217 (51%), Gaps = 10/217 (4%)

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 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR 416
           ++ ++ +P  + E   ++K+A  +L +E  R P   E+A+  G+S + +   +   K+ +
Sbjct: 101 KTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQ 160

Query: 417 SLDQKIGINQNLKPSEV-IAD--PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWR 473
           +L     I  +   S V + D   + E   +L  ++ +   LEK+L  L+ RE+ +++  
Sbjct: 161 ALSVDHSIEADSDGSTVTLLDIVGQQEDGYELTEQRMI---LEKILPVLSDREKSIIQCT 217

Query: 474 FGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           F   +    + +E GE +G+S+  + +++  A +KL+
Sbjct: 218 F--IEN--LSQKETGERLGISQMHVSRLQRQAIKKLR 250

Length = 257

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

 Score = 62.5 bits (153), Expect = 9e-11
 Identities = 24/56 (42%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 455 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           L   L+ L+ R R ++  R+  +D    TLQE+    GVS ER+RQIE +A +KLK
Sbjct: 224 LADALEGLDERSRDIIEARWLDDDK--STLQELAAEYGVSAERVRQIEKNAMKKLK 277

Length = 284

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

 Score = 59.7 bits (145), Expect = 4e-10
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query: 434 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGV 493
           I   + ++  + +      + L K L  L+ RER+V+  R+GL DGR KT +EI +++G+
Sbjct: 147 ILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGI 206

Query: 494 SRERIRQIESSAFRKL 509
           SR  + +IE  A  KL
Sbjct: 207 SRSYVSRIEKRALMKL 222

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

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

 Score = 59.6 bits (145), Expect = 6e-10
 Identities = 29/76 (38%), Positives = 43/76 (56%), Gaps = 3/76 (3%)

Query: 436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSR 495
           DPE    E+   +   ++ L   L +L+ R R+++  R+  +D    TLQE+    GVS 
Sbjct: 194 DPEDTLEEEQWEEL-QRQALANALGSLDARSRRIIEARWLDDDK--LTLQELAAEYGVSA 250

Query: 496 ERIRQIESSAFRKLKN 511
           ERIRQIE +A +KLK 
Sbjct: 251 ERIRQIEKNAMKKLKA 266

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

 Score = 56.2 bits (136), Expect = 2e-09
 Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 438 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRER 497
              + E+ L ++  +E L + L+ L  RER+V+  R+        + +EI E++G+S   
Sbjct: 87  SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGT 142

Query: 498 IRQIESSAFRKLKNK 512
           +++    A +KL+  
Sbjct: 143 VKRRLKRARKKLREL 157

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 = 57.5 bits (139), Expect = 2e-09
 Identities = 22/59 (37%), Positives = 38/59 (64%)

Query: 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           +E L K L  LN RE++++  RFGL  G  KT +E+ +++G+S+  I ++E    ++LK
Sbjct: 169 RELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLK 227

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

 Score = 56.5 bits (137), Expect = 5e-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|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed

 Score = 53.3 bits (129), Expect = 5e-08
 Identities = 21/59 (35%), Positives = 39/59 (66%)

Query: 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           ++ L+K L  L+ RE+Q++  RFGL  G  KT +E+ +++G+S+  I ++E    ++LK
Sbjct: 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227

Length = 234

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

 Score = 52.4 bits (126), Expect = 1e-07
 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|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family

 Score = 50.8 bits (122), Expect = 1e-07
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 2/97 (2%)

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

Query: 348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSE 384
             +   L  + R  R    + E         ++L  E
Sbjct: 62  NLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQE 98

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 = 52.5 bits (126), Expect = 1e-07
 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|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed

 Score = 46.0 bits (110), Expect = 1e-05
 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|224511 COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]

 Score = 40.5 bits (95), Expect = 8e-04
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 435 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVS 494
               A    +LL+ +   E L + L  L PR+R+    R+        + +EI E++G+S
Sbjct: 101 EADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEG----LSYEEIAEILGIS 156

Query: 495 RERIRQIESSAFRKLKNK 512
              ++     A +KL+ +
Sbjct: 157 VGTVKSRLHRARKKLREQ 174

Length = 182

>gnl|CDD|225360 COG2771, CsgD, DNA-binding HTH domain-containing proteins [Transcription]

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 6/62 (9%)

Query: 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
           L PRER+++R    +  G  K+ +EI  ++G+S E ++    + +RKL  K R   L+  
Sbjct: 5   LTPREREILRL---VAQG--KSNKEIARILGISEETVKTHLRNIYRKLGVKNRV-ELVAL 58

Query: 522 AI 523
           A+
Sbjct: 59  AL 60

Length = 65

>gnl|CDD|197715 smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 518
           L +L PRER+V+R    L +G   T +EI E +G+S + ++   S+  RKL  + RT   
Sbjct: 1   LASLTPREREVLRL---LAEG--LTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRT-QA 54

Query: 519 MQYA 522
           ++ A
Sbjct: 55  VRLA 58

lux regulon (activates the bioluminescence operon. Length = 58

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	525
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	100.0
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	100.0
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	100.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	100.0
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	100.0
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	100.0
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	100.0
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	100.0
PRK08215	258	sporulation sigma factor SigG; Reviewed	100.0
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	100.0
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	100.0
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	100.0
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	100.0
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	100.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	100.0
PRK08583	257	RNA polymerase sigma factor SigB; Validated	100.0
PRK05572	252	sporulation sigma factor SigF; Validated	100.0
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	100.0
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	100.0
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	100.0
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.96
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.94
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.94
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.93
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.91
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.9
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.9
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.89
PRK12513	194	RNA polymerase sigma factor; Provisional	99.89
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.89
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.89
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.89
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.89
PRK11922	231	RNA polymerase sigma factor; Provisional	99.88
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.88
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.88
PRK12519	194	RNA polymerase sigma factor; Provisional	99.88
PRK12514	179	RNA polymerase sigma factor; Provisional	99.88
PRK12524	196	RNA polymerase sigma factor; Provisional	99.88
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.87
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.87
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.87
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.87
PRK12537	182	RNA polymerase sigma factor; Provisional	99.87
PRK12534	187	RNA polymerase sigma factor; Provisional	99.87
PRK12538	233	RNA polymerase sigma factor; Provisional	99.87
PRK12542	185	RNA polymerase sigma factor; Provisional	99.87
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.87
PRK11924	179	RNA polymerase sigma factor; Provisional	99.86
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.86
PRK12515	189	RNA polymerase sigma factor; Provisional	99.86
PRK12526	206	RNA polymerase sigma factor; Provisional	99.86
PRK12543	179	RNA polymerase sigma factor; Provisional	99.86
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.85
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.85
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.85
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.85
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.85
PRK12531	194	RNA polymerase sigma factor; Provisional	99.85
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.84
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.84
PRK12536	181	RNA polymerase sigma factor; Provisional	99.84
PRK12522	173	RNA polymerase sigma factor; Provisional	99.84
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.84
PRK12520	191	RNA polymerase sigma factor; Provisional	99.84
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.83
PRK12539	184	RNA polymerase sigma factor; Provisional	99.83
PRK12533	216	RNA polymerase sigma factor; Provisional	99.83
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.83
PRK12529	178	RNA polymerase sigma factor; Provisional	99.83
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.83
PRK12518	175	RNA polymerase sigma factor; Provisional	99.83
PRK12512	184	RNA polymerase sigma factor; Provisional	99.82
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.82
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.82
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.82
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.82
PRK12516	187	RNA polymerase sigma factor; Provisional	99.82
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.81
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.81
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.81
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.81
PRK12528	161	RNA polymerase sigma factor; Provisional	99.81
PRK12541	161	RNA polymerase sigma factor; Provisional	99.81
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.8
PRK12532	195	RNA polymerase sigma factor; Provisional	99.8
PRK12530	189	RNA polymerase sigma factor; Provisional	99.8
PRK12547	164	RNA polymerase sigma factor; Provisional	99.8
PRK12545	201	RNA polymerase sigma factor; Provisional	99.8
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.8
PRK12535	196	RNA polymerase sigma factor; Provisional	99.8
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.8
PRK12544	206	RNA polymerase sigma factor; Provisional	99.79
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.79
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.79
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.78
PRK12517	188	RNA polymerase sigma factor; Provisional	99.78
PRK12540	182	RNA polymerase sigma factor; Provisional	99.78
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.78
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.78
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.77
PRK12546	188	RNA polymerase sigma factor; Provisional	99.76
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.76
PRK12511	182	RNA polymerase sigma factor; Provisional	99.75
PRK12525	168	RNA polymerase sigma factor; Provisional	99.75
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.73
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.72
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.69
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.69
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.69
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.55
PRK09191	261	two-component response regulator; Provisional	99.53
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.39
PF07638	185	Sigma70_ECF: ECF sigma factor	99.39
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.28
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.25
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	99.11
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	98.94
PRK06930	170	positive control sigma-like factor; Validated	98.69
PRK00118	104	putative DNA-binding protein; Validated	98.48
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.3
PRK04217	110	hypothetical protein; Provisional	98.12
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.1
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.03
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.03
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	97.98
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	97.9
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.8
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.78
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	97.68
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.66
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.66
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.57
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.4
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.16
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.1
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.08
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.05
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.05
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.04
PRK10840	216	transcriptional regulator RcsB; Provisional	97.01
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	96.99
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	96.96
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	96.94
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	96.9
PRK13870	234	transcriptional regulator TraR; Provisional	96.9
COG2197	211	CitB Response regulator containing a CheY-like rec	96.87
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.83
COG3413	215	Predicted DNA binding protein [General function pr	96.79
COG4566	202	TtrR Response regulator [Signal transduction mecha	96.71
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.7
PRK15369	211	two component system sensor kinase SsrB; Provision	96.7
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.66
PRK09483	217	response regulator; Provisional	96.62
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	96.6
COG4941	415	Predicted RNA polymerase sigma factor containing a	96.46
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	96.34
PRK09390	202	fixJ response regulator FixJ; Provisional	96.27
PRK10651	216	transcriptional regulator NarL; Provisional	96.2
COG1342	99	Predicted DNA-binding proteins [General function p	96.09
PRK01381	99	Trp operon repressor; Provisional	96.02
PRK13558	665	bacterio-opsin activator; Provisional	95.46
COG1356	143	tfx Transcriptional regulator [DNA replication, re	95.32
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	95.12
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	95.11
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.05
PRK09935	210	transcriptional regulator FimZ; Provisional	95.05
PRK10403	215	transcriptional regulator NarP; Provisional	94.99
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.95
PRK15320	251	transcriptional activator SprB; Provisional	94.9
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	94.81
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	94.41
PRK04841	903	transcriptional regulator MalT; Provisional	94.32
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	94.31
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	94.22
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	93.98
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	93.91
PRK15418	318	transcriptional regulator LsrR; Provisional	93.87
PF10668	60	Phage_terminase: Phage terminase small subunit; In	93.66
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	93.61
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	93.37
PF13730	55	HTH_36: Helix-turn-helix domain	93.33
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	93.32
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	93.1
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	93.05
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	92.9
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	92.84
PRK05901	509	RNA polymerase sigma factor; Provisional	92.84
PHA00675	78	hypothetical protein	92.44
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	92.02
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	91.85
PRK07598	415	RNA polymerase sigma factor SigC; Validated	91.71
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	91.65
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	91.13
PF13518	52	HTH_28: Helix-turn-helix domain	91.1
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	90.89
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	90.62
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	90.59
smart00351	125	PAX Paired Box domain.	90.49
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	89.97
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	89.97
COG3355	126	Predicted transcriptional regulator [Transcription	89.82
PHA02591	83	hypothetical protein; Provisional	89.33
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	88.86
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	88.66
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	88.62
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	88.62
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	88.57
PRK15479	221	transcriptional regulatory protein TctD; Provision	88.24
PRK12423	202	LexA repressor; Provisional	88.18
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	88.16
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	88.0
PHA02547	179	55 RNA polymerase sigma factor; Provisional	87.96
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	87.94
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	87.79
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	87.69
PRK11083	228	DNA-binding response regulator CreB; Provisional	87.63
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	87.59
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	87.11
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	87.08
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	87.03
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	87.02
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	86.8
cd00131	128	PAX Paired Box domain	86.8
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	86.66
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	86.59
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	86.57
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	86.57
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	86.5
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	86.5
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	86.49
PRK05949	327	RNA polymerase sigma factor; Validated	86.45
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	86.16
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	86.08
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	85.77
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	85.39
PF12728	51	HTH_17: Helix-turn-helix domain	85.36
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	85.33
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	85.24
COG1522	154	Lrp Transcriptional regulators [Transcription]	85.15
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	84.91
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	84.71
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	84.59
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	84.46
PRK00215	205	LexA repressor; Validated	84.34
PRK10046	225	dpiA two-component response regulator DpiA; Provis	84.2
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	84.15
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	84.08
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	84.04
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	83.68
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	83.56
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	83.52
PRK11169	164	leucine-responsive transcriptional regulator; Prov	83.49
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	83.36
COG3415	138	Transposase and inactivated derivatives [DNA repli	83.34
TIGR01764	49	excise DNA binding domain, excisionase family. An	83.27
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	83.22
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	82.89
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	82.82
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	82.76
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	82.73
PRK07405	317	RNA polymerase sigma factor SigD; Validated	82.52
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	82.48
COG1654	79	BirA Biotin operon repressor [Transcription]	82.4
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	81.29
COG1510	177	Predicted transcriptional regulators [Transcriptio	81.18
PRK07670	251	RNA polymerase sigma factor SigD; Validated	81.01
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	80.26
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	80.11
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	80.07

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=1.6e-65  Score=540.57  Aligned_cols=312  Identities=39%  Similarity=0.699  Sum_probs=295.0

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH--------------------HHhHHHHHHhhcCCCCchHHhHHh
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAAA  268 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~--------------------le~~~~~l~~~~g~~pt~~ewa~a  268 (525)
                      ..|+++ ||++| +++||||++||++|+++||.++.                    |++++..|++++|++||..+||.+
T Consensus        58 ~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~  136 (415)
T PRK07598         58 STDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKT  136 (415)
T ss_pred             CCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHH
Confidence            479999 99999 99999999999999999999999                    899999999999999999999966


Q ss_pred             hcCC----------------------HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHh
Q 009803          269 AGVD----------------------QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRG  326 (525)
Q Consensus       269 ~g~d----------------------~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirA  326 (525)
                      +|++                      ...|.+.++.|..|+++||.+|+++|+++|++|.++|++++||||||++|||+|
T Consensus       137 ~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ra  216 (415)
T PRK07598        137 ADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERA  216 (415)
T ss_pred             hCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence            6554                      555555567888999999999999999999999999999999999999999999


Q ss_pred             hhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHH
Q 009803          327 AEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH  406 (525)
Q Consensus       327 iekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~  406 (525)
                      +++|||++|++|+||++||||++|.+++.+++++||+|.|+.+.+++++++++.+.+++||.||.+|||+.+|+++++|+
T Consensus       217 vekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr  296 (415)
T PRK07598        217 VEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVR  296 (415)
T ss_pred             HHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHH
Q 009803          407 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQE  486 (525)
Q Consensus       407 ~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~E  486 (525)
                      .++.....++|||.+++++++..+.+.+.++ ..+|++.+....+...|..+|..||++||.||.||||++||.++|++|
T Consensus       297 ~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~-~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~E  375 (415)
T PRK07598        297 EVLLRVPRSVSLETKVGKDKDTELGDLLETD-DISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAE  375 (415)
T ss_pred             HHHHHccCCcccccccCCCccccHHHhccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHHH
Confidence            9999889999999999988888888877654 458999999999999999999999999999999999999999999999


Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          487 IGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       487 IAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      ||+.||||+++|||++++|++|||++-....|++|+.
T Consensus       376 IA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~  412 (415)
T PRK07598        376 IGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE  412 (415)
T ss_pred             HHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence            9999999999999999999999999999999999986

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2.8e-63  Score=519.99  Aligned_cols=311  Identities=48%  Similarity=0.794  Sum_probs=299.3

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e  288 (525)
                      ..|++. ||++| +++|+||++||++|+++|+.++.+++++.+|+...|+.|+..+||.++|++...|.+++..|..|++
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             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (525)
Q Consensus       289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~  368 (525)
                      .||.+|+++|+++|++|.++|.+++||+|||++|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.|+.
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             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  448 (525)
Q Consensus       369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~  448 (525)
                      ..+++++++...|.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++++. .+|++.+..
T Consensus       220 ~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~~-~~pee~~~~  298 (373)
T PRK07406        220 ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADG-ETPEDDVAK  298 (373)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCCC-CCHHHHHHH
Confidence            9999999999999999999999999999999999999999988889999999998777777888888763 478888888


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhh
Q 009803          449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA  522 (525)
Q Consensus       449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl  522 (525)
                      ..+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+......|+.|+
T Consensus       299 ~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~  372 (373)
T PRK07406        299 NLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI  372 (373)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence            99999999999999999999999999998888899999999999999999999999999999999999999986

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=5.5e-62  Score=504.07  Aligned_cols=310  Identities=37%  Similarity=0.688  Sum_probs=296.5

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e  288 (525)
                      ..|++. ||++| +++|+||++||++|+++|+.++.++..+..|+...|+.|+..+|+.++++++..|...++.|..|++
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            468999 99999 9999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (525)
Q Consensus       289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~  368 (525)
                      .||.+|+++|+++|++|.+++.+++|||||||+|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+.
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             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  448 (525)
Q Consensus       369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~  448 (525)
                      ..+++++++.+.+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+.++++. .+|++.+..
T Consensus       175 ~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~~-~~pe~~~~~  253 (327)
T PRK05949        175 EKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSPDQYITQ  253 (327)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCCC-CCHHHHHHH
Confidence            9999999999999999999999999999999999999999998899999999998777777788887765 589999999


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      ..+...|..+|+.||++||.||.+|||++|++++|++|||+.||||+++|||++++|++|||+.  ...|+.|+.
T Consensus       254 ~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~  326 (327)
T PRK05949        254 ELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA  326 (327)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            9999999999999999999999999999988999999999999999999999999999999994  467888875

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

Probab=100.00  E-value=2.4e-61  Score=493.79  Aligned_cols=297  Identities=45%  Similarity=0.778  Sum_probs=284.0

Q ss_pred             CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHH
Q 009803          212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM  290 (525)
Q Consensus       212 d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~L  290 (525)
                      |++. ||++| +++|+||++||.+|+++|+.++.+++++..|+++.|++||..+||+++|++...|...++.|..|++.|
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            4677 99999 999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHH
Q 009803          291 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA  370 (525)
Q Consensus       291 v~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~  370 (525)
                      |.+|+++|+++|++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.+++++||+|.++...
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             HHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHH
Q 009803          371 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF  450 (525)
Q Consensus       371 ~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~  450 (525)
                      +++++++...+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.+++. ..+|++.+....
T Consensus       160 ~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~-~~~pe~~~~~~~  238 (298)
T TIGR02997       160 LNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERES  238 (298)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccCC-CCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999999888999999998766666677777764 458899999888


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      +...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++++|++|||
T Consensus       239 ~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr  298 (298)
T TIGR02997       239 LRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR  298 (298)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            999999999999999999999999998888899999999999999999999999999996

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

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=5.4e-61  Score=495.09  Aligned_cols=309  Identities=41%  Similarity=0.705  Sum_probs=295.2

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHH
Q 009803          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  289 (525)
Q Consensus       211 ~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~  289 (525)
                      +|++. ||++| +++|+||++||++|+++|+.++.+++++..|++++|++|+..+||.++++++..|...+..|..|+++
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            57899 99999 99999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHH
Q 009803          290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE  369 (525)
Q Consensus       290 Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~  369 (525)
                      ||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
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             HHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHH
Q 009803          370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK  449 (525)
Q Consensus       370 ~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~  449 (525)
                      .+++++++.+.+...+|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+.++++. .+|++.+...
T Consensus       166 ~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~~-~~pe~~~~~~  244 (317)
T PRK07405        166 KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQS  244 (317)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCCC-CCHHHHHHHH
Confidence            999999999999999999999999999999999999999988888999999998777777788887764 5799999989


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       450 ~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      .+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+.  ...|..|+.
T Consensus       245 ~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~  316 (317)
T PRK07405        245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA  316 (317)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            999999999999999999999999999888999999999999999999999999999999995  457788875

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

Probab=100.00  E-value=1.2e-60  Score=489.49  Aligned_cols=312  Identities=42%  Similarity=0.708  Sum_probs=288.1

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHh-hcCCCCchH---------------HhHHhhcCCH
Q 009803          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVDQ  273 (525)
Q Consensus       211 ~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~-~~g~~pt~~---------------ewa~a~g~d~  273 (525)
                      .|.+. |+.++ +..+++++++|..+...++....+..+...|.. ..|..|+..               +|+.....++
T Consensus         8 ~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E   86 (342)
T COG0568           8 ADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE   86 (342)
T ss_pred             hhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence            56778 99999 999999999999999999887777677777776 677888876               6666665554


Q ss_pred             -HHHHHHHhcc---HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHH
Q 009803          274 -RELRRRLNYG---ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (525)
Q Consensus       274 -~~L~~~l~~g---~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqa  349 (525)
                       ..|..++..|   ..|+.+||.+|+|||++||++|.|+|+++.|||||||||||+|+++|||++||+|||||+|||||+
T Consensus        87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqa  166 (342)
T COG0568          87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQA  166 (342)
T ss_pred             HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHH
Confidence             5677776666   459999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCC
Q 009803          350 VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLK  429 (525)
Q Consensus       350 I~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~  429 (525)
                      |.++|.+++|+||+|+|+.+.+++++++.+.+.+++|++|+.+|||+.+|+++++|..++.....++|||.+++++++..
T Consensus       167 I~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~ded~~  246 (342)
T COG0568         167 ITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSE  246 (342)
T ss_pred             HHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCCCcccH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998889


Q ss_pred             CCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 009803          430 PSEVIADPEAETAEDLLIKKFMKEDLEKVLDT-LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK  508 (525)
Q Consensus       430 l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~-L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkK  508 (525)
                      +.|+++|+...+|++.+....+...+...|.. |+|+|+.||++|||++|++|.|++|||+.+|||++|||||+.+||+|
T Consensus       247 l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~kAl~K  326 (342)
T COG0568         247 LGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRK  326 (342)
T ss_pred             HHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence            99999999877999999999999999999999 99999999999999999999999999999999999999999999999


Q ss_pred             HH-hHHhhchhhhhhc
Q 009803          509 LK-NKKRTKHLMQYAI  523 (525)
Q Consensus       509 LR-~~l~~~~L~~yl~  523 (525)
                      || .......+++|++
T Consensus       327 Lr~~~~~~~~~~~~l~  342 (342)
T COG0568         327 LRRHPERSALLRSYLD  342 (342)
T ss_pred             HHHhhhhhhHHHHhhC
Confidence            99 5555566788864

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=3.8e-60  Score=510.83  Aligned_cols=302  Identities=40%  Similarity=0.674  Sum_probs=276.7

Q ss_pred             CCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHH
Q 009803          208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC  286 (525)
Q Consensus       208 ~~~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A  286 (525)
                      ....|+++ ||++| +++|+||++||++|+++|+.+..++..   +.       ...+|+..   ....|++.+..|..|
T Consensus       207 ~~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~~---~~~~l~~~~~~g~~A  272 (509)
T PRK05901        207 TATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDPE---LRRDLQWIGRDGKRA  272 (509)
T ss_pred             cccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchhh---hhhhhhhhccchHHH
Confidence            34578999 99999 999999999999999999976433221   11       11224422   456788889999999


Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (525)
Q Consensus       287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~  366 (525)
                      +++||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|
T Consensus       273 r~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~  352 (509)
T PRK05901        273 KNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVH  352 (509)
T ss_pred             HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  446 (525)
Q Consensus       367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~  446 (525)
                      +.+.+++++++.+.|.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|+....|++.+
T Consensus       353 ~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~  432 (509)
T PRK05901        353 MVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAV  432 (509)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHH
Confidence            99999999999999999999999999999999999999999999888999999999877777788999988777899999


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      ....++..|..+|..|++|||.||.+|||+++++++|++|||+.||||++|||||+.+||+|||.......|++|++
T Consensus       433 ~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~  509 (509)
T PRK05901        433 SFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD  509 (509)
T ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            99999999999999999999999999999998899999999999999999999999999999999999999999974

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=3.8e-59  Score=481.98  Aligned_cols=300  Identities=42%  Similarity=0.710  Sum_probs=275.4

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e  288 (525)
                      .+|++. ||++| +++|+||++||++|+++|+.+..++..           |+..+|....  ....|...++.|..|++
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            368899 99999 999999999999999999986655432           2233333211  34678889999999999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (525)
Q Consensus       289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~  368 (525)
                      +||..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.+++++++++||+|.|+.
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             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  448 (525)
Q Consensus       369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~  448 (525)
                      +.+++++++...|.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+..
T Consensus       170 ~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~~~  249 (324)
T PRK07921        170 EQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIA  249 (324)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHHHH
Confidence            99999999999999999999999999999999999999999888889999999987766678888988766789988888


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      ..+...|..+|+.|+++|+.||.+|||++|++++|++|||+.||||++|||||+.+|++|||.......|+.|+.
T Consensus       250 ~~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~~  324 (324)
T PRK07921        250 GLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYAS  324 (324)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhhC
Confidence            899999999999999999999999999998999999999999999999999999999999999998889998863

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=3.6e-55  Score=460.09  Aligned_cols=273  Identities=45%  Similarity=0.767  Sum_probs=260.9

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e  288 (525)
                      ..|+++ ||++| +++|+||++||.+|+.+++.                                        |+..|++
T Consensus        94 ~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~~  132 (367)
T PRK09210         94 INDPVRMYLKEI-GRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAKQ  132 (367)
T ss_pred             cCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHHH
Confidence            468999 99999 99999999999999988864                                        4578999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (525)
Q Consensus       289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~  368 (525)
                      .||..|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+|||+||||++|.++|++++|++|+|.|+.
T Consensus       133 ~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~  212 (367)
T PRK09210        133 RLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV  212 (367)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  448 (525)
Q Consensus       369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~  448 (525)
                      +.++++.++.+.|.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|+...+|++.+..
T Consensus       213 ~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~~  292 (367)
T PRK09210        213 ETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAY  292 (367)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHHH
Confidence            99999999999999999999999999999999999999999888889999999987777788899998877789999999


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      ..++..|..+|..||++||.||.+|||++||+++|++|||+.||||++|||||+.+||+|||++.....|+.|++
T Consensus       293 ~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~  367 (367)
T PRK09210        293 ELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE  367 (367)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999974

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2.7e-52  Score=464.69  Aligned_cols=270  Identities=40%  Similarity=0.667  Sum_probs=251.3

Q ss_pred             HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHH
Q 009803          216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI  295 (525)
Q Consensus       216 yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nl  295 (525)
                      ||.++ ...+.||++++..++++|+.               |..                      .+..|+++||.+|+
T Consensus       349 ~L~~i-e~~~~Ls~eElk~l~~~i~~---------------g~~----------------------~~~~a~~~Li~~nl  390 (619)
T PRK05658        349 ELEAI-EEETGLTIEELKEINRQISK---------------GEA----------------------KARRAKKEMVEANL  390 (619)
T ss_pred             HHHHH-HHHhCCCHHHHHHHHHHHhc---------------cch----------------------hhhHHHHHHHHHHH
Confidence            67777 66777777777777776664               210                      12478999999999


Q ss_pred             HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHH
Q 009803          296 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK  375 (525)
Q Consensus       296 rLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~  375 (525)
                      |||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+.+.+++++
T Consensus       391 rlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~k~~  470 (619)
T PRK05658        391 RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN  470 (619)
T ss_pred             HHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHH
Q 009803          376 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDL  455 (525)
Q Consensus       376 ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L  455 (525)
                      ++.+.+.+++|+.||.+|||+.||+++++|..++.....++|||.+++++++.++.++++|+...+|++.+....++..|
T Consensus       471 ~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~~p~~~~~~~~~~~~l  550 (619)
T PRK05658        471 RISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREAT  550 (619)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCCChHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999888999999999888777889999988777899999999999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          456 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       456 ~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      ..+|..||+||+.||++|||++++.++|++|||+.||||++|||||+.+|++|||++.....|+.|++
T Consensus       551 ~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~  618 (619)
T PRK05658        551 TDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD  618 (619)
T ss_pred             HHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence            99999999999999999999988899999999999999999999999999999999999999999986

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

Probab=100.00  E-value=4.5e-48  Score=383.49  Aligned_cols=238  Identities=45%  Similarity=0.777  Sum_probs=226.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (525)
Q Consensus       286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~  365 (525)
                      |+++||..|+++|+++|++|.++|.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+|+|.
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             chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803          366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  445 (525)
Q Consensus       366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~  445 (525)
                      ++...++++.++.+.+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++|+...+|++.
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p~~~  160 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDY  160 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCChHHH
Confidence            99999999999999999999999999999999999999999999887789999999877666677788888777789988


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      +....+...|..+|+.||++||.||.+|||+++++++|++|||+.||||+++|+|++.+|++|||+.+....|+.|++
T Consensus       161 ~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~~  238 (238)
T TIGR02393       161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFLD  238 (238)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhhC
Confidence            888889999999999999999999999999887788999999999999999999999999999999999999999875

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.

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=2.8e-45  Score=373.90  Aligned_cols=262  Identities=26%  Similarity=0.418  Sum_probs=226.5

Q ss_pred             CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHH
Q 009803          212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM  290 (525)
Q Consensus       212 d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~L  290 (525)
                      +..+ ||+++ +++|+||+++|.+|+++++.                                       .|+..|+++|
T Consensus         6 ~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~---------------------------------------~gd~~A~~~L   45 (289)
T PRK07500          6 SADRSMIRSA-MKAPYLEREEEHALAYRWKD---------------------------------------HRDEDALHRI   45 (289)
T ss_pred             hHHHHHHHHH-hcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHH
Confidence            4566 99999 99999999999999987752                                       1457899999


Q ss_pred             HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHH-
Q 009803          291 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE-  369 (525)
Q Consensus       291 v~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~-  369 (525)
                      |..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++++++++++|+|.+... 
T Consensus        46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~  125 (289)
T PRK07500         46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQK  125 (289)
T ss_pred             HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999765 


Q ss_pred             -HHHHHHHHHHHHHH---HcCCCCCHHHHHHHcCCCHHHHHHHH-hCCCCCCCcccccccccCC--CCCcccCCCCCCCH
Q 009803          370 -ATYRVKEARKQLYS---ENGRHPNNEEVAEATGLSMKRLHAVL-LSPKAPRSLDQKIGINQNL--KPSEVIADPEAETA  442 (525)
Q Consensus       370 -~~~ki~ka~~~L~~---~lgr~Pt~eEIA~~lgis~~~v~~~l-~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~p  442 (525)
                       ...++++.+..+.+   .+|+.||.+|||+.||+++++|..+. .....++|||.+++++++.  ++.+.++++.. +|
T Consensus       126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~~~-~p  204 (289)
T PRK07500        126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP-LP  204 (289)
T ss_pred             HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCCCC-Cc
Confidence             45566666666655   68999999999999999999998875 3455799999998765443  46777877643 56


Q ss_pred             HHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          443 EDLLIK----KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       443 ee~~~~----~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      ++.+..    ......|..+|+.||++||.||.+||+..  +++|++|||+.||||++||+|++++|++|||..+...
T Consensus       205 e~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~~--~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~~  280 (289)
T PRK07500        205 DEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRE--DGATLEALGEELGISKERVRQIEARALEKLRRALLSQ  280 (289)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            665443    34567799999999999999999999732  2399999999999999999999999999999988754

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=4.3e-45  Score=371.60  Aligned_cols=261  Identities=28%  Similarity=0.440  Sum_probs=223.8

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHH
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e  288 (525)
                      +.+++. |++++ +++|+||.++|.+|+.+++.                                       .|+..|++
T Consensus        12 ~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a~~   51 (284)
T PRK06596         12 PEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEAAK   51 (284)
T ss_pred             CccHHHHHHHHH-hccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHHHH
Confidence            457888 99999 99999999999999887542                                       25578999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (525)
Q Consensus       289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~  368 (525)
                      .||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++++++++||+|.+..
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            99999999999999999999999999999999999999999999999999999999999999999999988999999864


Q ss_pred             --HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh-CCCCCCCcccccccccC--CCCCcccCCCCCCCHH
Q 009803          369 --EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQN--LKPSEVIADPEAETAE  443 (525)
Q Consensus       369 --~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~-~~~~~~SLD~~i~~d~~--~~l~d~l~d~~~~~pe  443 (525)
                        ....++++....+.  .+++||.+|||+.||+++++|..++. ....++|||.+++++++  .++.+.++++. .+|+
T Consensus       132 ~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~~-~~p~  208 (284)
T PRK06596        132 QRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKS-SDPA  208 (284)
T ss_pred             HHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCCC-CCch
Confidence              23445555555543  35999999999999999999999875 34578999999865532  34667777763 4677


Q ss_pred             HHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          444 DLLIKK----FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       444 e~~~~~----~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      +.+...    .+...|..+|+.||++||.||.+||+.+  +++|++|||+.||||++||||++.+|++|||..+..
T Consensus       209 ~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~~--~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~~  282 (284)
T PRK06596        209 DVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD--DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA  282 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            766654    3577899999999999999999999853  459999999999999999999999999999997754

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=100.00  E-value=2.1e-44  Score=372.88  Aligned_cols=268  Identities=36%  Similarity=0.573  Sum_probs=249.2

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHH
Q 009803          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  289 (525)
Q Consensus       211 ~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~  289 (525)
                      .|... ||.+| +..|+||+++|..|..+++.                                        |+..|++.
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            56778 99999 99999999999999887763                                        56789999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHH
Q 009803          290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE  369 (525)
Q Consensus       290 Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~  369 (525)
                      ||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||++|.++++++.+.+|+|.++.+
T Consensus        91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~~~  170 (325)
T PRK05657         91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK  170 (325)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHH
Q 009803          370 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK  449 (525)
Q Consensus       370 ~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~  449 (525)
                      .++.+.++.+.+...+|+.|+.+|||+.+|+++++|..++.......|||.++..+...++.+.+.++...+|++.+...
T Consensus       171 ~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~  250 (325)
T PRK05657        171 ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDD  250 (325)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHHHHHH
Confidence            99989999999999999999999999999999999999998888889999998776666777888877666899998888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhh
Q 009803          450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLM  519 (525)
Q Consensus       450 ~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~  519 (525)
                      +....|..+|..||+++|.||.+|||+.+.+.+|++|||+.||||+++|++++++|+++||+.+...++.
T Consensus       251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~  320 (325)
T PRK05657        251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS  320 (325)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            8889999999999999999999999876666699999999999999999999999999999999877664

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=1.8e-44  Score=364.38  Aligned_cols=257  Identities=29%  Similarity=0.489  Sum_probs=217.0

Q ss_pred             HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHH
Q 009803          213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI  291 (525)
Q Consensus       213 ~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv  291 (525)
                      ++. ||+++ +++|+|++++|.+|+.++..                                       .|+..|++.||
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 99999999999999886532                                       25678999999


Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH--H
Q 009803          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV--E  369 (525)
Q Consensus       292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~--~  369 (525)
                      ..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++++++|+|.+..  +
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            99999999999999999999999999999999999999999999999999999999999999999988999998764  3


Q ss_pred             HHHHHHHHHHHHHHHcCCCC-CHHHHHHHcCCCHHHHHHHHh-CCCCCCCcccccccccCC--CCCcccCCCCCCCHHHH
Q 009803          370 ATYRVKEARKQLYSENGRHP-NNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDL  445 (525)
Q Consensus       370 ~~~ki~ka~~~L~~~lgr~P-t~eEIA~~lgis~~~v~~~l~-~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~pee~  445 (525)
                      ...++++....+.  .++.| +.+|||+.||+++++|..++. ....++|||.+++++++.  .+.+.++++. .+|++.
T Consensus       122 ~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe~~  198 (270)
T TIGR02392       122 LFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPEDT  198 (270)
T ss_pred             HHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChHHH
Confidence            4555666555543  22556 699999999999999999865 334589999998765432  4556677654 367776


Q ss_pred             HHHH----HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          446 LIKK----FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       446 ~~~~----~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      +...    .+...|..+|..||++||.||.+||+.+  +++|++|||+.||||.++|+|++.+|++|||+.+.
T Consensus       199 ~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~~--~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~  269 (270)
T TIGR02392       199 LEEEQWEELQRQALANALGSLDARSRRIIEARWLDD--DKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA  269 (270)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence            6543    3567899999999999999999999753  34999999999999999999999999999998663

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

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=7.4e-44  Score=359.02  Aligned_cols=221  Identities=25%  Similarity=0.372  Sum_probs=200.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi  363 (525)
                      ..++++||.+|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+
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             ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhC--CCCCCCcccccccccCC--CCCcccCCCCC
Q 009803          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNL--KPSEVIADPEA  439 (525)
Q Consensus       364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~--~~~~~SLD~~i~~d~~~--~l~d~l~d~~~  439 (525)
                      |.++.+.+++++++...+.+++|+.||.+|||+.||+++++|.+++..  ...++|||.+++++++.  .+.+.++    
T Consensus       119 Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~d~~~----  194 (264)
T PRK07122        119 PRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDARAIADTLG----  194 (264)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCcccchhccC----
Confidence            999999999999999999999999999999999999999999998853  45789999998653322  3333333    


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                       +++..+...+....|..+|+.||+++|.||.++|+.+    +|++|||+.||||.++|++++++|+++||..+
T Consensus       195 -~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y~~~----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l  263 (264)
T PRK07122        195 -DVDAGLDQIENREALRPLLAALPERERTVLVLRFFES----MTQTQIAERVGISQMHVSRLLAKTLARLRDQL  263 (264)
T ss_pred             -CcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence             3455566667788899999999999999999999876    99999999999999999999999999999865

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=3.3e-42  Score=345.44  Aligned_cols=227  Identities=27%  Similarity=0.453  Sum_probs=201.7

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~-g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~  360 (525)
                      ++..|+++||..|+++|+++|++|.+. +.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.++
T Consensus        22 gd~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~  101 (256)
T PRK07408         22 PSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPT  101 (256)
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCe
Confidence            457899999999999999999999875 6679999999999999999999999999999999999999999999999999


Q ss_pred             eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh--CCCCCCCcccccccccC--CCCCcccCC
Q 009803          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQN--LKPSEVIAD  436 (525)
Q Consensus       361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~--~~~~~~SLD~~i~~d~~--~~l~d~l~d  436 (525)
                      ||+|.++...+++++++...|.+++|++||.+|||+.+|+++++|..++.  .....+|||.+++++++  ..+.+.+++
T Consensus       102 vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~~~d  181 (256)
T PRK07408        102 VRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGDLLPD  181 (256)
T ss_pred             eeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCccccccccCC
Confidence            99999999999999999999999999999999999999999999999864  34568899998865433  245666666


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      +... +..  ...+....|..+|..||+++|.||.++|+.+    +|++|||+.||||.++|++++++|++|||+.+..
T Consensus       182 ~~~~-~~~--~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~----~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~  253 (256)
T PRK07408        182 PRYR-SFQ--LAQEDRIRLQQALAQLEERTREVLEFVFLHD----LTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQP  253 (256)
T ss_pred             cccc-hhh--hhHHHHHHHHHHHHcCCHHHHHHHHHHHHCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhc
Confidence            5432 221  2334557799999999999999999999877    9999999999999999999999999999998764

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=8e-41  Score=340.20  Aligned_cols=271  Identities=37%  Similarity=0.561  Sum_probs=245.6

Q ss_pred             CCCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHH
Q 009803          207 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL  285 (525)
Q Consensus       207 ~~~~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~  285 (525)
                      +...+|.++ ||.+| +.+|.||.++|.+|..+++.                                        |+..
T Consensus         8 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~   46 (285)
T TIGR02394         8 ETRVADVTQLYLREI-GFKPLLTAEEEIAYARRALA----------------------------------------GDFE   46 (285)
T ss_pred             ccCcchHHHHHHHHH-hccCCCCHHHHHHHHHHHHc----------------------------------------CCHH
Confidence            345678999 99999 99999999999999887663                                        4578


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (525)
Q Consensus       286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~  365 (525)
                      |++.||..|.++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||+.|||+.++.+++.++.+.+++|.
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             chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803          366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  445 (525)
Q Consensus       366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~  445 (525)
                      ++...++.+.+..+.+.+.+|+.|+..++|..+|++++++..++......+|+|.++..++...+.+.+.++...+|++.
T Consensus       127 ~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~  206 (285)
T TIGR02394       127 HVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESL  206 (285)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHH
Confidence            99999999999888888899999999999999999999999999888889999988765554455566666655679999


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 009803          446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  518 (525)
Q Consensus       446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L  518 (525)
                      +...+....|..+|..||+++|.||.|+||+.+.+.+|++|||+.||||.++|++++++|+++||+.+...+.
T Consensus       207 ~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~  279 (285)
T TIGR02394       207 VQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV  279 (285)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            9999999999999999999999999999975444459999999999999999999999999999999876443

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

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=100.00  E-value=7e-41  Score=335.23  Aligned_cols=242  Identities=28%  Similarity=0.425  Sum_probs=215.4

Q ss_pred             hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 009803          221 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS  300 (525)
Q Consensus       221 ~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~  300 (525)
                      ++++|+||+++|.+|+.+++.                                        ++..|++.||..|+++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQS----------------------------------------GDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHHH
Confidence            478999999999999877653                                        4578999999999999999


Q ss_pred             HHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHH
Q 009803          301 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQ  380 (525)
Q Consensus       301 IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~  380 (525)
                      +|++|.+++.+++||+||||+|||+++++|||.+|.+|+||++|||++.|.++++++. .+|+|.++...++++.++...
T Consensus        50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~  128 (254)
T TIGR02850        50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK  128 (254)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999975 789999999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHH
Q 009803          381 LYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKV  458 (525)
Q Consensus       381 L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~pee~~~~~~~~~~L~~a  458 (525)
                      +.+++|+.||.+|||+.+|+++++|..++.....++|||.++.++++.  ++.+.+.++.. .++    .......|..+
T Consensus       129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~-~~~----~~~~~~~l~~~  203 (254)
T TIGR02850       129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN-KDS----QWLEGIALKEA  203 (254)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc-cHH----HHHhHHHHHHH
Confidence            999999999999999999999999999998888899999987544332  35566665432 222    12234578999


Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      ++.||+++|.||.+||+.+    +|++|||+.||+|+++|++++.+|++|||+.
T Consensus       204 l~~L~~rer~vi~~~~~~~----~t~~eIA~~lgis~~~V~~~~~ral~kLr~~  253 (254)
T TIGR02850       204 MKRLNEREKMILNMRFFEG----KTQMEVAEEIGISQAQVSRLEKAALKHMRKY  253 (254)
T ss_pred             HHcCCHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999866    9999999999999999999999999999975

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

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=100.00  E-value=2.6e-40  Score=332.02  Aligned_cols=227  Identities=30%  Similarity=0.422  Sum_probs=205.0

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~---~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~  358 (525)
                      ++..|+++||..|+++|+++|++|.+   .+++++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++.
T Consensus        20 ~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~   99 (257)
T PRK05911         20 QEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD   99 (257)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            45789999999999999999999862   456899999999999999999999999999999999999999999999987


Q ss_pred             cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCC--CCCCccccccc--cc--CCCCCc
Q 009803          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK--APRSLDQKIGI--NQ--NLKPSE  432 (525)
Q Consensus       359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~--~~~SLD~~i~~--d~--~~~l~d  432 (525)
                      |   +|.++.+.++++.++...|.+.+|+.||.+|||+.+|+++++|..++....  .++|||.++..  ++  +.++.+
T Consensus       100 ~---~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~  176 (257)
T PRK05911        100 W---VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE  176 (257)
T ss_pred             C---CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence            7   899999999999999999999999999999999999999999999986543  46899987643  11  234677


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .++|+....|++.+...+....|..+|+.||+++|.||.++|+.+    +|++|||+.||||.++|++++++|+++||+.
T Consensus       177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y~e~----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~  252 (257)
T PRK05911        177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKLRAT  252 (257)
T ss_pred             hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            788776667888888888889999999999999999999999877    9999999999999999999999999999998


Q ss_pred             Hhh
Q 009803          513 KRT  515 (525)
Q Consensus       513 l~~  515 (525)
                      +..
T Consensus       253 l~~  255 (257)
T PRK05911        253 LSA  255 (257)
T ss_pred             HHh
Confidence            753

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=100.00  E-value=3.5e-39  Score=323.51  Aligned_cols=242  Identities=28%  Similarity=0.444  Sum_probs=214.7

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 009803          222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  301 (525)
Q Consensus       222 ~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~I  301 (525)
                      .++|+|+++|+..|+.+++.                                        ++..|+++||..|.++|+++
T Consensus        14 ~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~~   53 (258)
T PRK08215         14 SKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLSV   53 (258)
T ss_pred             CCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHHH
Confidence            66899999999998877653                                        45789999999999999999


Q ss_pred             HHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHH
Q 009803          302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL  381 (525)
Q Consensus       302 A~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L  381 (525)
                      |++|.+++.+++||+|||++|||+++++|||.+|++|+||+++||+++|.++++++. .+|+|.++.....++.++...+
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            999999999999999999999999999999999999999999999999999999985 7899999999999999999999


Q ss_pred             HHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009803          382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKVL  459 (525)
Q Consensus       382 ~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL  459 (525)
                      .+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++.  ++.+.++++.. .++..    .....|..+|
T Consensus       133 ~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~~~~~----~~~~~l~~~l  207 (258)
T PRK08215        133 INENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-KDENW----LEEIALKEAM  207 (258)
T ss_pred             HHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-cHHHH----HhHHHHHHHH
Confidence            99999999999999999999999999988777888999988655432  24555555432 22222    2345788999


Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      +.||++++.||.++|+.+    +|++|||+.||||.++|++++++|+++||+.+
T Consensus       208 ~~L~~~er~vi~~~~~~~----~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l  257 (258)
T PRK08215        208 KKLNDREKLILNLRFFQG----KTQMEVAEEIGISQAQVSRLEKAALKHMRKYI  257 (258)
T ss_pred             HcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999866    99999999999999999999999999999865

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

Probab=100.00  E-value=1.5e-38  Score=315.43  Aligned_cols=222  Identities=31%  Similarity=0.477  Sum_probs=202.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGM-NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~-~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~  360 (525)
                      ++..++ .||+.|+|||.++|++|.+++. +.+||+|-|++||++|+++|||++|.+|+|||...|+++|.+++|++. .
T Consensus        21 g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~   98 (247)
T COG1191          21 GDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-S   98 (247)
T ss_pred             cCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-C
Confidence            457888 9999999999999999998877 999999999999999999999999999999999999999999999999 8


Q ss_pred             eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCC--CCCCCcccccccccCCCCCcccCCCC
Q 009803          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPE  438 (525)
Q Consensus       361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~d~~  438 (525)
                      +++|.++.+..+++..+...+.+++||+||++|||+.+|++.+++..++...  ...+|+|..+..+++..     .++.
T Consensus        99 v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~-----~~~~  173 (247)
T COG1191          99 VKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD-----VDDQ  173 (247)
T ss_pred             ccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc-----hhhc
Confidence            9999999999999999999999999999999999999999999999998765  36788887765443333     2223


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ..+|.+.+...+....|.+++..|++|||.||.+||..+    +|++|||++||||..+|+|++.+|++|||+.+.
T Consensus       174 ~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~ee----lt~kEI~~~LgISes~VSql~kkai~kLr~~l~  245 (247)
T COG1191         174 IENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVSRLHKKAIKKLRKELN  245 (247)
T ss_pred             cccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc----cCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhc
Confidence            346778888888888899999999999999999999988    999999999999999999999999999999775

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=100.00  E-value=5.1e-38  Score=316.91  Aligned_cols=249  Identities=24%  Similarity=0.355  Sum_probs=222.0

Q ss_pred             hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 009803          221 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS  300 (525)
Q Consensus       221 ~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~  300 (525)
                      +|++|+||+++|.+|+.+++.                                       .++..+++.|+..|.++|+.
T Consensus         6 ~~~~~~~~~~~e~~l~~~~~~---------------------------------------~~d~~a~~~l~~~y~~lv~~   46 (268)
T PRK06288          6 SGKIPKYAQQDETELWREYKK---------------------------------------TGDPKIREYLILKYSPLVKY   46 (268)
T ss_pred             cCCCccccchHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHH
Confidence            588999999999999987663                                       14578999999999999999


Q ss_pred             HHHHhh-C--CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHH
Q 009803          301 IAKNYQ-G--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEA  377 (525)
Q Consensus       301 IA~~y~-~--~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka  377 (525)
                      +|++|. +  .+.+++||+||||+|||+++++|||.+|++|+||++||||+.|.+++++..   ++|.++....++++++
T Consensus        47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~~---~~p~~~~~~~~~i~~~  123 (268)
T PRK06288         47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSID---WIPRSVRQKARQIERA  123 (268)
T ss_pred             HHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---ccCHHHHHHHHHHHHH
Confidence            999986 2  567899999999999999999999999999999999999999999999764   4899999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCC--CCCCCccccccccc---CCCCCcccCCCCCCCHHHHHHHHHHH
Q 009803          378 RKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQ---NLKPSEVIADPEAETAEDLLIKKFMK  452 (525)
Q Consensus       378 ~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~--~~~~SLD~~i~~d~---~~~l~d~l~d~~~~~pee~~~~~~~~  452 (525)
                      ...|.+++|+.||.+|||+.+|++.+++..++...  ...+|||..+..++   ...+.+.++++...+|++.+...+..
T Consensus       124 ~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~  203 (268)
T PRK06288        124 IAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIK  203 (268)
T ss_pred             HHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999988543  46789998764221   23456777777677899988888888


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      ..|..+|+.||+++|.||.++|+.+    +|++|||+.||+|.++|++++++|+++||.++..
T Consensus       204 ~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  262 (268)
T PRK06288        204 RVIVEAIKTLPEREKKVLILYYYED----LTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAE  262 (268)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999887    9999999999999999999999999999998864

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=100.00  E-value=2.8e-37  Score=309.01  Aligned_cols=245  Identities=26%  Similarity=0.347  Sum_probs=216.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHH
Q 009803          224 SRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAK  303 (525)
Q Consensus       224 ~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~  303 (525)
                      .|.||+++|.+|..+++.                                       .++..|+++||..|.++|+.+|+
T Consensus         7 ~~~l~~~~~~~li~~~~~---------------------------------------~gd~~a~~~l~~~y~~~v~~~a~   47 (255)
T TIGR02941         7 PTNLTKEDVIQWIAEFQQ---------------------------------------NQNGEAQEKLVDHYQNLVYSIAY   47 (255)
T ss_pred             CCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHHHHHHhHHHHHHHHH
Confidence            367999999988877663                                       13578999999999999999999


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHH
Q 009803          304 NYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYS  383 (525)
Q Consensus       304 ~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~  383 (525)
                      +|.+++.+++||+||||+|||+++++||+..|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+.+
T Consensus        48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~  127 (255)
T TIGR02941        48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTD  127 (255)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HcCCCCCHHHHHHHcCCCHHHHHHHHhC--CCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q 009803          384 ENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT  461 (525)
Q Consensus       384 ~lgr~Pt~eEIA~~lgis~~~v~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~  461 (525)
                      .+|+.|+.+|||+.+|++.+++..++..  .....|||.+++.+++......+ +. ..+|++.+...+....+..+|+.
T Consensus       128 ~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~e~~~~l~~~l~~  205 (255)
T TIGR02941       128 HLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARL-DS-VGEVEDGYDQTERRMVLEKILPI  205 (255)
T ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccc-cc-cCCcchHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999999888754  34678999988765443322221 11 12456666677777889999999


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      ||+++|.||.++|+.+    +|++|||+.||||.++|++++++|+++||+.+
T Consensus       206 L~~~~r~ii~l~~~~g----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~  253 (255)
T TIGR02941       206 LSEREKSIIHCTFEEN----LSQKETGERLGISQMHVSRLQRQAISKLKEAA  253 (255)
T ss_pred             CCHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999877    99999999999999999999999999999865

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

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=100.00  E-value=3.8e-37  Score=303.38  Aligned_cols=223  Identities=32%  Similarity=0.487  Sum_probs=199.1

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803          281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (525)
Q Consensus       281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~  360 (525)
                      .++..|+++||..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .
T Consensus         7 ~gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~   85 (231)
T TIGR02885         7 NGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-I   85 (231)
T ss_pred             cCCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-C
Confidence            466889999999999999999999999999999999999999999999999999999999999999999999999986 7


Q ss_pred             eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCC--CCCcccCCCC
Q 009803          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPE  438 (525)
Q Consensus       361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~  438 (525)
                      +++|.++...+++++++...+..++|+.||.+|||+.+|++++++..++.....+.|||.+++++++.  ++.+.+.++.
T Consensus        86 i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~  165 (231)
T TIGR02885        86 IKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIADKG  165 (231)
T ss_pred             eECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhhcCCCC
Confidence            99999999999999999999999999999999999999999999999988777889999988655432  3455665543


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      .  +++..   .....|..+++.||++++.||.++|+.+    +|++|||+.||||+++|++++++|++|||..+
T Consensus       166 ~--~~~~~---~~~~~l~~~l~~L~~~e~~i~~~~~~~~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l  231 (231)
T TIGR02885       166 S--EDSDW---LEKIALKEAISKLDERERQIIMLRYFKD----KTQTEVANMLGISQVQVSRLEKKVLKKMKEKL  231 (231)
T ss_pred             c--cHHhH---HHHHHHHHHHHcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence            2  22222   2356788999999999999999999876    99999999999999999999999999999753

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

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

Probab=100.00  E-value=1.4e-36  Score=298.33  Aligned_cols=221  Identities=29%  Similarity=0.445  Sum_probs=198.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi  363 (525)
                      ..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+++++||+.+|.+|+||++|||++.|.++++++.|.+++
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             ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCC--CCCcccccccccC--CCCCcccCCCCC
Q 009803          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKA--PRSLDQKIGINQN--LKPSEVIADPEA  439 (525)
Q Consensus       364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~--~~SLD~~i~~d~~--~~l~d~l~d~~~  439 (525)
                      |.++...+++++++...+.+.+|+.|+.+|+|+.+|++.+++..++.....  +.|||.++.++++  ..+.+.+.    
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~----  157 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG----  157 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence            999999999999999999999999999999999999999999998876544  8999998763222  12333333    


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                       ++++.+........|..+|..||++++.||.++|+.+    +|++|||+.||+|+++|++++++|+++||+.+
T Consensus       158 -~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y~~~----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l  226 (227)
T TIGR02980       158 -DEDDALETVEDRLALKPLLAALPERERRILLLRFFED----KTQSEIAERLGISQMHVSRLLRRALKKLREQL  226 (227)
T ss_pred             -CcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence             3344445556677899999999999999999999877    99999999999999999999999999999864

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

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=5.3e-36  Score=299.41  Aligned_cols=226  Identities=30%  Similarity=0.358  Sum_probs=202.8

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~---~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~  358 (525)
                      ++..|++.||..|.++|+++|++|.+   ++.+.+||+||||+|||+++++|||.+|.+|+||+++||++.|.++++++.
T Consensus        19 ~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~   98 (251)
T PRK07670         19 RDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED   98 (251)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            45889999999999999999999975   678999999999999999999999999999999999999999999999876


Q ss_pred             cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh--CCCCCCCcccccccccCC-CCCcccC
Q 009803          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQNL-KPSEVIA  435 (525)
Q Consensus       359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~--~~~~~~SLD~~i~~d~~~-~l~d~l~  435 (525)
                         ++|.++.+.+++++++...+.+.+|+.|+.+|||..+|+++++|..++.  ....+.|||.++.++++. .+.+.+.
T Consensus        99 ---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~  175 (251)
T PRK07670         99 ---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIR  175 (251)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhc
Confidence               4899999999999999999999999999999999999999999999985  456789999987654432 2233444


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      +....+|++.+...+....|..+|..||+++|.||.++|+.+    +|++|||+.||+|.++|+++++||+++||.++.
T Consensus       176 ~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~  250 (251)
T PRK07670        176 DDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEE----LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE  250 (251)
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            555557888888888888999999999999999999999877    999999999999999999999999999998764

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=2.7e-35  Score=295.02  Aligned_cols=248  Identities=25%  Similarity=0.329  Sum_probs=215.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHH
Q 009803          223 SSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA  302 (525)
Q Consensus       223 ~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA  302 (525)
                      ..|.|++++|.+|..+++.                                       .++..|+++||..|.++|+++|
T Consensus         6 ~~~~l~~~e~~~li~~~~~---------------------------------------~gd~~a~~~l~~~~~~~v~~~a   46 (257)
T PRK08583          6 QPTKLTKEEVNKWIAEYQE---------------------------------------NQDEEAQEKLVKHYKNLVESLA   46 (257)
T ss_pred             cCCcCChHHHHHHHHHHHH---------------------------------------cCCHHHHHHHHHHHHHHHHHHH
Confidence            3478999999888776653                                       1457899999999999999999


Q ss_pred             HHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHH
Q 009803          303 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLY  382 (525)
Q Consensus       303 ~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~  382 (525)
                      ++|.+++.+++||+||||+|||+++++||+.+|.+|+||+++||++.|.++++++.|.+++|.+.....++++++...+.
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            99999999999999999999999999999999989999999999999999999999999999999999999999999999


Q ss_pred             HHcCCCCCHHHHHHHcCCCHHHHHHHHhCC--CCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHh
Q 009803          383 SENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD  460 (525)
Q Consensus       383 ~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~  460 (525)
                      ..+++.|+.+++|+.+|++.+++..+....  ..+.|+|.+++.+++.....+. + ...+|++.+...+....|..+|.
T Consensus       127 ~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~-~-~~~~~e~~~~~~~~~~~l~~~l~  204 (257)
T PRK08583        127 TELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLL-D-IVGQQEDGYELTEQRMILEKILP  204 (257)
T ss_pred             HHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHh-h-hcCCcchhHHHHHHHHHHHHHHH
Confidence            999999999999999999999998877543  4678999887654332111111 1 11245566666677788999999


Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      .||+++|.||.++|+.+    +|++|||+.||||.++|++++++|+++||+.+..
T Consensus       205 ~L~~~~r~vl~l~~~~g----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~  255 (257)
T PRK08583        205 VLSDREKSIIQCTFIEN----LSQKETGERLGISQMHVSRLQRQAIKKLREAAFL  255 (257)
T ss_pred             hCCHHHHHHHHHHHhCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999887    9999999999999999999999999999998754

>PRK05572 sporulation sigma factor SigF; Validated

Probab=100.00  E-value=4.4e-35  Score=292.89  Aligned_cols=241  Identities=29%  Similarity=0.452  Sum_probs=211.0

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 009803          222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  301 (525)
Q Consensus       222 ~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~I  301 (525)
                      .+.|.||.+++.+|..+++.                                        ++..|+++||..|.++|+++
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            56899999999888765542                                        45789999999999999999


Q ss_pred             HHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHH
Q 009803          302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL  381 (525)
Q Consensus       302 A~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L  381 (525)
                      |++|.+++.+++||+|||++++|+++++|++.+|.+|.||+++||++.|.+++++.. .+|+|.++....++++++...+
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            999999999999999999999999999999998889999999999999999999885 7899999999999999999999


Q ss_pred             HHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHHH
Q 009803          382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKVL  459 (525)
Q Consensus       382 ~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL  459 (525)
                      ..++|+.|+..|+|+.+|++++++..++.....+.||+.++.+++..  +..+.+.++..   +.    ......|..+|
T Consensus       128 ~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~~---~~----~~~~~~l~~~l  200 (252)
T PRK05572        128 SKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQSE---ED----WFDKIALKEAI  200 (252)
T ss_pred             HHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCch---hh----HHHHHHHHHHH
Confidence            99999999999999999999999999988777889999887654322  22344443221   11    22356789999


Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      +.||++++.||.++|+.+    +|++|||+.+|+|.++|++++++|+++||..+.
T Consensus       201 ~~L~~~~~~v~~l~~~~~----~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~  251 (252)
T PRK05572        201 RELDERERLIVYLRYFKD----KTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD  251 (252)
T ss_pred             HcCCHHHHHHHHHHHhCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999866    999999999999999999999999999998764

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

Probab=100.00  E-value=2.7e-35  Score=289.09  Aligned_cols=217  Identities=30%  Similarity=0.467  Sum_probs=195.5

Q ss_pred             HHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803          290 MITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (525)
Q Consensus       290 Lv~~nlrLV~~IA~~y~~---~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~  366 (525)
                      |+..|.++|+++|++|.+   ++.+++||+|||++|||+++++|||.+|++|+||+++||++.|.+++++..   ++|.+
T Consensus         1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~   77 (224)
T TIGR02479         1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS   77 (224)
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence            588999999999999986   789999999999999999999999999999999999999999999999875   48999


Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh--CCCCCCCcccccccc-cCCCCCcccCCCCCCCHH
Q 009803          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGIN-QNLKPSEVIADPEAETAE  443 (525)
Q Consensus       367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~--~~~~~~SLD~~i~~d-~~~~l~d~l~d~~~~~pe  443 (525)
                      +...++++.++...+.+.+|+.|+.+|||+.+|+++++|..++.  .....+|+|....++ +..++.+.++++...+|+
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE  157 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence            99999999999999999999999999999999999999999985  345577888766533 233455666655566888


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      +.+...+....|..+|+.||+++|+||.++|+.+    +|++|||+.||+|.++|++++++|+++||+++
T Consensus       158 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y~~~----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l  223 (224)
T TIGR02479       158 EELEREELREALAEAIESLSEREQLVLSLYYYEE----LNLKEIGEVLGLTESRVSQIHSQALKKLRAKL  223 (224)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence            8888888889999999999999999999999887    99999999999999999999999999999865

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

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=100.00  E-value=1.5e-34  Score=286.15  Aligned_cols=210  Identities=20%  Similarity=0.364  Sum_probs=182.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccccee
Q 009803          286 CKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  362 (525)
Q Consensus       286 A~e~Lv~~nlrLV~~IA~~y~~---~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iR  362 (525)
                      -...|+..|+++|.++|++|.+   .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..|   
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            4567899999999999999875   4679999999999999999999998666 89999999999999999998776   


Q ss_pred             cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhC--CCCCCCcccccccccCCCCCcccCCCCCC
Q 009803          363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIADPEAE  440 (525)
Q Consensus       363 iP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~d~~~~  440 (525)
                      +|.++...+++++++...+.+++|+.||.+|||+.+|+++++|..++..  .....|||.+++++++.   +.+++   .
T Consensus        92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~---~~~~~---~  165 (231)
T PRK12427         92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN---DILQS---R  165 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCcc---cccCC---C
Confidence            6888888999999999999999999999999999999999999998753  45789999998665432   22222   2


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .+++..   .....|..++..||+++|.||.++|+.+    +|++|||+.||||.++|+|++.+|++|||.+
T Consensus       166 ~~~~~~---~~~~~l~~~l~~L~~~er~vi~l~~~~~----~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~  230 (231)
T PRK12427        166 DLEENI---IIEDNLKQALSQLDEREQLILHLYYQHE----MSLKEIALVLDLTEARICQLNKKIAQKIKSF  230 (231)
T ss_pred             CHHHHH---HHHHHHHHHHHcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            344332   2455789999999999999999999876    9999999999999999999999999999964

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=100.00  E-value=7.4e-34  Score=281.20  Aligned_cols=225  Identities=30%  Similarity=0.435  Sum_probs=198.6

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~---~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~  358 (525)
                      .|.-++++|+..|.++|+++|++|.   +++.+++||+||||+|||+++++|||.+|.+|+||+++||++.|.++++++.
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            4567899999999999999999997   6789999999999999999999999999999999999999999999999987


Q ss_pred             cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhC--CCCCCCcccccccccCCCCCcccCC
Q 009803          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIAD  436 (525)
Q Consensus       359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~d  436 (525)
                      +   +|.++....+++.++...+.+.+|++|+.+|||+.+|++.++|..++..  ...++|++..++++++. +.. ..+
T Consensus        85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~-~~~-~~~  159 (236)
T PRK06986         85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDS-ILV-TED  159 (236)
T ss_pred             C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcc-ccc-ccC
Confidence            5   6888888888899999999999999999999999999999999998864  34567888887654443 222 223


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      +...+|++.+...+....|..+|+.||+++|.||.++|+.+    +|++|||+.||||.++|+++++||+++||+.+..
T Consensus       160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  234 (236)
T PRK06986        160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEE----LNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGE  234 (236)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            33457888888888889999999999999999999999877    9999999999999999999999999999997753

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.96  E-value=3.3e-28  Score=240.58  Aligned_cols=209  Identities=29%  Similarity=0.484  Sum_probs=168.0

Q ss_pred             HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHH
Q 009803          213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI  291 (525)
Q Consensus       213 ~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv  291 (525)
                      .+. |+.++ ++.|+||+++|..|...++.                                        ++..|++.|+
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 99999999999988766542                                        4578999999


Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT  371 (525)
Q Consensus       292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~  371 (525)
                      ..|.++|+++|.+|.+++.+++||+|||++++|+++++||+++|.+|.||+++|+|+.+.++++++.+..+         
T Consensus        56 ~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~---------  126 (233)
T PRK05803         56 ERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKK---------  126 (233)
T ss_pred             HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence            99999999999999999999999999999999999999999889999999999999999999987643100         


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccccc---CCCCCcccCCCCCCCHHHHHHH
Q 009803          372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ---NLKPSEVIADPEAETAEDLLIK  448 (525)
Q Consensus       372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~---~~~l~d~l~d~~~~~pee~~~~  448 (525)
                                                                 ..+++...+.++   ..++.+..++. .+++++.+..
T Consensus       127 -------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  162 (233)
T PRK05803        127 -------------------------------------------EVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVEL  162 (233)
T ss_pred             -------------------------------------------CCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHH
Confidence                                                       011111111010   11122223322 2357777777


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      +.....|..+|+.||+++|+||.++|+.++.+.+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus       163 ~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~  229 (233)
T PRK05803        163 KMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYR  229 (233)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            7778889999999999999999999975433449999999999999999999999999999998765

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.94  E-value=5.7e-25  Score=217.24  Aligned_cols=180  Identities=28%  Similarity=0.498  Sum_probs=137.5

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||+++++||.+.++++++.+..
T Consensus        49 gd~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~  128 (234)
T PRK08301         49 GDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVK  128 (234)
T ss_pred             cCHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            55789999999999999999999999999999999999999999999999988889999999999999999998765410


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccc--ccC-CCCCcccCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI--NQN-LKPSEVIADPE  438 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~--d~~-~~l~d~l~d~~  438 (525)
                      .                                                    ..+++.+...  ++. ....+...+. 
T Consensus       129 ~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-  155 (234)
T PRK08301        129 A----------------------------------------------------EVSFDEPLNIDWDGNELLLSDVLGTD-  155 (234)
T ss_pred             c----------------------------------------------------ccccccccccccCCCcccHHHhccCc-
Confidence            0                                                    0111111100  000 0011111111 


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ...++..+........|..+|+.||+++|.||.|+|++...+.+|++|||+.||||.++|+++++||+++||+.+.
T Consensus       156 ~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~  231 (234)
T PRK08301        156 NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN  231 (234)
T ss_pred             ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            1233344444555667999999999999999999995211111999999999999999999999999999999765

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.94  E-value=7.5e-25  Score=215.93  Aligned_cols=205  Identities=28%  Similarity=0.489  Sum_probs=157.3

Q ss_pred             HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHH
Q 009803          216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI  295 (525)
Q Consensus       216 yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nl  295 (525)
                      |.-.-.+..+.|++.+|.+|..+++.                                        ++..|++.|+..|.
T Consensus        19 ~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~af~~l~~~y~   58 (227)
T TIGR02846        19 YVTNNGSFPQPLSEEEEKKYLDRLKE----------------------------------------GDEEARNVLIERNL   58 (227)
T ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhH
Confidence            54333266778999998888776653                                        45789999999999


Q ss_pred             HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHH
Q 009803          296 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK  375 (525)
Q Consensus       296 rLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~  375 (525)
                      ++|+++|.+|.++..+++||+||+|+++|+++++|+++.+.+|.||+++|+++.|.+++++..+..+             
T Consensus        59 ~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~-------------  125 (227)
T TIGR02846        59 RLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKG-------------  125 (227)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhcccc-------------
Confidence            9999999999999999999999999999999999999888899999999999999999987653100             


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccccc---CCCCCcccCCCCCCCHHHHHHHHHHH
Q 009803          376 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ---NLKPSEVIADPEAETAEDLLIKKFMK  452 (525)
Q Consensus       376 ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~---~~~l~d~l~d~~~~~pee~~~~~~~~  452 (525)
                                                             ..+++...+.+.   .....+...+ ...++++........
T Consensus       126 ---------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  165 (227)
T TIGR02846       126 ---------------------------------------EVSLQDPIGVDKEGNEISLIDILGS-DGDSVIEQVELNLEI  165 (227)
T ss_pred             ---------------------------------------ceeccccccCCcccCcccHHHHhcC-CCCChHHHHHHHHHH
Confidence                                                   011111110000   0011112221 123566666666666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      ..|..+|+.||+++|+||.++|.++..+.+|++|||++||+|.++|++++++|+++||+.+
T Consensus       166 ~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~  226 (227)
T TIGR02846       166 KKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL  226 (227)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            7899999999999999999999732112299999999999999999999999999999864

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=99.93  E-value=5.7e-24  Score=210.59  Aligned_cols=180  Identities=30%  Similarity=0.517  Sum_probs=139.1

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++..|++.|+..|.+.|+++|++|.+++.+++|++||+++++|+++++|++..+++|.||++.+++|.+.++++++.+..
T Consensus        49 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~  128 (234)
T TIGR02835        49 GDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTR  128 (234)
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhcccc
Confidence            55889999999999999999999999999999999999999999999999988889999999999999999999865410


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccc--ccC-CCCCcccCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI--NQN-LKPSEVIADPE  438 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~--d~~-~~l~d~l~d~~  438 (525)
                      .                                                    ..+++..+..  +++ ....+. .++.
T Consensus       129 ~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~-~~~~  155 (234)
T TIGR02835       129 S----------------------------------------------------EVSFDEPLNVDWDGNELLLSDV-LGTD  155 (234)
T ss_pred             C----------------------------------------------------cccccccccCCCCCCcchHHHh-cCCC
Confidence            0                                                    0111111100  000 000111 1112


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ...+++.+........|..+|+.||+++|.||.++|++.+++.+|++|||+.||||..+|+++.+||+++||+.+.
T Consensus       156 ~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~  231 (234)
T TIGR02835       156 SDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEIN  231 (234)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence            2234444555556678999999999999999999996322223999999999999999999999999999999775

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

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.91  E-value=6.4e-23  Score=197.91  Aligned_cols=189  Identities=24%  Similarity=0.309  Sum_probs=144.8

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      .....++..|++.|+..|.++|+.+|++|.++..+++|++||++++||+++.+||+.++.+|.||++.++++.+.+++++
T Consensus        16 ~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~~r~   95 (208)
T PRK08295         16 ELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKT   95 (208)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHH
Confidence            33445669999999999999999999999999999999999999999999999999887899999999999999999886


Q ss_pred             cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccc-ccCCCCCcccC
Q 009803          357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI-NQNLKPSEVIA  435 (525)
Q Consensus       357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~-d~~~~l~d~l~  435 (525)
                      ..+..+.|.                                               ....|++..+.+ +.+..+.+.+.
T Consensus        96 ~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~~~~~~~~  128 (208)
T PRK08295         96 ANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDRTLLDVIS  128 (208)
T ss_pred             hhhhccccc-----------------------------------------------cceeecCCcccCCccchhHHHHhc
Confidence            543211110                                               011222222211 11112223333


Q ss_pred             CCCCCCHHHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          436 DPEAETAEDLLIKKFMKEDL-EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       436 d~~~~~pee~~~~~~~~~~L-~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ++...+|++.+........+ ..+++.||+++|.||.+ |..+    +|++|||+.||+|.++|+.+++||+++||+++.
T Consensus       129 ~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~e~----~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~  203 (208)
T PRK08295        129 EAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YLDG----KSYQEIAEELNRHVKSIDNALQRVKRKLEKYLE  203 (208)
T ss_pred             CcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            33334677766555555555 45679999999999999 8776    999999999999999999999999999999886


Q ss_pred             hch
Q 009803          515 TKH  517 (525)
Q Consensus       515 ~~~  517 (525)
                      ...
T Consensus       204 ~~~  206 (208)
T PRK08295        204 NRE  206 (208)
T ss_pred             hhc
Confidence            543

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.90  E-value=3.3e-22  Score=190.21  Aligned_cols=170  Identities=15%  Similarity=0.229  Sum_probs=140.5

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803          276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  355 (525)
Q Consensus       276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir  355 (525)
                      +.....++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.++++
T Consensus        11 ~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~d~~R   89 (186)
T PRK05602         11 LARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCYDRLR   89 (186)
T ss_pred             HHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHHHHHH
Confidence            3445556699999999999999999999999999999999999999999999999986 458999999999999999998


Q ss_pred             hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803          356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  435 (525)
Q Consensus       356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  435 (525)
                      ++...                                                        +.+.         ..+ ..
T Consensus        90 ~~~~~--------------------------------------------------------~~~~---------~~~-~~  103 (186)
T PRK05602         90 RRREV--------------------------------------------------------PVED---------APD-VP  103 (186)
T ss_pred             hcCCC--------------------------------------------------------Cccc---------ccc-cC
Confidence            66420                                                        0000         000 01


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      +. ...+++.+...+....+..+|+.||+++|.||.++|..+    +|++|||+.||+|..+|+++++||+++||+.+..
T Consensus       104 ~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  178 (186)
T PRK05602        104 DP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQG----LSNIEAAAVMDISVDALESLLARGRRALRAQLAD  178 (186)
T ss_pred             CC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence            11 124566666666677899999999999999999999887    9999999999999999999999999999998876


Q ss_pred             ch
Q 009803          516 KH  517 (525)
Q Consensus       516 ~~  517 (525)
                      .+
T Consensus       179 ~~  180 (186)
T PRK05602        179 LP  180 (186)
T ss_pred             cc
Confidence            44

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.90  E-value=3.5e-22  Score=191.80  Aligned_cols=174  Identities=14%  Similarity=0.169  Sum_probs=138.9

Q ss_pred             HHHHH-HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803          274 RELRR-RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  352 (525)
Q Consensus       274 ~~L~~-~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~  352 (525)
                      ..|.. ...++..++++|+..|.++|+++|.+|.++..+++|++||+|+++|+++.+||+.+| .|.+|++..+++.+.+
T Consensus        18 ~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d   96 (194)
T PRK09646         18 DALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVD   96 (194)
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHH
Confidence            34444 444569999999999999999999999999999999999999999999999998765 6999999999999999


Q ss_pred             HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803          353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE  432 (525)
Q Consensus       353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d  432 (525)
                      +++++.+..+.                                                       +....   ..   +
T Consensus        97 ~~r~~~~~~~~-------------------------------------------------------~~~~~---~~---~  115 (194)
T PRK09646         97 RVRSEQAASQR-------------------------------------------------------EVRYG---AR---N  115 (194)
T ss_pred             HHHhhcccccc-------------------------------------------------------ccccc---cc---c
Confidence            99876531110                                                       00000   00   0


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .  +.....+++.+...+....|..+|..||+++|.||.|+|..|    +|++|||+.||+|..+|+++++||+++||++
T Consensus       116 ~--~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~  189 (194)
T PRK09646        116 V--DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGG----LTYREVAERLAVPLGTVKTRMRDGLIRLRDC  189 (194)
T ss_pred             c--cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence            0  001113444444455567899999999999999999999887    9999999999999999999999999999998


Q ss_pred             Hhh
Q 009803          513 KRT  515 (525)
Q Consensus       513 l~~  515 (525)
                      +..
T Consensus       190 l~~  192 (194)
T PRK09646        190 LGV  192 (194)
T ss_pred             hcc
Confidence            753

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.89  E-value=4.7e-22  Score=188.36  Aligned_cols=180  Identities=15%  Similarity=0.237  Sum_probs=142.3

Q ss_pred             HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803          273 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  352 (525)
Q Consensus       273 ~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~  352 (525)
                      ...+.....++..|+.+|+..|.++|+.+|++|.+++.+++|++||+++++|+++.+|++..  .|.+|++..+++.+.+
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            34455556677999999999999999999999999999999999999999999999999865  6999999999999999


Q ss_pred             HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803          353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE  432 (525)
Q Consensus       353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d  432 (525)
                      ++++..+...                                                       ++.....++...+.+
T Consensus        84 ~~rk~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~  108 (187)
T TIGR02948        84 RLRKRKPDFY-------------------------------------------------------LDDEVQGTDGLTMES  108 (187)
T ss_pred             HHHhhccccc-------------------------------------------------------ccccccCcccccccc
Confidence            9886432100                                                       000000000111111


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      ...+ ..+.|++.+...+....+..+|..||+++|.||.++|..|    +|++|||+.||+|.++|+++++||+++||..
T Consensus       109 ~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  183 (187)
T TIGR02948       109 QLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMED----LSLKEISEILDLPVGTVKTRIHRGREALRKQ  183 (187)
T ss_pred             cccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            1111 1235677777777777899999999999999999999877    9999999999999999999999999999997


Q ss_pred             Hh
Q 009803          513 KR  514 (525)
Q Consensus       513 l~  514 (525)
                      +.
T Consensus       184 l~  185 (187)
T TIGR02948       184 LR  185 (187)
T ss_pred             hh
Confidence            75

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

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=3.5e-22  Score=191.28  Aligned_cols=179  Identities=17%  Similarity=0.183  Sum_probs=144.6

Q ss_pred             HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803          273 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  352 (525)
Q Consensus       273 ~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~  352 (525)
                      ...+.....++..|++.|+..|.+.|+++|+++.++..+++|++||+|+++|+++++|++.  ..|.+|++.++++.+.+
T Consensus        14 ~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~~~~   91 (194)
T PRK12513         14 EALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNLLID   91 (194)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHHHHH
Confidence            3445555556699999999999999999999999999999999999999999999999974  36999999999999999


Q ss_pred             HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803          353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE  432 (525)
Q Consensus       353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d  432 (525)
                      +++++.+....+                                                     .+.    +..  . .
T Consensus        92 ~~R~~~~~~~~~-----------------------------------------------------~~~----~~~--~-~  111 (194)
T PRK12513         92 HWRRHGARQAPS-----------------------------------------------------LDA----DEQ--L-H  111 (194)
T ss_pred             HHHHhccccccc-----------------------------------------------------ccc----chh--h-h
Confidence            998776421110                                                     000    000  0 0


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      ...+ ...+|++.+...+....|..+|+.||+++|.||.|+|+.|    +|++|||+.||+|.++|+++++||+++||+.
T Consensus       112 ~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~  186 (194)
T PRK12513        112 ALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGD----LELEEIAELTGVPEETVKSRLRYALQKLREL  186 (194)
T ss_pred             hcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            0111 1235677667777778899999999999999999999887    9999999999999999999999999999998


Q ss_pred             Hhhchh
Q 009803          513 KRTKHL  518 (525)
Q Consensus       513 l~~~~L  518 (525)
                      +...++
T Consensus       187 l~~~~~  192 (194)
T PRK12513        187 LAEEVA  192 (194)
T ss_pred             HHHhhc
Confidence            876543

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.89  E-value=1.2e-21  Score=186.77  Aligned_cols=165  Identities=16%  Similarity=0.261  Sum_probs=135.7

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          281 NYGILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~----g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      .++..|+++|+..|.+.|+.+|.++.++    +.+++|++||+|+++|+++.+|++. +..|.||++..+++.+.+++++
T Consensus        20 ~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~d~~r~   98 (189)
T PRK09648         20 AGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVADAHRA   98 (189)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHH
Confidence            4558999999999999999999998865    3689999999999999999999864 4589999999999999999987


Q ss_pred             cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803          357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  436 (525)
Q Consensus       357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d  436 (525)
                      +.+....                                                     ..+         ...+... 
T Consensus        99 ~~r~~~~-----------------------------------------------------~~~---------~~~~~~~-  115 (189)
T PRK09648         99 AGRDKAV-----------------------------------------------------PTE---------EVPERPS-  115 (189)
T ss_pred             hCCCccc-----------------------------------------------------ccc---------ccccccc-
Confidence            6541100                                                     000         0000111 


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                       ...+|++.+...+....|..+|..||+++|+||.++|+.|    +|++|||+.||+|..+|+++++||+++||+.+.
T Consensus       116 -~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~  188 (189)
T PRK09648        116 -DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVG----LSAEETAEAVGSTPGAVRVAQHRALARLRAEIE  188 (189)
T ss_pred             -cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence             1225777777777778899999999999999999999987    999999999999999999999999999998763

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.89  E-value=6.1e-22  Score=189.48  Aligned_cols=189  Identities=21%  Similarity=0.262  Sum_probs=139.9

Q ss_pred             HHHHHHH-HhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHH
Q 009803          273 QRELRRR-LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  351 (525)
Q Consensus       273 ~~~L~~~-l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~  351 (525)
                      +..|... ..++..|++.||..|.+.|+++|+++.++..+++||+||+|+.+|+++.+|++..+..|.||++.+|++.+.
T Consensus         6 ~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~   85 (198)
T TIGR02859         6 DEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQII   85 (198)
T ss_pred             hHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHH
Confidence            3344444 445589999999999999999999999999999999999999999999999998878999999999999998


Q ss_pred             HHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccc-ccCCCC
Q 009803          352 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI-NQNLKP  430 (525)
Q Consensus       352 ~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~-d~~~~l  430 (525)
                      ++++...+..+.+.                                               ....|++.+... +++.++
T Consensus        86 ~~~r~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~~  118 (198)
T TIGR02859        86 TAIKTATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESDRTL  118 (198)
T ss_pred             HHHHHHHHhcccch-----------------------------------------------hhhcCcccccccccccchH
Confidence            88875422111000                                               011233322111 111112


Q ss_pred             CcccCCCCCCCHHHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803          431 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTL-NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL  509 (525)
Q Consensus       431 ~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L-~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL  509 (525)
                      .+.+.+....+|++.+...+....|.++|+.| ++.++.|+ ++|..+    +|++|||+.||+|.++|+...+||+++|
T Consensus       119 ~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~-~~~~~~----~s~~eIA~~l~~s~~tV~~~l~r~r~~L  193 (198)
T TIGR02859       119 LDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVL-QSYLDG----KSYQEIACDLNRHVKSIDNALQRVKRKL  193 (198)
T ss_pred             HHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHH-HHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            22222222346787777777778899999995 55566665 557666    9999999999999999999999999999


Q ss_pred             HhHH
Q 009803          510 KNKK  513 (525)
Q Consensus       510 R~~l  513 (525)
                      |+.+
T Consensus       194 ~~~l  197 (198)
T TIGR02859       194 EKYL  197 (198)
T ss_pred             HHhc
Confidence            9865

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.

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.89  E-value=1.3e-21  Score=185.33  Aligned_cols=175  Identities=14%  Similarity=0.183  Sum_probs=139.8

Q ss_pred             HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803          278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  357 (525)
Q Consensus       278 ~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~  357 (525)
                      ....++..+++.++..|.++|+++|+++.++..+++|++||++++||+++.+|++..  .|.+|++..+|+.+.++++++
T Consensus        11 ~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R~~   88 (187)
T PRK09641         11 QVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLRKR   88 (187)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHHhc
Confidence            334456999999999999999999999999999999999999999999999999853  799999999999999999876


Q ss_pred             ccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCC
Q 009803          358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP  437 (525)
Q Consensus       358 ~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~  437 (525)
                      .+...                                                       ++.....++.....+.+.+.
T Consensus        89 ~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~~~~~~  113 (187)
T PRK09641         89 KPDYY-------------------------------------------------------LDAEVAGTEGLTMYSQLAAD  113 (187)
T ss_pred             Ccccc-------------------------------------------------------ccccccCCcchhhhcccccC
Confidence            43100                                                       00000001111111111221


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          438 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       438 ~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                       ..+|++.+...+....|..+|+.||+++++||.++|..+    +|++|||+.||||.++|++.++||+++||+.+.
T Consensus       114 -~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~  185 (187)
T PRK09641        114 -DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIED----LSLKEISEILDLPVGTVKTRIHRGREALRKQLR  185 (187)
T ss_pred             -cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence             235777777777778899999999999999999999877    999999999999999999999999999999775

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.89  E-value=1.5e-21  Score=182.96  Aligned_cols=174  Identities=18%  Similarity=0.180  Sum_probs=139.5

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803          279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (525)
Q Consensus       279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~  358 (525)
                      ...++..|+++|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+  .+.+|.+|++.++++.+.+++++..
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            34567899999999999999999999999999999999999999999999999  4568999999999999999998765


Q ss_pred             cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC
Q 009803          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE  438 (525)
Q Consensus       359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~  438 (525)
                      +....+                                                    +++  ..+.++....+...+  
T Consensus        82 ~~~~~~----------------------------------------------------~~~--~~~~~~~~~~~~~~~--  105 (182)
T PRK09652         82 RRPPAS----------------------------------------------------DVD--AEEAEDFDLADALRD--  105 (182)
T ss_pred             CCCCcc----------------------------------------------------ccc--ccccccccccccccc--
Confidence            411110                                                    000  000011111111111  


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ..+|++.+........+..+|..||+++++||.++|+.+    +|++|||+.||+|..+|++.++||+++||+.+.
T Consensus       106 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~  177 (182)
T PRK09652        106 ISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEG----LSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ  177 (182)
T ss_pred             ccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            135777777777788899999999999999999999877    999999999999999999999999999999775

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=1.3e-21  Score=193.36  Aligned_cols=193  Identities=19%  Similarity=0.192  Sum_probs=153.5

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 009803          222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  301 (525)
Q Consensus       222 ~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~I  301 (525)
                      ...|+|++..+..|...++.                                        ++..|++.|+..|.+.|+++
T Consensus         7 ~~~~~~~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~y~~~l~~~   46 (231)
T PRK11922          7 SRPPPLSAASDRELVARVLA----------------------------------------GDEAAFEALMRRHNRRLYRT   46 (231)
T ss_pred             CCCCCcCcccHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHHH
Confidence            56788888888777665542                                        56789999999999999999


Q ss_pred             HHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHH
Q 009803          302 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL  381 (525)
Q Consensus       302 A~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L  381 (525)
                      ++++.+++.+++|++||+|+++|+++++|++.  ..|.+|++..+++.+.+++++..+..+++..               
T Consensus        47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~~~~~~---------------  109 (231)
T PRK11922         47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLVNLAEM---------------  109 (231)
T ss_pred             HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccccchhc---------------
Confidence            99999999999999999999999999999985  4799999999999999999876542111000               


Q ss_pred             HHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q 009803          382 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT  461 (525)
Q Consensus       382 ~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~  461 (525)
                                                         ..+. .. .++  ...... ....+|++.+...+....|..+|+.
T Consensus       110 -----------------------------------~~~~-~~-~~~--~~~~~~-~~~~~~e~~~~~~e~~~~l~~~l~~  149 (231)
T PRK11922        110 -----------------------------------VMAS-TI-AGG--ERTPLA-DPAEDPERAAARREIRALLERAIDA  149 (231)
T ss_pred             -----------------------------------cccc-cc-ccc--cccccC-cccCChHHHHHHHHHHHHHHHHHHh
Confidence                                               0000 00 000  000011 1223577777777888889999999


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      ||+++|+||.++|..+    +|++|||+.||+|.++|+++++||+++||+.+..
T Consensus       150 L~~~~r~i~~l~~~~g----~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~  199 (231)
T PRK11922        150 LPDAFRAVFVLRVVEE----LSVEETAQALGLPEETVKTRLHRARRLLRESLAR  199 (231)
T ss_pred             CCHHHhhhheeehhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999887    9999999999999999999999999999998864

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

Probab=99.88  E-value=2.7e-21  Score=180.24  Aligned_cols=165  Identities=19%  Similarity=0.309  Sum_probs=136.9

Q ss_pred             HhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccc
Q 009803          280 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  359 (525)
Q Consensus       280 l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r  359 (525)
                      ..++..|++.|+..|.+.+++++.++.++..+++|++||+++.+|+.+++|+...+ .|.+|++.++++.+.++++++.+
T Consensus         6 ~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~   84 (170)
T TIGR02952         6 QDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKR   84 (170)
T ss_pred             HccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCC
Confidence            34668999999999999999999999998899999999999999999999997555 89999999999999999997754


Q ss_pred             ceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCC
Q 009803          360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEA  439 (525)
Q Consensus       360 ~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~  439 (525)
                      ....                                                     +.+..         .+...  ..
T Consensus        85 ~~~~-----------------------------------------------------~~~~~---------~~~~~--~~  100 (170)
T TIGR02952        85 HPLF-----------------------------------------------------SLDVF---------KELLS--NE  100 (170)
T ss_pred             CCCC-----------------------------------------------------cHHHH---------hhcCC--CC
Confidence            1110                                                     00000         00000  11


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      .+|++.+...+....+..+|..|||++|+||.++|..|    +|++|||+.||||..+|++..+||+++||+.+
T Consensus       101 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l  170 (170)
T TIGR02952       101 PNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQN----LPIAEVARILGKTEGAVKILQFRAIKKLARQM  170 (170)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            25676666677778899999999999999999999987    99999999999999999999999999999753

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.

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.88  E-value=1.2e-21  Score=180.10  Aligned_cols=151  Identities=20%  Similarity=0.254  Sum_probs=123.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi  363 (525)
                      ..|++.|+..|.++|+.+++++ +...+++|++|||++++|+++++|++..| .|.+|++..+++.+.++++++.+... 
T Consensus         3 ~~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~~-   79 (154)
T PRK06759          3 PATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQE-   79 (154)
T ss_pred             cccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhcc-
Confidence            4689999999999999999986 55679999999999999999999998766 79999999999999999987632000 


Q ss_pred             ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  443 (525)
Q Consensus       364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe  443 (525)
                                                                              .... +         +     .|+
T Consensus        80 --------------------------------------------------------~~~~-~---------~-----~~~   88 (154)
T PRK06759         80 --------------------------------------------------------KCVC-V---------G-----EYE   88 (154)
T ss_pred             --------------------------------------------------------cccc-c---------C-----CCc
Confidence                                                                    0000 0         0     111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      +.....+....|..+|..||+++|.||.++|+.|    +|++|||+.||+|..+|+++++||+++||+.
T Consensus        89 ~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~  153 (154)
T PRK06759         89 DHFHFEDVEMKVKDFMSVLDEKEKYIIFERFFVG----KTMGEIALETEMTYYQVRWIYRQALEKMRNS  153 (154)
T ss_pred             ccccHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence            1122233456799999999999999999999988    9999999999999999999999999999973

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=2.6e-21  Score=185.17  Aligned_cols=170  Identities=16%  Similarity=0.197  Sum_probs=135.8

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      .+...++..|++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++..+ .|.||++.++++.+.+++++
T Consensus        21 ~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~Rk   98 (194)
T PRK12519         21 SALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLRS   98 (194)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHHh
Confidence            33444668999999999999999999999999899999999999999976 67887654 79999999999999999987


Q ss_pred             cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803          357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  436 (525)
Q Consensus       357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d  436 (525)
                      +.+..+..                                                      +.    . ...   ...+
T Consensus        99 ~~~~~~~~------------------------------------------------------~~----~-~~~---~~~~  116 (194)
T PRK12519         99 RRSRQRLL------------------------------------------------------ER----W-QQE---LLGE  116 (194)
T ss_pred             cccccchh------------------------------------------------------hh----h-hhh---hccc
Confidence            65411000                                                      00    0 000   0000


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      .....+++.+...+....|..+|..||+++++||.++|..|    +|++|||+.||+|..+|+++++||+++||+.+.
T Consensus       117 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~  190 (194)
T PRK12519        117 ASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEG----LSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ  190 (194)
T ss_pred             ccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence            11124556666666667899999999999999999999887    999999999999999999999999999999765

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=5.3e-21  Score=180.74  Aligned_cols=169  Identities=14%  Similarity=0.123  Sum_probs=136.6

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803          276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  355 (525)
Q Consensus       276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir  355 (525)
                      +.....++..|+..|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++..+ .|.||++..++|.+.++++
T Consensus        10 i~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R   88 (179)
T PRK12514         10 IVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLR   88 (179)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHH
Confidence            333455668999999999999999999999999999999999999999999999987543 6999999999999999998


Q ss_pred             hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803          356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  435 (525)
Q Consensus       356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  435 (525)
                      ++.+. ..                                                     .++.      .   .+ ..
T Consensus        89 ~~~~~-~~-----------------------------------------------------~~~~------~---~~-~~  104 (179)
T PRK12514         89 ARKAV-AV-----------------------------------------------------DIDE------A---HD-LA  104 (179)
T ss_pred             hcCCc-cc-----------------------------------------------------cccc------c---hh-cc
Confidence            75431 00                                                     0000      0   00 00


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      +. ..+|++.+...+....|..+|..||+++++||.++|..|    +|++|||+.||+|..+|++.++||+++||+++.
T Consensus       105 ~~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  178 (179)
T PRK12514        105 DP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEG----LSYKELAERHDVPLNTMRTWLRRSLLKLRECLS  178 (179)
T ss_pred             cc-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCChHHHHHHHHHHHHHHHHHhc
Confidence            11 124565555555556789999999999999999999877    999999999999999999999999999999764

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=5.7e-21  Score=183.69  Aligned_cols=173  Identities=23%  Similarity=0.196  Sum_probs=140.4

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHH
Q 009803          275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  354 (525)
Q Consensus       275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~i  354 (525)
                      .+.+...++..|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.||++..+++.+.+++
T Consensus        16 li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d~~   94 (196)
T PRK12524         16 LLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLCTDRL   94 (196)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHHHHHH
Confidence            344444556999999999999999999999999999999999999999999999998533 4799999999999999998


Q ss_pred             HhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCccc
Q 009803          355 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  434 (525)
Q Consensus       355 r~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  434 (525)
                      +++.+..                                                      ..++..         .+. 
T Consensus        95 Rk~~~~~------------------------------------------------------~~~~~~---------~~~-  110 (196)
T PRK12524         95 RRRRRAS------------------------------------------------------VDLDDA---------PEP-  110 (196)
T ss_pred             HhhcCCC------------------------------------------------------CCcccc---------ccc-
Confidence            8654300                                                      000000         000 


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          435 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       435 ~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      .+. ..++++.+...+....|..+|+.||+++|.||.|+|..+    ++++|||+.||||..+|+++++||+++||+++.
T Consensus       111 ~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g----~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~  185 (196)
T PRK12524        111 ADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEG----LSNPEIAEVMEIGVEAVESLTARGKRALAALLA  185 (196)
T ss_pred             ccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            111 124566666667778899999999999999999999987    999999999999999999999999999999887


Q ss_pred             hch
Q 009803          515 TKH  517 (525)
Q Consensus       515 ~~~  517 (525)
                      ..+
T Consensus       186 ~~~  188 (196)
T PRK12524        186 GQR  188 (196)
T ss_pred             hcc
Confidence            543

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.87  E-value=6.7e-21  Score=180.90  Aligned_cols=177  Identities=15%  Similarity=0.156  Sum_probs=138.8

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803          276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  355 (525)
Q Consensus       276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir  355 (525)
                      +.....++..+++.|+..|.+.|+.+|+++.++..+++|++||+++++|+++.+|++.  ..|.+|++..+++.+.++++
T Consensus        11 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~~~~r   88 (190)
T TIGR02939        11 VERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAKNHLV   88 (190)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHHHHHH
Confidence            3334445689999999999999999999999999999999999999999999999975  36999999999999999987


Q ss_pred             hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803          356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  435 (525)
Q Consensus       356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  435 (525)
                      ++.+.....                                                  ..+.+..      ....+...
T Consensus        89 ~~~r~~~~~--------------------------------------------------~~~~~~~------~~~~~~~~  112 (190)
T TIGR02939        89 AQGRRPPTS--------------------------------------------------DVEIEDA------EHFEGADR  112 (190)
T ss_pred             HhccCCCcc--------------------------------------------------cccccch------hhhccccc
Confidence            654311000                                                  0000000      00000000


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      .....+|++.+...+....|..+|+.||+++|.||.++|..+    +|++|||+.||+|..+|++.++||+++||+++.
T Consensus       113 ~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~  187 (190)
T TIGR02939       113 LREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEG----LSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR  187 (190)
T ss_pred             ccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            001235676667777778899999999999999999999877    999999999999999999999999999999875

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.

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.87  E-value=7.6e-21  Score=181.81  Aligned_cols=173  Identities=20%  Similarity=0.264  Sum_probs=139.1

Q ss_pred             CHHHHHH-HHhccHHHHHHHHHHHHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHH
Q 009803          272 DQRELRR-RLNYGILCKDKMITSNIRLVISIAKNYQGAG---MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK  347 (525)
Q Consensus       272 d~~~L~~-~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g---~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIR  347 (525)
                      ++..|.. ...++..|++.|+..|.+.|+.++.++.+++   .+++|++||+++++|+++++|++..+ .|.||++..++
T Consensus         4 ~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iar   82 (189)
T PRK06811          4 NEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISK   82 (189)
T ss_pred             cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHH
Confidence            3444444 4445589999999999999999999998853   47999999999999999999997655 79999999999


Q ss_pred             HHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccC
Q 009803          348 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN  427 (525)
Q Consensus       348 qaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~  427 (525)
                      +.+.++++++.+....                                                    .+.+.      .
T Consensus        83 n~~~d~~rk~~~~~~~----------------------------------------------------~~~~~------~  104 (189)
T PRK06811         83 YKAIDYKRKLTKNNEI----------------------------------------------------DSIDE------F  104 (189)
T ss_pred             HHHHHHHHHhcccccc----------------------------------------------------ccchh------h
Confidence            9999999876541100                                                    00000      0


Q ss_pred             CCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803          428 LKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR  507 (525)
Q Consensus       428 ~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk  507 (525)
                            ..+ ...+|++.+...+....|..+|..|||++|.||.|+|..|    +|++|||+.||+|..+|+++++||++
T Consensus       105 ------~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIAe~lgis~~~V~~~l~Ra~~  173 (189)
T PRK06811        105 ------ILI-SEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLG----EKIEEIAKKLGLTRSAIDNRLSRGRK  173 (189)
T ss_pred             ------hhc-ccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcc----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                  000 1125666667777778899999999999999999999877    99999999999999999999999999


Q ss_pred             HHHhHHh
Q 009803          508 KLKNKKR  514 (525)
Q Consensus       508 KLR~~l~  514 (525)
                      +||+...
T Consensus       174 ~Lr~~~~  180 (189)
T PRK06811        174 KLQKNKL  180 (189)
T ss_pred             HHHHccc
Confidence            9998653

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.87  E-value=6e-21  Score=181.23  Aligned_cols=170  Identities=16%  Similarity=0.191  Sum_probs=131.5

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      .....++..|++.|+..|.+.|+.++++|.+++.+++|++||+++++|+++++|++.. ..|.+|++..+++.+.+++++
T Consensus        15 ~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d~~rk   93 (186)
T PRK13919         15 ALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRR-GSARAWLLALAHHAAVDHVRR   93 (186)
T ss_pred             HHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCccc-cchHHHHHHHHHHHHHHHHHh
Confidence            3334566999999999999999999999999989999999999999999999998754 369999999999999999987


Q ss_pred             cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803          357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  436 (525)
Q Consensus       357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d  436 (525)
                      ..+..+.                                                    .+.+     .......+ .++
T Consensus        94 ~~~~~~~----------------------------------------------------~~~~-----~~~~~~~~-~~~  115 (186)
T PRK13919         94 RAARPQP----------------------------------------------------LEPD-----EREPEAFD-LPG  115 (186)
T ss_pred             hhccccc----------------------------------------------------cccc-----cccccccc-CCC
Confidence            6431000                                                    0000     00000000 001


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      +.  .++   ........|..+|+.||+++|.||.++|..+    +|++|||+.||+|..+|+.+++||+++||..+.
T Consensus       116 ~~--~~~---~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~  184 (186)
T PRK13919        116 PG--LDE---EGHLDRTRLGRALKALSPEERRVIEVLYYQG----YTHREAAQLLGLPLGTLKTRARRALSRLKEVLR  184 (186)
T ss_pred             cc--ccH---HHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            10  111   1222345689999999999999999999887    999999999999999999999999999999764

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.87  E-value=1.1e-20  Score=180.75  Aligned_cols=175  Identities=13%  Similarity=0.126  Sum_probs=138.3

Q ss_pred             HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803          278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  357 (525)
Q Consensus       278 ~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~  357 (525)
                      ....|+..+++.|+..|.+.|+.++++|.++..+++|++||+++++|+++.+|++..  .|.+|++..+++.+.++++++
T Consensus        13 ~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~rk~   90 (193)
T PRK11923         13 RVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLVSR   90 (193)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHHHh
Confidence            333456899999999999999999999999989999999999999999999999863  599999999999999999865


Q ss_pred             ccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCC
Q 009803          358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP  437 (525)
Q Consensus       358 ~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~  437 (525)
                      .+....                                                  ....++.....++.    ..+.  
T Consensus        91 ~~~~~~--------------------------------------------------~~~~~~~~~~~~~~----~~~~--  114 (193)
T PRK11923         91 GRRPPD--------------------------------------------------SDVSSEDAEFYDGD----HALK--  114 (193)
T ss_pred             cCCCcc--------------------------------------------------ccccccchhhhccc----cccc--
Confidence            441100                                                  00000000000000    0011  


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          438 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       438 ~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ...+|++.+...+....+..+|..||+++|.||.++|..|    +|++|||+.||+|..+|+++.+||+++||+++.
T Consensus       115 ~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~  187 (193)
T PRK11923        115 DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDG----LSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ  187 (193)
T ss_pred             CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            1235676666777778899999999999999999999877    999999999999999999999999999999876

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=7.9e-21  Score=180.51  Aligned_cols=169  Identities=14%  Similarity=0.141  Sum_probs=135.5

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHH
Q 009803          275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  354 (525)
Q Consensus       275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~i  354 (525)
                      .+.....++..|++.|+..|.+.++.+++++.++..+++|++||+|+.+|+.+++|++.. ..|.+|++..+++.+.+++
T Consensus        13 l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~   91 (182)
T PRK12537         13 CLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPAR-GSARGWIYSVTRHLALNVL   91 (182)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCccc-ccHHHHHHHHHHHHHHHHH
Confidence            344445566999999999999999999999999999999999999999999999998644 3799999999999999999


Q ss_pred             HhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCccc
Q 009803          355 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  434 (525)
Q Consensus       355 r~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  434 (525)
                      +++.+...+                                                       +..     .   .+..
T Consensus        92 r~~~~~~~~-------------------------------------------------------~~~-----~---~~~~  108 (182)
T PRK12537         92 RDTRREVVL-------------------------------------------------------DDD-----A---EETA  108 (182)
T ss_pred             HhccccCcc-------------------------------------------------------ccc-----h---hhhc
Confidence            876531100                                                       000     0   0000


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          435 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       435 ~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      .+  ..++++..........|..+|+.||+++|+||.++|..|    +|++|||+.||||.++|+.+++||+++||.++
T Consensus       109 ~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l  181 (182)
T PRK12537        109 QT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDG----CSHAEIAQRLGAPLGTVKAWIKRSLKALRECM  181 (182)
T ss_pred             cc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCChhhHHHHHHHHHHHHHHHh
Confidence            00  112333444444556789999999999999999999888    99999999999999999999999999999875

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=7.5e-21  Score=180.91  Aligned_cols=171  Identities=13%  Similarity=0.127  Sum_probs=137.2

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803          276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  355 (525)
Q Consensus       276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir  355 (525)
                      +.....++..+++.|+..|.++|+++|++|.++..+++|++||+|+++|+++++|++.++ .|.||++..+++.+.++++
T Consensus        16 ~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~R   94 (187)
T PRK12534         16 LTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHLR   94 (187)
T ss_pred             HHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHH
Confidence            444455668999999999999999999999999999999999999999999999998654 6899999999999999998


Q ss_pred             hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803          356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  435 (525)
Q Consensus       356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  435 (525)
                      ++.+..+.                                                    .+++..         .+.. 
T Consensus        95 ~~~~~~~~----------------------------------------------------~~~~~~---------~~~~-  112 (187)
T PRK12534         95 ANAPQRRN----------------------------------------------------VALDDA---------GELR-  112 (187)
T ss_pred             hccccccc----------------------------------------------------ccccch---------hhhc-
Confidence            76431000                                                    000000         0000 


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ++ ..++++.....+....|..+|..||++++.|+.++|..|    +|++|||+.||+|.++|+++++||+++||+.+.
T Consensus       113 ~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~  186 (187)
T PRK12534        113 AA-DASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEG----ITYEELAARTDTPIGTVKSWIRRGLAKLKACLE  186 (187)
T ss_pred             cc-cCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCChhHHHHHHHHHHHHHHHHHc
Confidence            00 113444445556677899999999999999999999877    999999999999999999999999999999764

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=9.4e-21  Score=187.89  Aligned_cols=165  Identities=17%  Similarity=0.214  Sum_probs=135.6

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803          281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (525)
Q Consensus       281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~  360 (525)
                      .|+..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..+++.++++++++.+.
T Consensus        59 ~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~~~~  137 (233)
T PRK12538         59 TDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKPRTE  137 (233)
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhhccc
Confidence            3568999999999999999999999999899999999999999999999987544 799999999999999998764210


Q ss_pred             eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCC
Q 009803          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE  440 (525)
Q Consensus       361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~  440 (525)
                       .                                                       ++. .  .      +. .+ ...
T Consensus       138 -~-------------------------------------------------------~~~-~--~------~~-~~-~~~  150 (233)
T PRK12538        138 -N-------------------------------------------------------VDA-V--P------EV-AD-GKP  150 (233)
T ss_pred             -c-------------------------------------------------------ccc-c--c------cc-cc-CCC
Confidence             0                                                       000 0  0      00 00 012


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      .+++.+...+....|..+|..||+++|+||.|+|..|    +|++|||+.||+|.++|+++++||+++||+.+....
T Consensus       151 ~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~~  223 (233)
T PRK12538        151 DAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHEN----MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRHE  223 (233)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3455555566667899999999999999999999988    999999999999999999999999999999887543

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=3.6e-21  Score=183.11  Aligned_cols=175  Identities=19%  Similarity=0.220  Sum_probs=138.8

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803          281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (525)
Q Consensus       281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~  360 (525)
                      .++..|+..|+..|.+.++.+|.++.++..+++|++||+|+.+|+++.+|++..+..|.||++..++|.+.++++++.+.
T Consensus         5 ~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~   84 (185)
T PRK12542          5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRH   84 (185)
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            35688999999999999999999999998999999999999999999999875445899999999999999999876431


Q ss_pred             eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCC
Q 009803          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE  440 (525)
Q Consensus       361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~  440 (525)
                      ...                  .                                    +. .    ..   +.... ..+
T Consensus        85 ~~~------------------~------------------------------------~~-~----~~---~~~~~-~~~  101 (185)
T PRK12542         85 ETF------------------L------------------------------------EE-Y----ER---ESIEA-VDE  101 (185)
T ss_pred             hhh------------------h------------------------------------hh-c----cc---cchhh-hhc
Confidence            000                  0                                    00 0    00   00000 011


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhh
Q 009803          441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ  520 (525)
Q Consensus       441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~  520 (525)
                      .+++..........|..+|..||+++|+||.|+|..|    +|++|||+.||+|.++|+++++||+++||+.+....-..
T Consensus       102 ~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~  177 (185)
T PRK12542        102 NIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYN----LTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQHDE  177 (185)
T ss_pred             cHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            3444333444456799999999999999999999988    999999999999999999999999999999987765555


Q ss_pred             hh
Q 009803          521 YA  522 (525)
Q Consensus       521 yl  522 (525)
                      |+
T Consensus       178 ~~  179 (185)
T PRK12542        178 FK  179 (185)
T ss_pred             HH
Confidence            53

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.87  E-value=4.3e-21  Score=183.21  Aligned_cols=172  Identities=20%  Similarity=0.286  Sum_probs=134.4

Q ss_pred             CCHHHHHHHHh----ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHH
Q 009803          271 VDQRELRRRLN----YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI  346 (525)
Q Consensus       271 ~d~~~L~~~l~----~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wI  346 (525)
                      +++..|...++    ++..|++.|+..|.+.|+++|.+|.++..+++|++||+++.+|+++++|++.  ..|.||++.++
T Consensus         8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia   85 (188)
T PRK09640          8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSIT   85 (188)
T ss_pred             CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHH
Confidence            44555555554    4699999999999999999999999999999999999999999999999863  47999999999


Q ss_pred             HHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccccc
Q 009803          347 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ  426 (525)
Q Consensus       347 RqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~  426 (525)
                      ++.+.+++++..+....                                                     ..+...    
T Consensus        86 ~n~~~d~~R~~~~~~~~-----------------------------------------------------~~~~~~----  108 (188)
T PRK09640         86 YNECITQYRKERRKRRL-----------------------------------------------------MDALSL----  108 (188)
T ss_pred             HHHHHHHHHHhcccccC-----------------------------------------------------cchhhh----
Confidence            99999999875431100                                                     000000    


Q ss_pred             CCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803          427 NLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  506 (525)
Q Consensus       427 ~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL  506 (525)
                           +...++.    ++.....+....|..+|+.||+++|+||.|+|..|    +|++|||+.||||..+|+.+++||+
T Consensus       109 -----~~~~~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~  175 (188)
T PRK09640        109 -----DPLEEAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAE----LEFQEIADIMHMGLSATKMRYKRAL  175 (188)
T ss_pred             -----ccccccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence                 0000000    00011123345689999999999999999999987    9999999999999999999999999


Q ss_pred             HHHHhHHh
Q 009803          507 RKLKNKKR  514 (525)
Q Consensus       507 kKLR~~l~  514 (525)
                      ++||+.+.
T Consensus       176 ~~Lr~~l~  183 (188)
T PRK09640        176 DKLREKFA  183 (188)
T ss_pred             HHHHHHHH
Confidence            99999774

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=2.7e-20  Score=174.01  Aligned_cols=170  Identities=19%  Similarity=0.167  Sum_probs=141.2

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803          279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (525)
Q Consensus       279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~  358 (525)
                      ...++..|++.|+..|.+.|+++|+++.++..+++|++||+++.||++.++|+  .+..|.+|++..+++.+.+++++..
T Consensus         7 ~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~   84 (179)
T PRK11924          7 DATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRR   84 (179)
T ss_pred             HHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhcc
Confidence            34567899999999999999999999999999999999999999999999998  3458999999999999999998765


Q ss_pred             cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC
Q 009803          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE  438 (525)
Q Consensus       359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~  438 (525)
                      +....                                                     ..+     +.    .+...+..
T Consensus        85 ~~~~~-----------------------------------------------------~~~-----~~----~~~~~~~~  102 (179)
T PRK11924         85 REKAV-----------------------------------------------------LSD-----DA----LEPEFAET  102 (179)
T ss_pred             ccccc-----------------------------------------------------Ccc-----cc----cccccCCc
Confidence            41110                                                     000     00    00000002


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      ..+|++.+...+....+..+|+.||++++.||.++|..+    +|++|||+.||+|+.+|+++++||+++||+.+...
T Consensus       103 ~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~  176 (179)
T PRK11924        103 AETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEG----LSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ  176 (179)
T ss_pred             cCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            346888888888889999999999999999999999877    99999999999999999999999999999988653

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

Probab=99.86  E-value=1.8e-20  Score=177.65  Aligned_cols=179  Identities=15%  Similarity=0.152  Sum_probs=137.9

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQG----AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  357 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~----~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~  357 (525)
                      ++..|++.|+..|.+.|+.+|++|.+    +..+++|++||+++.+|+++.+|++..+.+|.+|++..+++.+.++++++
T Consensus         4 ~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~   83 (189)
T TIGR02984         4 GDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRH   83 (189)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHH
Confidence            56899999999999999999999853    56789999999999999999999976667899999999999999998865


Q ss_pred             cc-ceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCccccccccc-CCCCCcccC
Q 009803          358 SR-TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ-NLKPSEVIA  435 (525)
Q Consensus       358 ~r-~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~-~~~l~d~l~  435 (525)
                      .+ -.+.                         +                       ....+++.....++ ...+.+.+.
T Consensus        84 ~~~~~r~-------------------------~-----------------------~~~~~~~~~~~~~~~~~~~~~~~~  115 (189)
T TIGR02984        84 LGAQKRD-------------------------I-----------------------RREQSLDAGGRLDESSVRLAAQLA  115 (189)
T ss_pred             HHHHhhh-------------------------c-----------------------ccccCCCcccccCCcchhHHHHcc
Confidence            21 0000                         0                       00012221110011 111222222


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      + ...+|++.+...+....|..+|..|||++|.||.++|+.|    +|++|||+.||||.++|++.++||+++||+.+
T Consensus       116 ~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l  188 (189)
T TIGR02984       116 A-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEG----LSFAEVAERMDRSEGAVSMLWVRGLARLRQIL  188 (189)
T ss_pred             C-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            2 2335777777777778899999999999999999999877    99999999999999999999999999999865

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=2.3e-20  Score=178.15  Aligned_cols=174  Identities=20%  Similarity=0.230  Sum_probs=141.4

Q ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHH
Q 009803          274 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  353 (525)
Q Consensus       274 ~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~  353 (525)
                      ..+.....++..|++.|+..|.+.++.++.++.++..+++|++||+|+.+|+++++|++.  ..|.+|++..+++.+.++
T Consensus        11 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~   88 (189)
T PRK12515         11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKALSA   88 (189)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHHHH
Confidence            344445556699999999999999999999999999999999999999999999999964  479999999999999999


Q ss_pred             HHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcc
Q 009803          354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV  433 (525)
Q Consensus       354 ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~  433 (525)
                      +++..+. .+                                                       ..    + .  . ..
T Consensus        89 ~r~~~~~-~~-------------------------------------------------------~~----~-~--~-~~  104 (189)
T PRK12515         89 LRRRKHE-EI-------------------------------------------------------DD----E-A--A-AA  104 (189)
T ss_pred             HHccCCC-CC-------------------------------------------------------cc----c-c--c-cc
Confidence            9865420 00                                                       00    0 0  0 00


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          434 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       434 l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      ..+ ..++|++.....+....+..+|+.||+++|+||.++|..+    +|++|||+.||+|..+|+++++||+++||+.+
T Consensus       105 ~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l  179 (189)
T PRK12515        105 IED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHE----KSVEEVGEIVGIPESTVKTRMFYARKKLAELL  179 (189)
T ss_pred             cCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            111 1235666666666677899999999999999999999987    99999999999999999999999999999988


Q ss_pred             hhchh
Q 009803          514 RTKHL  518 (525)
Q Consensus       514 ~~~~L  518 (525)
                      ...+.
T Consensus       180 ~~~~~  184 (189)
T PRK12515        180 KAAGV  184 (189)
T ss_pred             HHhcc
Confidence            76543

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=2.4e-20  Score=181.12  Aligned_cols=172  Identities=15%  Similarity=0.168  Sum_probs=134.3

Q ss_pred             HhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccc
Q 009803          280 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  359 (525)
Q Consensus       280 l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r  359 (525)
                      .+++..++++|+..|.+.|+.++.++.++..+++|++||+|+.+|+++..|++.++ .|.||++.++|+.+.++++++.+
T Consensus        33 ~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~  111 (206)
T PRK12526         33 ISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKA  111 (206)
T ss_pred             HcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhcc
Confidence            34668999999999999999999999999889999999999999999999997665 59999999999999999987654


Q ss_pred             ceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCC
Q 009803          360 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEA  439 (525)
Q Consensus       360 ~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~  439 (525)
                      .....                                                     ++.    + .....+.+.+. .
T Consensus       112 ~~~~~-----------------------------------------------------~~~----~-~~~~~~~~~~~-~  132 (206)
T PRK12526        112 KKEQN-----------------------------------------------------LGD----D-IWPIEQALAES-Q  132 (206)
T ss_pred             ccccc-----------------------------------------------------ccc----c-cchhhhhcccc-c
Confidence            11000                                                     000    0 00000111111 1


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      ..+. ..........|..+|..||+++|.||.++|+.+    +|++|||+.||+|.++|+.+++||+++||+.+...
T Consensus       133 ~~~~-~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~  204 (206)
T PRK12526        133 SESE-EFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQE----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ  204 (206)
T ss_pred             CchH-HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            1222 222233446789999999999999999999988    99999999999999999999999999999988643

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=3e-20  Score=176.10  Aligned_cols=165  Identities=16%  Similarity=0.241  Sum_probs=134.3

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++..|+..|+..|.+.|+.+++.|.++..+++|++||+|+.+|+++.+|++..  .|.+|++..+++.+.++++...+..
T Consensus         4 ~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~   81 (179)
T PRK12543          4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRF   81 (179)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhcccc
Confidence            56789999999999999999999999999999999999999999999999864  6999999999999999877654210


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                      +.                                                      ++.. . +    ..+   ......
T Consensus        82 ~~------------------------------------------------------~~~~-~-~----~~~---~~~~~~   98 (179)
T PRK12543         82 RI------------------------------------------------------FEKA-E-E----QRK---PVSIDF   98 (179)
T ss_pred             cc------------------------------------------------------cccc-c-c----ccc---cccccC
Confidence            00                                                      0000 0 0    000   001113


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      |+. +...+....|..+|..||+++|.||.|+|..|    +|++|||+.||||..+|+..++||+++||+.+...
T Consensus        99 ~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~  168 (179)
T PRK12543         99 SED-VLSKESNQELIELIHKLPYKLRQVIILRYLHD----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE  168 (179)
T ss_pred             hHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            444 55666778899999999999999999999988    99999999999999999999999999999998754

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.85  E-value=4.9e-20  Score=173.04  Aligned_cols=164  Identities=12%  Similarity=0.081  Sum_probs=131.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++..+++.|+..|.+.++++|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+..
T Consensus         6 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~   84 (173)
T PRK09645          6 AEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARP   84 (173)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhcccc
Confidence            46889999999999999999999999888999999999999999999997533 47999999999999999998764310


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                      ..                                                     ..      ++.   .+ .++.   .
T Consensus        85 ~~-----------------------------------------------------~~------~~~---~~-~~~~---~   98 (173)
T PRK09645         85 VE-----------------------------------------------------GG------DDV---LG-VPEQ---S   98 (173)
T ss_pred             cc-----------------------------------------------------cc------ccc---cc-CCCC---C
Confidence            00                                                     00      000   00 0011   1


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      +++..........|..+|+.||+++|+||.|+|..|    +|++|||+.||+|.++|+.+++||+++||+.+...
T Consensus        99 ~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~  169 (173)
T PRK09645         99 APDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRG----WSTAQIAADLGIPEGTVKSRLHYALRALRLALQER  169 (173)
T ss_pred             CchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence            122233333445789999999999999999999988    99999999999999999999999999999988653

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.85  E-value=7.9e-20  Score=175.47  Aligned_cols=171  Identities=15%  Similarity=0.147  Sum_probs=137.0

Q ss_pred             CHHH-HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHH
Q 009803          272 DQRE-LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (525)
Q Consensus       272 d~~~-L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI  350 (525)
                      ++.. +.....++..+++.|+..|.+.|++++.++.++..+++|++||+|+.+|+++++|++.  ..|.+|++..+++.+
T Consensus        13 ~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~--~~f~~wL~~i~rn~~   90 (192)
T PRK09643         13 SDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD--AAVSSWLHRIVVNAC   90 (192)
T ss_pred             CHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCC--CccHHHHHHHHHHHH
Confidence            3444 4445556699999999999999999999999999999999999999999999999975  369999999999999


Q ss_pred             HHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCC
Q 009803          351 RKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP  430 (525)
Q Consensus       351 ~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l  430 (525)
                      .+++++..+..+.                                                     +++     +..   
T Consensus        91 ~d~~Rk~~~~~~~-----------------------------------------------------~~~-----~~~---  109 (192)
T PRK09643         91 LDRLRRAKARPTV-----------------------------------------------------PLD-----DVY---  109 (192)
T ss_pred             HHHHHccccCCCC-----------------------------------------------------Ccc-----ccc---
Confidence            9999876531000                                                     000     000   


Q ss_pred             CcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          431 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       431 ~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                       +. ..    .+++.+...+....|..+|+.||+++|+||.|+|..+    +|++|||+.||+|..+|+.+++||+++||
T Consensus       110 -~~-~~----~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g----~s~~EIA~~lg~s~~tV~~rl~rar~~Lr  179 (192)
T PRK09643        110 -PV-AQ----LERDPTARVETALAVQRALMRLPVEQRAALVAVDMQG----YSVADAARMLGVAEGTVKSRCARGRARLA  179 (192)
T ss_pred             -cc-cC----CcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence             00 00    1222333445566799999999999999999999987    99999999999999999999999999999


Q ss_pred             hHHhh
Q 009803          511 NKKRT  515 (525)
Q Consensus       511 ~~l~~  515 (525)
                      +.+..
T Consensus       180 ~~l~~  184 (192)
T PRK09643        180 ELLGY  184 (192)
T ss_pred             HHHHH
Confidence            98864

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

Probab=99.85  E-value=7e-20  Score=164.67  Aligned_cols=157  Identities=23%  Similarity=0.345  Sum_probs=132.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (525)
Q Consensus       286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~  365 (525)
                      |++.++..|.++|+++++++.+++.+.+|++|||++++|++++.|++.  .+|.+|+++++++.+.++++++.+   .+.
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~~   76 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LRR   76 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CCc
Confidence            789999999999999999999999999999999999999999999998  689999999999999999998765   111


Q ss_pred             chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803          366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  445 (525)
Q Consensus       366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~  445 (525)
                      ..                                                   ...      ..    .. .....+++.
T Consensus        77 ~~---------------------------------------------------~~~------~~----~~-~~~~~~~~~   94 (158)
T TIGR02937        77 EL---------------------------------------------------DLL------EE----LL-DSDPSPEEE   94 (158)
T ss_pred             ch---------------------------------------------------hhh------hh----cc-cccCCHHHH
Confidence            00                                                   000      00    00 112246666


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      .........|..+++.||+.++.||.++|+.|    +|..|||+.||+|+.+|+++..+++++||+.+
T Consensus        95 ~~~~~~~~~l~~~l~~L~~~~~~ii~~~~~~g----~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l  158 (158)
T TIGR02937        95 LEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGTVKRRLKRARKKLRELL  158 (158)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            66777778899999999999999999998877    99999999999999999999999999999753

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.

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.85  E-value=4.3e-20  Score=173.67  Aligned_cols=166  Identities=15%  Similarity=0.137  Sum_probs=130.9

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      .....++..|++.|+..|.+.|+.+|++|.++..+++|++||+|+++|++++.|++.  .+|.+|++..+++.+.+++++
T Consensus        10 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~   87 (176)
T PRK09638         10 QKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYKDHLRK   87 (176)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHH
Confidence            344456699999999999999999999999999999999999999999999999874  479999999999999999987


Q ss_pred             cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803          357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  436 (525)
Q Consensus       357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d  436 (525)
                      ..+....                            .+                           ... +       ...+
T Consensus        88 ~~~~~~~----------------------------~~---------------------------~~~-~-------~~~~  104 (176)
T PRK09638         88 QKREKLR----------------------------LQ---------------------------RAK-E-------ETLR  104 (176)
T ss_pred             hccccch----------------------------hh---------------------------hcc-c-------ccCC
Confidence            6431100                            00                           000 0       0000


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      .  ... +..........|..+|+.||+++|+||.++|..|    +|++|||+.||+|..+|++.++||+++||+.+.
T Consensus       105 ~--~~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l~  175 (176)
T PRK09638        105 K--EKW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYG----YTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWG  175 (176)
T ss_pred             c--cch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcC----CCHHHHHHHHCCChhHHHHHHHHHHHHHHHHhc
Confidence            0  000 1112223345688999999999999999999877    999999999999999999999999999999763

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

Probab=99.85  E-value=3.2e-20  Score=170.31  Aligned_cols=160  Identities=16%  Similarity=0.170  Sum_probs=129.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (525)
Q Consensus       286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~  365 (525)
                      |+++|+..|.+.|+++++++.++..+.+|++||+++++|+++.+|++.  .+|.+|++.++|+.+.+++++..+....  
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~--   77 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKY--   77 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHH--
Confidence            789999999999999999999998999999999999999999999864  4799999999999999998876531000  


Q ss_pred             chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803          366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  445 (525)
Q Consensus       366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~  445 (525)
                                  ...+                                         .++..       .....+++++.
T Consensus        78 ------------~~~~-----------------------------------------~~~~~-------~~~~~~~~~~~   97 (161)
T TIGR02985        78 ------------QEEI-----------------------------------------LEIEV-------DELSENDPEEE   97 (161)
T ss_pred             ------------HHHH-----------------------------------------Hhhcc-------cccCCCCcHHH
Confidence                        0000                                         00000       00011245566


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      +...+....|..++..||+++++||.++|..+    +|..|||+.||+|+++|+++++||+++||+.+
T Consensus        98 ~~~~e~~~~l~~~l~~L~~~~r~il~l~~~~~----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l  161 (161)
T TIGR02985        98 LEAKELQLIIYKAIEKLPEQCRKIFILSRFEG----KSYKEIAEELGISVKTVEYHISKALKELRKEL  161 (161)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            66667777899999999999999999999877    99999999999999999999999999999753

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

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=6.6e-20  Score=176.03  Aligned_cols=175  Identities=18%  Similarity=0.142  Sum_probs=134.0

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      .+...++..+++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++..+ .|.+|++..++|.+.+++++
T Consensus        19 ~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~Rk   97 (194)
T PRK12531         19 EKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLRK   97 (194)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHHH
Confidence            34445668999999999999999999999999889999999999999999999997544 69999999999999999987


Q ss_pred             cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803          357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  436 (525)
Q Consensus       357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d  436 (525)
                      ..+....                                                    ...+.... + + .......+
T Consensus        98 ~~~~~~~----------------------------------------------------~~~~~~~~-~-~-~~~~~~~~  122 (194)
T PRK12531         98 QKGKDLH----------------------------------------------------IHADDIWP-S-D-YYPPDLVD  122 (194)
T ss_pred             hcccccc----------------------------------------------------cchhhccc-c-c-cccccccc
Confidence            6531000                                                    00000000 0 0 00000000


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                        ...++..    .....+..+|..||+++|+||.++|..+    +|++|||+.||||.++|+.+++||+++||+.+...
T Consensus       123 --~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~eg----~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~~  192 (194)
T PRK12531        123 --HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYLEE----LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDAE  192 (194)
T ss_pred             --ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhhc
Confidence              1123322    2235688899999999999999999987    99999999999999999999999999999988754


Q ss_pred             h
Q 009803          517 H  517 (525)
Q Consensus       517 ~  517 (525)
                      .
T Consensus       193 ~  193 (194)
T PRK12531        193 S  193 (194)
T ss_pred             c
Confidence            3

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

Probab=99.84  E-value=1e-19  Score=170.44  Aligned_cols=162  Identities=19%  Similarity=0.245  Sum_probs=129.7

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803          276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  355 (525)
Q Consensus       276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir  355 (525)
                      +.....++..|++.++..|.+.+++++.++.++..+++|++||+++.+|+.+++|++.  .+|.||++..+++.+.++++
T Consensus         7 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   84 (169)
T TIGR02954         7 VKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHP--KYFNTWLTRILINECIDLLK   84 (169)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCc--cccHHHHHHHHHHHHHHHHH
Confidence            3444556699999999999999999999999999999999999999999999999975  36999999999999999998


Q ss_pred             hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803          356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  435 (525)
Q Consensus       356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  435 (525)
                      +..+.  .|                                                     ++....          ..
T Consensus        85 ~~~~~--~~-----------------------------------------------------~~~~~~----------~~   99 (169)
T TIGR02954        85 KKKKV--IP-----------------------------------------------------FDPNTS----------IE   99 (169)
T ss_pred             hcCCc--Cc-----------------------------------------------------cccccc----------cc
Confidence            76431  00                                                     000000          00


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      +.   .++.  .. .....+..+|+.||+++|+||.++|+.|    +|++|||+.||||..+|+.+.+||+++||+.+.
T Consensus       100 ~~---~~~~--~~-~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l~  168 (169)
T TIGR02954       100 KG---ECET--HA-DSRLDLYKAIDTLNDKYQTAIILRYYHD----LTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE  168 (169)
T ss_pred             cc---hhhh--ch-HHHHHHHHHHHhCCHHHhHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence            00   0110  00 1123688999999999999999999987    999999999999999999999999999999763

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.

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.84  E-value=1e-19  Score=172.64  Aligned_cols=165  Identities=16%  Similarity=0.138  Sum_probs=135.3

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      .+..|+++|+..|.+.|+++++++.++..+++|++||+++.+|+++++|++.  ..|.+|++..+++.+.+++++..+-.
T Consensus        13 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~~~~~   90 (179)
T PRK09415         13 DKEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSWHNKK   90 (179)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhhcccc
Confidence            3478999999999999999999999998999999999999999999999864  36999999999999999998754310


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                      ..                                                     +.+.        ...+...  ...+
T Consensus        91 ~~-----------------------------------------------------~~~~--------~~~~~~~--~~~~  107 (179)
T PRK09415         91 VI-----------------------------------------------------VTED--------IFTYMES--QKES  107 (179)
T ss_pred             cc-----------------------------------------------------cccc--------ccccccc--cccC
Confidence            00                                                     0000        0000001  1224


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      |++.+...+....|..+|+.||+++|+||.|+|..|    +|++|||+.||||.++|+++++||+++||+.+..
T Consensus       108 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~  177 (179)
T PRK09415        108 VEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEE----LSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE  177 (179)
T ss_pred             cHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            666666667778899999999999999999999987    9999999999999999999999999999997753

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=7.7e-20  Score=173.56  Aligned_cols=168  Identities=20%  Similarity=0.202  Sum_probs=131.7

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHH
Q 009803          275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQG-AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  353 (525)
Q Consensus       275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~-~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~  353 (525)
                      .+....+++..|++.|+..|.+.|+.++.++.+ ...+++|++||+++.+|+.++.|++.  ..|.+|++..++|.+.++
T Consensus        11 ~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~d~   88 (181)
T PRK12536         11 LLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLMDF   88 (181)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHHHH
Confidence            345566677999999999999999999998764 57899999999999999999999974  469999999999999999


Q ss_pred             HHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcc
Q 009803          354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV  433 (525)
Q Consensus       354 ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~  433 (525)
                      ++++.+....                                                   ..+++.    .     .+.
T Consensus        89 ~Rk~~~~~~~---------------------------------------------------~~~~~~----~-----~~~  108 (181)
T PRK12536         89 LRSRARREAL---------------------------------------------------HDPLDD----E-----SEL  108 (181)
T ss_pred             HHHHhccccc---------------------------------------------------cCCccc----h-----hhh
Confidence            9876431000                                                   000000    0     000


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          434 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       434 l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      ..+... .+.      +....+..+|+.||++++.||.++|..|    +|++|||+.||+|.++|+.+++||+++||+.+
T Consensus       109 ~~~~~~-~~~------~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l  177 (181)
T PRK12536        109 FATSDD-EAA------EARRDLGKLLEQLPDRQRLPIVHVKLEG----LSVAETAQLTGLSESAVKVGIHRGLKALAAKI  177 (181)
T ss_pred             cCCCCc-chH------HHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            011110 111      2344689999999999999999999887    99999999999999999999999999999987


Q ss_pred             hh
Q 009803          514 RT  515 (525)
Q Consensus       514 ~~  515 (525)
                      ..
T Consensus       178 ~~  179 (181)
T PRK12536        178 RG  179 (181)
T ss_pred             cC
Confidence            64

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.1e-19  Score=170.96  Aligned_cols=167  Identities=11%  Similarity=0.159  Sum_probs=131.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 009803          285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  364 (525)
Q Consensus       285 ~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP  364 (525)
                      ..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++..  +|.+|++..+++.+.++++++.+....+
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~   80 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI   80 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            45899999999999999999999999999999999999999999999753  7999999999999999998765411000


Q ss_pred             cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHH
Q 009803          365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED  444 (525)
Q Consensus       365 ~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee  444 (525)
                      ..                                                 . .+.    +   ...+.........++.
T Consensus        81 ~~-------------------------------------------------~-~~~----~---~~~~~~~~~~~~~~~~  103 (173)
T PRK12522         81 LD-------------------------------------------------L-FHK----E---DGGEIEFADDVNISEE  103 (173)
T ss_pred             cc-------------------------------------------------c-cch----h---hhhhhccccCCCChHH
Confidence            00                                                 0 000    0   0000000001112333


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          445 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       445 ~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                       ....+....|..+|..||+++++||.|+|..|    +|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus       104 -~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~  169 (173)
T PRK12522        104 -FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQ----YSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG  169 (173)
T ss_pred             -HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence             44455677899999999999999999999988    9999999999999999999999999999997754

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

Probab=99.84  E-value=2.2e-19  Score=179.45  Aligned_cols=183  Identities=13%  Similarity=0.152  Sum_probs=141.9

Q ss_pred             cCCHHHHHHHHh-ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhhcCCcCCCchhhH
Q 009803          270 GVDQRELRRRLN-YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR-------GAEKFDASKGFKFSTY  341 (525)
Q Consensus       270 g~d~~~L~~~l~-~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLir-------AiekFDp~kG~rFsTY  341 (525)
                      +.++..|...++ |+..|+..|+..|.+.|+.++.++.++..+++|++||+|+.+|.       .+.+|++.  ..|.||
T Consensus        23 ~~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tW  100 (244)
T TIGR03001        23 HAADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSW  100 (244)
T ss_pred             cccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhH
Confidence            345555655544 55899999999999999999999999999999999999999994       78889864  379999


Q ss_pred             HHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccc
Q 009803          342 AHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQK  421 (525)
Q Consensus       342 A~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~  421 (525)
                      ++.+++|.+.++++++.+...+                                                       +. 
T Consensus       101 L~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~~-  124 (244)
T TIGR03001       101 VRIVATRIALELQAQERRHSPV-------------------------------------------------------EE-  124 (244)
T ss_pred             HHHHHHHHHHHHHHHhcccCcc-------------------------------------------------------cc-
Confidence            9999999999999865431100                                                       00 


Q ss_pred             cccccCCCCCcccCCCCCCCHHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHH
Q 009803          422 IGINQNLKPSEVIADPEAETAEDLLIK----KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRER  497 (525)
Q Consensus       422 i~~d~~~~l~d~l~d~~~~~pee~~~~----~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~er  497 (525)
                         + + ...+. .+. ..+|++.+..    .+....|..+|++||+++|+||.|+|..|    +|++|||++||||.++
T Consensus       125 ---~-~-~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg----~S~~EIA~~Lgis~~T  193 (244)
T TIGR03001       125 ---P-T-ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDG----LSMDRIGAMYQVHRST  193 (244)
T ss_pred             ---c-c-ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHH
Confidence               0 0 00000 011 1234444432    23556799999999999999999999987    9999999999999999


Q ss_pred             HHHHHHHHHHHHHhHHhhchhhhh
Q 009803          498 IRQIESSAFRKLKNKKRTKHLMQY  521 (525)
Q Consensus       498 VRqie~RALkKLR~~l~~~~L~~y  521 (525)
                      |+.+++||+++||+.+.......|
T Consensus       194 Vk~rl~RAr~~Lr~~l~~~~~~~~  217 (244)
T TIGR03001       194 VSRWVAQARERLLERTRRRLAERL  217 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999987665544

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.5e-19  Score=172.81  Aligned_cols=181  Identities=15%  Similarity=0.163  Sum_probs=137.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (525)
Q Consensus       286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~  365 (525)
                      +++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+.+++|++.  .+|.||++..++|.+.++++++.+....+.
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  369999999999999999987754211100


Q ss_pred             chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803          366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  445 (525)
Q Consensus       366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~  445 (525)
                      ..                  .......++                       ++.... . + ......++. ..+|++.
T Consensus        81 ~~------------------~~~~~~~~~-----------------------~~~~~~-~-~-~~~~~~~~~-~~~~~~~  115 (191)
T PRK12520         81 DD------------------ADEQSDDDL-----------------------FDALFA-A-D-GHYREPPSD-WGDPDAA  115 (191)
T ss_pred             cc------------------cccchhhhh-----------------------hhhhcc-c-c-cccccCccc-cCCHHHH
Confidence            00                  000000000                       000000 0 0 000011111 2367777


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      +...+....|..+|..||+++|.||.|+|..+    +|++|||+.||+|.++|+++++||+++||+++....
T Consensus       116 ~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~  183 (191)
T PRK12520        116 LSRREFFEVLQACVDRLPPRTGRVFMMREWLE----LETEEICQELQITATNAWVLLYRARMRLRECLDLHW  183 (191)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777778899999999999999999999988    999999999999999999999999999999988765

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

Probab=99.83  E-value=2.8e-19  Score=170.00  Aligned_cols=172  Identities=20%  Similarity=0.265  Sum_probs=137.6

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      .....++..++..++..|.+.++.+++++.++..+++||+||+|+.+|+++..| +. +..|.||++.+++|.+++++++
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~   84 (182)
T COG1595           7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRK   84 (182)
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHH
Confidence            344556789999999999999999999999988899999999999999999999 33 3479999999999999999998


Q ss_pred             cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803          357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  436 (525)
Q Consensus       357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d  436 (525)
                      ..+....                                                      .+     +.+  ..+...+
T Consensus        85 ~~r~~~~------------------------------------------------------~~-----~~~--~~~~~~~  103 (182)
T COG1595          85 RKRRRAR------------------------------------------------------VE-----EAD--LLPEEAD  103 (182)
T ss_pred             hcccccc------------------------------------------------------cc-----ccc--ccccccC
Confidence            7652211                                                      00     000  0000111


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      +....+ +.+...+....|..+|..||+++|.+|.|+|+.|    +|++|||+.||||.++|+.+++||+++||+.+...
T Consensus       104 ~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~g----ls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~~  178 (182)
T COG1595         104 PAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRYLEG----LSYEEIAEILGISVGTVKSRLHRARKKLREQLEEA  178 (182)
T ss_pred             cccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHhhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            111011 2455566778899999999999999999999988    99999999999999999999999999999988653

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=2.6e-19  Score=170.35  Aligned_cols=165  Identities=13%  Similarity=0.107  Sum_probs=129.0

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHH----hhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803          277 RRRLNYGILCKDKMITSNIRLVISIAKN----YQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  352 (525)
Q Consensus       277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~----y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~  352 (525)
                      .....++..|++.|+..|.+.|+.++++    |.++..+++|++||+++.+|++++.|++..  .|.+|++..+++.+.+
T Consensus        13 ~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~d   90 (184)
T PRK12539         13 LASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLID   90 (184)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHHH
Confidence            3444566899999999999999999874    557788999999999999999999999753  6999999999999999


Q ss_pred             HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803          353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE  432 (525)
Q Consensus       353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d  432 (525)
                      ++++..+. ..+                                                   .+.+.    . +    .
T Consensus        91 ~~R~~~~~-~~~---------------------------------------------------~~~~~----~-~----~  109 (184)
T PRK12539         91 HLRRTRAS-LAD---------------------------------------------------VPIDD----A-D----E  109 (184)
T ss_pred             HHHHHhcc-ccc---------------------------------------------------cChhh----h-c----c
Confidence            99875431 000                                                   00000    0 0    0


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      ....    .+   ....+....|..+|..||+++|+||.|+|..|    +|++|||+.||+|..+|+++++||+++||+.
T Consensus       110 ~~~~----~~---~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  178 (184)
T PRK12539        110 LVAH----DD---HAAVESTLDLGRLLARLPEKMRLAIQAVKLEG----LSVAEAATRSGMSESAVKVSVHRGLKALAAL  178 (184)
T ss_pred             ccCC----cH---HhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            0000    11   11223345789999999999999999999877    9999999999999999999999999999998


Q ss_pred             Hhh
Q 009803          513 KRT  515 (525)
Q Consensus       513 l~~  515 (525)
                      +..
T Consensus       179 l~~  181 (184)
T PRK12539        179 IGR  181 (184)
T ss_pred             Hhh
Confidence            764

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=4.1e-19  Score=174.36  Aligned_cols=171  Identities=14%  Similarity=0.134  Sum_probs=137.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ....++..|+..|.+.++.+++++.++..+.+|++||+|+.+|+.+++|++.   .|.+|++.+++|.+.++++++.+..
T Consensus        15 ~~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~   91 (216)
T PRK12533         15 ARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAH   91 (216)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccc
Confidence            3467999999999999999999999999999999999999999999999853   4999999999999999998765310


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                      ..                                                    . ....+. + ...... .. +...+
T Consensus        92 ~~----------------------------------------------------~-~~~~~~-~-~~~~~~-~~-~~~~~  114 (216)
T PRK12533         92 EV----------------------------------------------------A-APDTLD-D-ADSLDD-WQ-PAGED  114 (216)
T ss_pred             cc----------------------------------------------------c-cccccc-c-cccccc-cc-cCCCC
Confidence            00                                                    0 000000 0 000000 11 11235


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      |++.+...+....|..+|+.||+++|+||.|+|..+    +|++|||+.||||.++|+++++||+++||+++...
T Consensus       115 ~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg----~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~  185 (216)
T PRK12533        115 PLALLLRAEDVRLVNAALAKLPVEYREVLVLRELED----MSYREIAAIADVPVGTVMSRLARARRRLAALLGGA  185 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence            777777777788899999999999999999999987    99999999999999999999999999999998654

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

Probab=99.83  E-value=3.3e-19  Score=168.68  Aligned_cols=166  Identities=22%  Similarity=0.208  Sum_probs=123.4

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803          279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGM-----NLQDLVQEGCRGLVR-GAEKFDASKGFKFSTYAHWWIKQAVRK  352 (525)
Q Consensus       279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~-----~~eDLIQEG~lGLir-AiekFDp~kG~rFsTYA~~wIRqaI~~  352 (525)
                      ...++..|++.|+..|.+.++.+|++|.++..     +++|++||+|+.+|+ ...+|++.  ..|.+|++.+++|.+.+
T Consensus        11 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d   88 (183)
T TIGR02999        11 WQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRILVD   88 (183)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHHHHH
Confidence            34456899999999999999999999998877     899999999999998 78889754  36999999999999999


Q ss_pred             HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803          353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE  432 (525)
Q Consensus       353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d  432 (525)
                      +++++.+..+..                                                   ...+..        ..+
T Consensus        89 ~~R~~~~~~~~~---------------------------------------------------~~~~~~--------~~~  109 (183)
T TIGR02999        89 HARRRRAQKRGG---------------------------------------------------GAVRVP--------LDE  109 (183)
T ss_pred             HHHHHHHHhccC---------------------------------------------------Cccccc--------ccc
Confidence            988654210000                                                   000000        000


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      ..++... ...+.   ......+...|+.||+++|.||.|+|..|    +|++|||+.||+|.++|+.+++||+++||+.
T Consensus       110 ~~~~~~~-~~~~~---~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~  181 (183)
T TIGR02999       110 VLPDAEA-DLDEE---LLDLDDALDKLAQVDPRQAEVVELRFFAG----LTVEEIAELLGVSVRTVERDWRFARAWLADE  181 (183)
T ss_pred             ccCCCCc-cHHHH---HHHHHHHHHHhhcCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            0001000 11111   11122344456779999999999999988    9999999999999999999999999999987


Q ss_pred             H
Q 009803          513 K  513 (525)
Q Consensus       513 l  513 (525)
                      +
T Consensus       182 l  182 (183)
T TIGR02999       182 L  182 (183)
T ss_pred             h
Confidence            5

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.

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=2.2e-19  Score=170.21  Aligned_cols=165  Identities=12%  Similarity=0.041  Sum_probs=131.2

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803          281 NYGILCKDKMITSNIRLVISIAKNYQG--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (525)
Q Consensus       281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~--~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~  358 (525)
                      .|+..+++.|+..|.+.|+.++..+.+  +..+++|++||+|+.+|+..++|++.....|.||++..++|.+.++++++.
T Consensus         9 ~~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~   88 (178)
T PRK12529          9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQS   88 (178)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999998766665  457899999999999999999998544457999999999999999887643


Q ss_pred             cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC
Q 009803          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE  438 (525)
Q Consensus       359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~  438 (525)
                      +.  .                ..                                    .+..         .+ .....
T Consensus        89 ~~--~----------------~~------------------------------------~~~~---------~~-~~~~~  104 (178)
T PRK12529         89 LE--L----------------AW------------------------------------LEAL---------AT-LPEPL  104 (178)
T ss_pred             HH--h----------------hh------------------------------------hhHh---------hh-ccCcC
Confidence            20  0                00                                    0000         00 00111


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      .++|++.+...+....|..+|..||+++|.||.|+|..|    +|++|||+.||+|.++|+.+++||+.+|++.+
T Consensus       105 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~  175 (178)
T PRK12529        105 HPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDG----MKQKDIAQALDIALPTVKKYIHQAYVTCLSLM  175 (178)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            235666666666667899999999999999999999987    99999999999999999999999999998864

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

Probab=99.83  E-value=1e-19  Score=168.02  Aligned_cols=157  Identities=18%  Similarity=0.240  Sum_probs=125.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (525)
Q Consensus       286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~  365 (525)
                      |++.++..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++..  .|.+|++..+++.+.++++++.+.-.. .
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~   78 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F   78 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence            7899999999999999999999999999999999999999999999753  699999999999999999987541100 0


Q ss_pred             chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803          366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  445 (525)
Q Consensus       366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~  445 (525)
                      .                         ++..                                    +.+.+..  +|.+.
T Consensus        79 ~-------------------------~~~~------------------------------------~~~~~~~--~~~~~   95 (159)
T TIGR02989        79 D-------------------------DELL------------------------------------EALAAEA--EATEA   95 (159)
T ss_pred             C-------------------------HHHH------------------------------------HHHHhhc--ccchH
Confidence            0                         0000                                    0000000  11111


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .........|..+++.||++++.||.++|..|    +|++|||+.||||.++|+...+||+++||++
T Consensus        96 ~~~~~~~~~l~~~i~~L~~~~r~v~~l~~~~g----~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~  158 (159)
T TIGR02989        96 DRSEDELQALEGCLEKLPERQRELLQLRYQRG----VSLTALAEQLGRTVNAVYKALSRLRVRLRDC  158 (159)
T ss_pred             hhHHHHHHHHHHHHHHCCHHHHHHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            22233446789999999999999999999877    9999999999999999999999999999975

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).

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=2e-19  Score=169.04  Aligned_cols=167  Identities=17%  Similarity=0.137  Sum_probs=129.5

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803          279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (525)
Q Consensus       279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~  358 (525)
                      ...++..+++.|+..|.+.|+.+++++.+. .+++|++||+|+.+|+.+++|++.  ..|.+|++..+++.+.+++++..
T Consensus         5 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~   81 (175)
T PRK12518          5 CQRGDRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFA   81 (175)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhh
Confidence            345678999999999999999999998754 689999999999999999999974  47999999999999999988653


Q ss_pred             cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC
Q 009803          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE  438 (525)
Q Consensus       359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~  438 (525)
                      +.-..                                                      .+..   ....   . .... 
T Consensus        82 ~~~~~------------------------------------------------------~~~~---~~~~---~-~~~~-   99 (175)
T PRK12518         82 QRPSR------------------------------------------------------IQDD---SLND---Q-PSRP-   99 (175)
T ss_pred             ccccc------------------------------------------------------hhcc---cccc---c-ccCC-
Confidence            21000                                                      0000   0000   0 0000 


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      ...++  ....+....+..+|+.||+++|.||.|+|+.|    +|++|||+.||+|..+|++..+||+++||+.+...
T Consensus       100 ~~~~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~  171 (175)
T PRK12518        100 SDTPD--LMQLHYQDLVQQGLQTLSLEHRAVLVLHDLED----LPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQ  171 (175)
T ss_pred             CCcHH--HHHHHHHHHHHHHHHhCCHHHeeeeeehHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            11222  22223345688999999999999999999988    99999999999999999999999999999988764

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=5.6e-19  Score=167.62  Aligned_cols=163  Identities=17%  Similarity=0.203  Sum_probs=128.4

Q ss_pred             HHHhccHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHH
Q 009803          278 RRLNYGILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  353 (525)
Q Consensus       278 ~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~----g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~  353 (525)
                      ....++..|++.|+..|.+.|+.+|++++++    ..+++|++||+++.+|...++|++.  ..|.+|++..+|+.+.++
T Consensus        15 ~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~d~   92 (184)
T PRK12512         15 SANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLIDA   92 (184)
T ss_pred             HHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHHHH
Confidence            3345679999999999999999999998862    4689999999999999999999863  479999999999999999


Q ss_pred             HHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcc
Q 009803          354 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV  433 (525)
Q Consensus       354 ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~  433 (525)
                      ++++.+....                                                     +++.         ..+.
T Consensus        93 ~Rr~~~~~~~-----------------------------------------------------~~~~---------~~~~  110 (184)
T PRK12512         93 LRRRGRRVFV-----------------------------------------------------DIDD---------FAET  110 (184)
T ss_pred             HHhhcccccC-----------------------------------------------------Cchh---------cccc
Confidence            9876431111                                                     0000         0011


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          434 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       434 l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      +++..   +.+    ......+..+|+.||+++|+||.++|..|    +|++|||+.||+|..+|+...+||+++||..+
T Consensus       111 ~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l  179 (184)
T PRK12512        111 LPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISVEG----ASIKETAAKLSMSEGAVRVALHRGLAALAAKF  179 (184)
T ss_pred             ccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            11110   111    11234578899999999999999999887    99999999999999999999999999999988


Q ss_pred             hh
Q 009803          514 RT  515 (525)
Q Consensus       514 ~~  515 (525)
                      ..
T Consensus       180 ~~  181 (184)
T PRK12512        180 RS  181 (184)
T ss_pred             hc
Confidence            65

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.82  E-value=4e-19  Score=169.60  Aligned_cols=167  Identities=14%  Similarity=0.081  Sum_probs=128.5

Q ss_pred             HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803          278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  357 (525)
Q Consensus       278 ~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~  357 (525)
                      +...++..|++.|+..|.+.++.++. +.++..+++|++||+|+.+|+..++|++.  ..|.+|++..+++.+.++++++
T Consensus        17 ~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~~Rk~   93 (185)
T PRK09649         17 SAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRHV   93 (185)
T ss_pred             HHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHHHHHh
Confidence            33446689999999999999999995 68888899999999999999999999864  4799999999999999999875


Q ss_pred             ccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCC
Q 009803          358 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP  437 (525)
Q Consensus       358 ~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~  437 (525)
                      .+..+.                                                     +.+.    .     .+...+.
T Consensus        94 ~~~~~~-----------------------------------------------------~~~~----~-----~~~~~~~  111 (185)
T PRK09649         94 RSRPRT-----------------------------------------------------TRGA----R-----PEHLIDG  111 (185)
T ss_pred             cccccc-----------------------------------------------------cccc----c-----hhhccCh
Confidence            431100                                                     0000    0     0000000


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          438 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       438 ~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                           +......+....|..+|+.||+++|+||.|+|..+    +|++|||+.||+|.++|+++++||+++||+.+....
T Consensus       112 -----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~~~~~  182 (185)
T PRK09649        112 -----DRHARGFEDLVEVTTMIADLTTDQREALLLTQLLG----LSYADAAAVCGCPVGTIRSRVARARDALLADAEPDD  182 (185)
T ss_pred             -----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCccc
Confidence                 00000111224588899999999999999999988    999999999999999999999999999999665544


Q ss_pred             h
Q 009803          518 L  518 (525)
Q Consensus       518 L  518 (525)
                      |
T Consensus       183 ~  183 (185)
T PRK09649        183 L  183 (185)
T ss_pred             c
Confidence            3

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.82  E-value=2.8e-19  Score=165.83  Aligned_cols=156  Identities=17%  Similarity=0.123  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT  371 (525)
Q Consensus       292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~  371 (525)
                      ..|.+.++.+|.++.++..+++|++||+|+.+|+++++|++.   .|.+|++..++|.+.++++++.+..+.        
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~--------   70 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE--------   70 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc--------
Confidence            568999999999999999999999999999999999999863   499999999999999999876431000        


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHH
Q 009803          372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM  451 (525)
Q Consensus       372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~  451 (525)
                                                                  ..+..    + .   .+...  ...+|++.+...+.
T Consensus        71 --------------------------------------------~~~~~----~-~---~~~~~--~~~~~~~~~~~~e~   96 (160)
T PRK09642         71 --------------------------------------------LSLCK----E-T---EENIK--SSHNIEDLLLTKEQ   96 (160)
T ss_pred             --------------------------------------------cccch----h-h---hhhcc--CCCChHHHHHHHHH
Confidence                                                        00000    0 0   00001  11245666666677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      ...|..+|+.||+++|.||.|+|..|    +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus        97 ~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  157 (160)
T PRK09642         97 KLLIAQKLRELPENYRDVVLAHYLEE----KSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE  157 (160)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence            78899999999999999999999988    99999999999999999999999999999988654

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.82  E-value=8.7e-19  Score=170.25  Aligned_cols=165  Identities=18%  Similarity=0.269  Sum_probs=136.5

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++..++++|+..|.+.++.++.++.++..+.+|++||+++.+|+...+|++  + .|.+|++..+|+.+.+++++..+ .
T Consensus        25 ~d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~  100 (203)
T PRK09647         25 ATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-I  100 (203)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-C
Confidence            458899999999999999999999999999999999999999999999985  3 69999999999999999987643 1


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                      +.                                                    ..++     + +  . +.... ...+
T Consensus       101 ~~----------------------------------------------------~~~~-----~-~--~-~~~~~-~~~~  118 (203)
T PRK09647        101 RM----------------------------------------------------EALP-----E-D--Y-DRVPG-DEPN  118 (203)
T ss_pred             cc----------------------------------------------------cccc-----c-c--c-cccCC-CCCC
Confidence            10                                                    0000     0 0  0 01111 1235


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      |+..+........|..+|..||++++.||.|+|+.|    ++++|||+.||||..+|++.++||+++||+.+...
T Consensus       119 ~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~~~g----~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~  189 (203)
T PRK09647        119 PEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEG----LSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAH  189 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            666666777778899999999999999999999888    99999999999999999999999999999988754

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

Probab=99.82  E-value=2.7e-19  Score=171.41  Aligned_cols=173  Identities=13%  Similarity=0.135  Sum_probs=132.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccccee
Q 009803          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  362 (525)
Q Consensus       283 g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iR  362 (525)
                      +..+|+.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+.+.+|++.  ..|.+|++..++|.+.++++++.+...
T Consensus         9 ~~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~   86 (193)
T TIGR02947         9 RAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQ   86 (193)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCcc
Confidence            378999999999999999999999998999999999999999999999864  469999999999999999987654110


Q ss_pred             cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCH
Q 009803          363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA  442 (525)
Q Consensus       363 iP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~p  442 (525)
                      ..                         ..+++.           .            .... +    ..+ ........+
T Consensus        87 ~~-------------------------~~~~~~-----------~------------~~~~-~----~~~-~~~~~~~~~  112 (193)
T TIGR02947        87 QS-------------------------DDDDIE-----------D------------WQLA-K----AAS-HTSNGLRSA  112 (193)
T ss_pred             cc-------------------------cchhhh-----------h------------hhhc-c----ccc-cccccccch
Confidence            00                         000000           0            0000 0    000 000011123


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          443 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       443 ee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      +...........|..+|+.||+++|+||.|+|..|    +|++|||+.||||.++|+.+++||+++||+.+..
T Consensus       113 e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~  181 (193)
T TIGR02947       113 ELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEG----FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD  181 (193)
T ss_pred             hHHHHhhhhHHHHHHHHHhCCHHHhhheeehhhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            33333444456789999999999999999999887    9999999999999999999999999999998864

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=99.82  E-value=6.9e-19  Score=168.59  Aligned_cols=162  Identities=14%  Similarity=0.148  Sum_probs=129.4

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++..++.+|+..|.+.++.+|++++++..+++|++||+|+.+|+..++|++.  ..|.+|++..++|.+.++++++.+..
T Consensus         7 ~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~awL~~Ia~n~~~d~~R~~~~~~   84 (187)
T PRK12516          7 EGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVG--TNMKAWLFTILRNEFYSQMRKRGREV   84 (187)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCc--ccHHHHHHHHHHHHHHHHHHhhcCCc
Confidence            4578999999999999999999999999999999999999999999999864  36999999999999999998765310


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                      ..                                                      .+..        ..+....  .+.
T Consensus        85 ~~------------------------------------------------------~~~~--------~~~~~~~--~~~  100 (187)
T PRK12516         85 QD------------------------------------------------------TDGM--------FTEQLAV--HPS  100 (187)
T ss_pred             cc------------------------------------------------------cccc--------cccccCC--Ccc
Confidence            00                                                      0000        0000000  001


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      ..    .......|..+|+.||+++|+||.|+|..|    +|++|||+.||||.++|+++++||+++||+.+....
T Consensus       101 ~~----~~~~~~~l~~~L~~Lp~~~r~i~~L~~~~g----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~  168 (187)
T PRK12516        101 QY----GTLDLQDFRAALDQLPDDQREAIILVGASG----FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG  168 (187)
T ss_pred             hh----hHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            11    111235689999999999999999999987    999999999999999999999999999999987654

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

Probab=99.81  E-value=5.6e-19  Score=163.95  Aligned_cols=159  Identities=15%  Similarity=0.163  Sum_probs=128.3

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803          281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (525)
Q Consensus       281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~  360 (525)
                      +|+..+++.|+..|.+.|+.++..+.++..+++|++||+|+.+|++.++|+.  ...|.+|++..+++.+.++++++.+.
T Consensus         2 ~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~   79 (162)
T TIGR02983         2 SATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL   79 (162)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc
Confidence            3568999999999999999999999999999999999999999999999964  34799999999999999998865430


Q ss_pred             eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCC
Q 009803          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE  440 (525)
Q Consensus       361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~  440 (525)
                       ..                                                     . +...        .+.  +..  
T Consensus        80 -~~-----------------------------------------------------~-~~~~--------~~~--~~~--   92 (162)
T TIGR02983        80 -EL-----------------------------------------------------P-TREL--------PDA--AAP--   92 (162)
T ss_pred             -cc-----------------------------------------------------c-cccc--------Ccc--cCC--
Confidence             00                                                     0 0000        000  000  


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      .+   .........|..+|..||+++|.||.|+|..|    +|.+|||+.||+|.++|+++++||+++||+.+..
T Consensus        93 ~~---~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~  160 (162)
T TIGR02983        93 DP---APDVALRAALARALRRLPARQRAVVVLRYYED----LSEAQVAEALGISVGTVKSRLSRALARLRELLEE  160 (162)
T ss_pred             cc---chhHHHHHHHHHHHHhCCHHHHHHhhhHHHhc----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            01   11233456788999999999999999999877    9999999999999999999999999999997753

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.81  E-value=5.7e-19  Score=166.14  Aligned_cols=163  Identities=13%  Similarity=0.095  Sum_probs=129.0

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++..++..|+..|.+.|+.++.++.++..+++|++||+|+.+|+. .+|+..  ..|.+|++.+++|.+.++++++.+-.
T Consensus         7 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~~   83 (172)
T PRK12523          7 PHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALEQ   83 (172)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            558899999999999999999999999999999999999999987 446543  36999999999999999998764200


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                                        ....         ++                        .       .      .......+
T Consensus        84 ------------------~~~~---------~~------------------------~-------~------~~~~~~~~   99 (172)
T PRK12523         84 ------------------AYLA---------EL------------------------A-------L------VPEAEQPS   99 (172)
T ss_pred             ------------------HHHH---------HH------------------------h-------h------cccccCCC
Confidence                              0000         00                        0       0      00001123


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      |++.....+....|..+|+.||+++|.||.|+|..|    +|++|||+.||+|.++|+++++||+++||..+..
T Consensus       100 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~  169 (172)
T PRK12523        100 PEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDG----MGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG  169 (172)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            555444444456799999999999999999999987    9999999999999999999999999999987754

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.81  E-value=7.3e-19  Score=164.14  Aligned_cols=157  Identities=17%  Similarity=0.152  Sum_probs=130.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (525)
Q Consensus       287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~  366 (525)
                      ++.|+..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++.   .|.+|++..+++.+.+++++..+....   
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~---   76 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV---   76 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc---
Confidence            67899999999999999999999999999999999999999999863   599999999999999999876531100   


Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  446 (525)
Q Consensus       367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~  446 (525)
                                             +.+++                                     +.+.   ..+|++.+
T Consensus        77 -----------------------~~~~~-------------------------------------~~~~---~~~~~~~~   93 (165)
T PRK09644         77 -----------------------GTDEI-------------------------------------EAIQ---AESTEEYV   93 (165)
T ss_pred             -----------------------chhHH-------------------------------------hhhc---ccChHHHH
Confidence                                   00000                                     0000   12455555


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      ...+....|..+|..||+++|+||.++|..|    +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus        94 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~  159 (165)
T PRK09644         94 VAKNSYEKLIQIIHTLPVIEAQAILLCDVHE----LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE  159 (165)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHhHHHhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            5666677899999999999999999999988    99999999999999999999999999999988654

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.81  E-value=1e-18  Score=162.61  Aligned_cols=160  Identities=18%  Similarity=0.172  Sum_probs=130.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi  363 (525)
                      ..+++.|+..|.+.++.+|+++.++..+++|++||+|+.+|++  .|+.  +..|.+|++..+++.+.+++++..+..+.
T Consensus         2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~   77 (166)
T PRK09639          2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR   77 (166)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence            3689999999999999999999999999999999999999999  6764  34799999999999999999876531110


Q ss_pred             ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  443 (525)
Q Consensus       364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe  443 (525)
                      .                                                      +..      ....+.  + ....|+
T Consensus        78 ~------------------------------------------------------~~~------~~~~~~--~-~~~~~e   94 (166)
T PRK09639         78 I------------------------------------------------------LGE------FQWQEV--D-NEPSPE   94 (166)
T ss_pred             c------------------------------------------------------cch------hhhhhc--c-CCCChH
Confidence            0                                                      000      000000  1 123566


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      +.....+....|..+|..||+++|.||.++| .|    +|++|||+.||+|..+|+..++||+++||+.+..
T Consensus        95 ~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-~g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~  161 (166)
T PRK09639         95 EIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SG----YSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ  161 (166)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            6666667777899999999999999999999 77    9999999999999999999999999999998764

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1e-18  Score=162.31  Aligned_cols=158  Identities=14%  Similarity=0.123  Sum_probs=125.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi  363 (525)
                      ..|+++|+..|.+.|+.++.++.++..+++|++||+|+.+|+..+.|++   ..|.+|++.++++.+.++++++.+.   
T Consensus         3 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~---   76 (161)
T PRK12528          3 SATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLE---   76 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHH---
Confidence            3689999999999999999999999899999999999999999988864   2699999999999999998865320   


Q ss_pred             ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  443 (525)
Q Consensus       364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe  443 (525)
                                     ....         .+                        ++            + .++.....++
T Consensus        77 ---------------~~~~---------~~------------------------~~------------~-~~~~~~~~~~   95 (161)
T PRK12528         77 ---------------RAYL---------EA------------------------LA------------Q-LPERVAPSEE   95 (161)
T ss_pred             ---------------HhhH---------HH------------------------hh------------c-cccccCCCHH
Confidence                           0000         00                        00            0 0000111344


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      ......+....|..+|..||+++|.||.|+|..|    +|++|||+.||+|.++|+++++||+++||..
T Consensus        96 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~  160 (161)
T PRK12528         96 ERAIILETLVELDQLLDGLPPLVKRAFLLAQVDG----LGYGEIATELGISLATVKRYLNKAAMRCYFA  160 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence            3333344456799999999999999999999988    9999999999999999999999999999964

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.8e-18  Score=160.72  Aligned_cols=158  Identities=13%  Similarity=0.146  Sum_probs=125.4

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++..+++.++..|.+.|+.++.++.++..+++|++||+++.+|+..++|++.   .|.||++..+++.+.++++++.+..
T Consensus         2 ~~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~   78 (161)
T PRK12541          2 KRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYK   78 (161)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccc
Confidence            3467999999999999999999999999999999999999999999999863   5999999999999999998775410


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                      ..                                                     ..+.       ..     .......
T Consensus        79 ~~-----------------------------------------------------~~~~-------~~-----~~~~~~~   93 (161)
T PRK12541         79 TT-----------------------------------------------------TIEE-------FH-----LPNVPST   93 (161)
T ss_pred             cc-----------------------------------------------------chhh-------hh-----ccCCCCc
Confidence            00                                                     0000       00     0000111


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      +++.....+. ..+..+|..||+++|.||.|+|..|    +|++|||+.||+|.++|++.++||+++||+.
T Consensus        94 ~~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541         94 EHEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDYYG----FSYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             HHHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            2233333333 3456789999999999999999988    9999999999999999999999999999974

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=99.80  E-value=2.2e-18  Score=165.01  Aligned_cols=178  Identities=15%  Similarity=0.083  Sum_probs=133.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccch
Q 009803          288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM  367 (525)
Q Consensus       288 e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~  367 (525)
                      .+.+..|.+.|+.+|+++.++..+++|++||+|+.+|+...+|++.  .+|.+|++..+++.+.++++++.+....+.- 
T Consensus         5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~-   81 (188)
T TIGR02943         5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDL-   81 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccc-
Confidence            3578889999999999999999999999999999999999999864  4799999999999999999877542111000 


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHH
Q 009803          368 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI  447 (525)
Q Consensus       368 ~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~  447 (525)
                                        ...+.                        .-.++.... ..+.......++ ..++|+..+.
T Consensus        82 ------------------~~~~~------------------------~~~~~~~~~-~~~~~~~~~~~~-~~~~~e~~~~  117 (188)
T TIGR02943        82 ------------------DDELD------------------------DEAFNALFT-QNGHWAQHGQPQ-HWNTPEKQLE  117 (188)
T ss_pred             ------------------ccccc------------------------cchhhhhhc-cccchhcccccc-ccCCHHHHHH
Confidence                              00000                        000000000 000000011111 1235777777


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          448 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       448 ~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      ..+....+..+|..||+++|+||.++|..+    +|++|||+.||+|.++|++++.||+++||+++...
T Consensus       118 ~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~  182 (188)
T TIGR02943       118 NKEFWEVFEACLYHLPEQTARVFMMREVLG----FESDEICQELEISTSNCHVLLYRARLSLRACLSIN  182 (188)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            777778899999999999999999999988    99999999999999999999999999999988753

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.

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.2e-18  Score=165.34  Aligned_cols=181  Identities=17%  Similarity=0.152  Sum_probs=133.3

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803          288 DKMITSNIRLVISIAKNYQGAGMN-LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (525)
Q Consensus       288 e~Lv~~nlrLV~~IA~~y~~~g~~-~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~  366 (525)
                      +..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++++|++.  .+|.+|++..++|.+.++++++.+.......
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            456788999999999999998888 9999999999999999999864  4799999999999999999876542111000


Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  446 (525)
Q Consensus       367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~  446 (525)
                      .                   ......+..                    .+.   .. .+.....+..++ ...+|++.+
T Consensus        86 ~-------------------~~~~~~~~~--------------------~~~---~~-~~~~~~~~~~~~-~~~~~e~~~  121 (195)
T PRK12532         86 L-------------------DDELLDEAF--------------------ESH---FS-QNGHWTPEGQPQ-HWNTPEKSL  121 (195)
T ss_pred             c-------------------cccccchhh--------------------hhh---hc-cccccccccCcc-ccCCHHHHH
Confidence            0                   000000000                    000   00 000000000111 123677777


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 009803          447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  518 (525)
Q Consensus       447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L  518 (525)
                      ...+....+..+|..||+++|+||.|+|..|    +|++|||+.||+|.++|+++++||+++||+++....+
T Consensus       122 ~~~e~~~~l~~~l~~L~~~~r~i~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~  189 (195)
T PRK12532        122 NNNEFQKILQSCLYNLPENTARVFTLKEILG----FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF  189 (195)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHhhhHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            7777778899999999999999999999987    9999999999999999999999999999999876543

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.6e-18  Score=164.59  Aligned_cols=176  Identities=17%  Similarity=0.121  Sum_probs=131.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccch
Q 009803          288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM  367 (525)
Q Consensus       288 e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~  367 (525)
                      +..|..|.+.++.+|.+|.++..+++|++||+|+.+|+.+++|++.  .+|.+|++..++|.+.++++++.+..... ..
T Consensus        10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~   86 (189)
T PRK12530         10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQ--SALKTWIFAILKNKIIDLIRYRKRFVNES-EL   86 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCC--ccHHHHHHHHHHHHHHHHHHhhccCCCcc-cc
Confidence            3457788999999999999998999999999999999999999865  36999999999999999998765421110 00


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHH
Q 009803          368 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI  447 (525)
Q Consensus       368 ~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~  447 (525)
                                        .     .+                   ..+....    +.......+........+|++.+.
T Consensus        87 ------------------~-----~~-------------------~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~  120 (189)
T PRK12530         87 ------------------I-----EE-------------------DSPNSFF----DEKGHWKPEYYEPSEWQEVENTVY  120 (189)
T ss_pred             ------------------c-----cc-------------------ccchhhh----cccccccccccCCccccCHHHHHH
Confidence                              0     00                   0000000    000000000111111235667777


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          448 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       448 ~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      ..+....|..+|+.||+++|+||.|+|..|    +|++|||+.||+|.++|+.+++||+++||+++...
T Consensus       121 ~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~  185 (189)
T PRK12530        121 KEEFWLIFEACLNHLPAQQARVFMMREYLE----LSSEQICQECDISTSNLHVLLYRARLQLQACLSKN  185 (189)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            777778899999999999999999999987    99999999999999999999999999999988644

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.4e-18  Score=160.80  Aligned_cols=158  Identities=11%  Similarity=0.134  Sum_probs=126.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi  363 (525)
                      ...+.+++..|.+.|+.+|+++.++..+++|++||+++.+|+..++|++.  ..|.+|++..++|.+.++++++.+....
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            46799999999999999999999999999999999999999999999854  3699999999999999999876431000


Q ss_pred             ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  443 (525)
Q Consensus       364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe  443 (525)
                                                                            .+...  .     ..  .+   ..++
T Consensus        83 ------------------------------------------------------~~~~~--~-----~~--~~---~~~~   96 (164)
T PRK12547         83 ------------------------------------------------------SDGVF--T-----AR--VA---VHPA   96 (164)
T ss_pred             ------------------------------------------------------ccccc--c-----cc--CC---CCch
Confidence                                                                  00000  0     00  00   0111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      ..  .......|..+|..||+++|+||.|+|..|    +|++|||+.||||.++|+++++||+++||..+..
T Consensus        97 ~~--~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  162 (164)
T PRK12547         97 QY--GSLDLQDFKKALNLLSADQREAIILIGASG----FSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV  162 (164)
T ss_pred             hh--hHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            11  112235688999999999999999999977    9999999999999999999999999999998764

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.7e-18  Score=166.07  Aligned_cols=180  Identities=16%  Similarity=0.147  Sum_probs=131.1

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (525)
Q Consensus       289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~  368 (525)
                      .++..|.+.++.+|+++.++..+++|++||+|+.+|+.+++|++.  ..|.+|++.+++|.+.++++++.+...++..  
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~--   87 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARQRTVNLSAL--   87 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhcccc--chHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence            348899999999999999999999999999999999999999975  3699999999999999999887542111000  


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  448 (525)
Q Consensus       369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~  448 (525)
                                            ..++.                  ....++............+..++. ..++++....
T Consensus        88 ----------------------~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~  126 (201)
T PRK12545         88 ----------------------DAELD------------------GEALLDRELFKDNGHWAAHAKPRP-WPKPETILQQ  126 (201)
T ss_pred             ----------------------ccccc------------------hhhhhhhhhhcccccccccccCcC-CCCHHHHHHH
Confidence                                  00000                  000000000000000000111111 2246666666


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      .+....|..+|..||+++|.||.|+|+.|    +|++|||+.||+|.++|+++++||+++||+++...+
T Consensus       127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~  191 (201)
T PRK12545        127 QQFWTLFETCLDHLPEQIGRVFMMREFLD----FEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKG  191 (201)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            66667889999999999999999999988    999999999999999999999999999999986544

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=99.80  E-value=2.4e-18  Score=177.46  Aligned_cols=183  Identities=17%  Similarity=0.134  Sum_probs=135.6

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      |+..++++|+..|.+.++++|+++.++..+++|++||.|+.+|+.+++|++.  ..|.+|++..++|.+.++++++.+..
T Consensus         2 gd~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~   79 (324)
T TIGR02960         2 VDGAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRP   79 (324)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCc
Confidence            4578999999999999999999999999999999999999999999999864  46999999999999999998765411


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC------
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA------  435 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~------  435 (525)
                      .....                  .. .                         ........ ..+......+.+.      
T Consensus        80 ~~~~~------------------~~-~-------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~  114 (324)
T TIGR02960        80 RPVGL------------------GA-P-------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDL  114 (324)
T ss_pred             Ccccc------------------CC-C-------------------------CCcccccc-cccccccccCCCCcccccc
Confidence            00000                  00 0                         00000000 0000000000000      


Q ss_pred             -CCCCCCHHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          436 -DPEAETAEDLLIKKF-MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       436 -d~~~~~pee~~~~~~-~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                       .....+|++.+...+ ....+..+|+.||+++|.||.|+|..+    +|++|||+.||+|.++|+++++||+++||+++
T Consensus       115 ~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  190 (324)
T TIGR02960       115 DDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLG----WRAAETAELLGTSTASVNSALQRARATLDEVG  190 (324)
T ss_pred             ccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence             111235666655544 456788999999999999999999988    99999999999999999999999999999988


Q ss_pred             hh
Q 009803          514 RT  515 (525)
Q Consensus       514 ~~  515 (525)
                      ..
T Consensus       191 ~~  192 (324)
T TIGR02960       191 PS  192 (324)
T ss_pred             cc
Confidence            74

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=3.7e-18  Score=164.84  Aligned_cols=168  Identities=16%  Similarity=0.071  Sum_probs=129.7

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          277 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       277 ~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      .....++..+++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++.  ..|.+|++..+|+.+.+++++
T Consensus        17 ~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk   93 (196)
T PRK12535         17 LAAGRGDRAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWVDNIRH   93 (196)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHHHHHHh
Confidence            344456689999999999999999975 67888899999999999999999999863  379999999999999999997


Q ss_pred             cccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCC
Q 009803          357 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  436 (525)
Q Consensus       357 ~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d  436 (525)
                      +.+..+.                                                     ..+ ...     ...+   .
T Consensus        94 ~~~~~~~-----------------------------------------------------~~~-~~~-----~~~~---~  111 (196)
T PRK12535         94 DMARPRK-----------------------------------------------------SAT-EYE-----DAAA---T  111 (196)
T ss_pred             hccCCCc-----------------------------------------------------ccc-ccc-----cccc---c
Confidence            6531110                                                     000 000     0000   0


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          437 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       437 ~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                       . ..++..... .....|..+|+.||+++|+||.|+|..|    +|++|||+.||+|.++|+++++||+++||+++...
T Consensus       112 -~-~~~~~~~~~-~~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~  184 (196)
T PRK12535        112 -T-ASNETTGSW-SEWIDVRTLIDALPPERREALILTQVLG----YTYEEAAKIADVRVGTIRSRVARARADLIAATATG  184 (196)
T ss_pred             -c-CCcchhHHH-HHHHHHHHHHHcCCHHHHHHhhhHHHhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence             0 011111111 1234689999999999999999999988    99999999999999999999999999999988654

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.80  E-value=5.1e-18  Score=176.42  Aligned_cols=186  Identities=19%  Similarity=0.188  Sum_probs=136.4

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHH
Q 009803          275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  354 (525)
Q Consensus       275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~i  354 (525)
                      .+.+...++..++++|+..|.+.|+.+|+++.++..+++|++||+|+.+|+.+++|++.  ..|.+|++..++|.+.+++
T Consensus         9 l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~   86 (339)
T PRK08241          9 LLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDAL   86 (339)
T ss_pred             HHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHHH
Confidence            34444556689999999999999999999999998999999999999999999999853  4699999999999999999


Q ss_pred             HhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCccc
Q 009803          355 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  434 (525)
Q Consensus       355 r~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  434 (525)
                      +++.+.. .+..                  .+. +                         ..........+....+.+.+
T Consensus        87 Rk~~~~~-~~~~------------------~~~-~-------------------------~~~~~~~~~~~~~~~~~~~~  121 (339)
T PRK08241         87 EGRARRP-LPTD------------------LGA-P-------------------------AADPVDELVERPEVPWLEPY  121 (339)
T ss_pred             Hhhcccc-Cccc------------------cCC-C-------------------------cCcccccccccccccccCCC
Confidence            8765310 0000                  000 0                         00000000000000011111


Q ss_pred             CCC----CCCCHHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803          435 ADP----EAETAEDLLIKKF-MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL  509 (525)
Q Consensus       435 ~d~----~~~~pee~~~~~~-~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL  509 (525)
                      .+.    ...+|++.+...+ ....|..+|++||+++|.||.|+|..+    +|++|||++||+|.++|+++++||+++|
T Consensus       122 ~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~RAr~~L  197 (339)
T PRK08241        122 PDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLG----WSAAEVAELLDTSVAAVNSALQRARATL  197 (339)
T ss_pred             CcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHhhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            111    1235666555544 445689999999999999999999988    9999999999999999999999999999


Q ss_pred             Hh
Q 009803          510 KN  511 (525)
Q Consensus       510 R~  511 (525)
                      |+
T Consensus       198 r~  199 (339)
T PRK08241        198 AE  199 (339)
T ss_pred             hh
Confidence            98

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=6.6e-18  Score=164.46  Aligned_cols=179  Identities=17%  Similarity=0.153  Sum_probs=134.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (525)
Q Consensus       287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~  366 (525)
                      -..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|++.  .+|.+|++.+++|.+.++++++.+....+..
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            45788999999999999999999999999999999999999999864  4799999999999999999977642111000


Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCC-CcccCCCCCCCHHHH
Q 009803          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP-SEVIADPEAETAEDL  445 (525)
Q Consensus       367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l-~d~l~d~~~~~pee~  445 (525)
                      .                  ....+  +         ..+..+             .  +....+ .....+ ...+|+..
T Consensus        98 ~------------------~~~~~--~---------~~~~~~-------------~--~~~~~~~~~~~~~-~~~~~e~~  132 (206)
T PRK12544         98 L------------------RDEEE--E---------EDFEEL-------------F--DESGHWQKDERPQ-AWGNPEES  132 (206)
T ss_pred             c------------------cccch--h---------hHHHHh-------------h--ccccccccccccc-ccCCHHHH
Confidence            0                  00000  0         000000             0  000000 000111 12357777


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      +...+....+..+|..||+++|+||.|+|..+    +|++|||+.||+|..+|+++++||+++||+.+...
T Consensus       133 ~~~~e~~~~l~~~L~~L~~~~r~v~~L~~~~g----~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~  199 (206)
T PRK12544        133 LEQEQFWRIFEACLDGLPAKYARVFMMREFIE----LETNEICHAVDLSVSNLNVLLYRARLRLRECLENK  199 (206)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777899999999999999999999988    99999999999999999999999999999998753

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.79  E-value=7.3e-18  Score=156.60  Aligned_cols=158  Identities=16%  Similarity=0.188  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (525)
Q Consensus       289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~  368 (525)
                      .++..|.+.++.+|.++.++..+++|++||+++.+|+....|++.   .|.+|++..+|+.+.++++++.+....     
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~-----   73 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKY-----   73 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcccccc-----
Confidence            367789999999999999999999999999999999999888763   488999999999999999876531100     


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  448 (525)
Q Consensus       369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~  448 (525)
                                                                      +      ....... +. .+. ..+|+..+..
T Consensus        74 ------------------------------------------------~------~~~~~~~-~~-~~~-~~~~~~~~~~   96 (163)
T PRK07037         74 ------------------------------------------------H------GDEEDGL-DV-PSP-EASPEAALIN   96 (163)
T ss_pred             ------------------------------------------------c------ccccccc-cc-CCC-CCCHHHHHHH
Confidence                                                            0      0000000 00 111 1246666666


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       449 ~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      .+....|..+|+.||+++|.||.++|..|    +|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus        97 ~~~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~  159 (163)
T PRK07037         97 RDTLRHVADALSELPARTRYAFEMYRLHG----ETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA  159 (163)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            66677899999999999999999999987    9999999999999999999999999999998764

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.79  E-value=1.3e-18  Score=159.78  Aligned_cols=152  Identities=17%  Similarity=0.153  Sum_probs=123.0

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT  371 (525)
Q Consensus       292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~  371 (525)
                      ..|.+.|+.++.++.++..+++|++||+++.+|+.+++|++   .+|.||++..+++.+.++++++.+....+       
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~-------   71 (154)
T TIGR02950         2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID-------   71 (154)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc-------
Confidence            57899999999999998889999999999999999999997   47999999999999999998765311000       


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHH
Q 009803          372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM  451 (525)
Q Consensus       372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~  451 (525)
                                          .+                           .        ..+...+ ....|++.+...+.
T Consensus        72 --------------------~~---------------------------~--------~~~~~~~-~~~~~~~~~~~~~~   95 (154)
T TIGR02950        72 --------------------DD---------------------------A--------IGDLEQH-PVESPEHHLLIKIE   95 (154)
T ss_pred             --------------------Hh---------------------------h--------hhhcccc-ccCChhHHHHHHHH
Confidence                                00                           0        0000001 11245666666666


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      ...|..+|+.||+++++||.++|+.|    +|++|||+.||+|..+|++..+||+++||+.+
T Consensus        96 ~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l  153 (154)
T TIGR02950        96 QEEITHHLSRLPENYRTVLILREFKE----FSYKEIAELLNLSLAKVKSNLFRARKELKKLL  153 (154)
T ss_pred             HHHHHHHHHhCCHhheeeeeehhhcc----CcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            67899999999999999999999877    99999999999999999999999999999865

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.

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.78  E-value=7.1e-18  Score=156.39  Aligned_cols=154  Identities=14%  Similarity=0.109  Sum_probs=124.3

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT  371 (525)
Q Consensus       292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~  371 (525)
                      ..|.+.++.++.++.++..+++|++||+|+.+|+..+.|++   .+|.||++..+++.+.++++++.+...         
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~---~~~~~wL~~ia~n~~~d~~R~~~~~~~---------   69 (159)
T PRK12527          2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI---EHPRAFLYRTALNLVVDRHRRHRVRQA---------   69 (159)
T ss_pred             hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc---cchHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence            56888999999999998889999999999999999999875   279999999999999999986532000         


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHH
Q 009803          372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM  451 (525)
Q Consensus       372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~  451 (525)
                                                                  .+++. .. +.     ..   ...++|++.+..++.
T Consensus        70 --------------------------------------------~~~~~-~~-~~-----~~---~~~~~~~~~~~~~~~   95 (159)
T PRK12527         70 --------------------------------------------EPLEV-LD-EE-----ER---LHSPSPQTRLDLGQR   95 (159)
T ss_pred             --------------------------------------------cchhh-hh-cc-----cc---ccCCCHHHHHHHHHH
Confidence                                                        00000 00 00     00   012256777666677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      ...|..+|..||+++++||.|+|+.+    +|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus        96 ~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~  155 (159)
T PRK12527         96 LALLQRALAELPPACRDSFLLRKLEG----LSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ  155 (159)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            77899999999999999999999988    9999999999999999999999999999998764

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=1.1e-17  Score=160.25  Aligned_cols=161  Identities=14%  Similarity=0.111  Sum_probs=127.4

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803          281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (525)
Q Consensus       281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~  360 (525)
                      ..+..+++.++..|.+.|+.+|+++.++..+++|++||+|+.+|+.++.|++.  ..|.+|++..+++.+.+..+++.+.
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            45688999999999999999999999999999999999999999999999864  3699999999999876655432210


Q ss_pred             eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCC
Q 009803          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE  440 (525)
Q Consensus       361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~  440 (525)
                        .                                                    ...+       .    +...+....
T Consensus        97 --~----------------------------------------------------~~~~-------~----~~~~~~~~~  111 (188)
T PRK12517         97 --L----------------------------------------------------VDIE-------D----DSIEDDASH  111 (188)
T ss_pred             --c----------------------------------------------------cCcc-------c----ccccCcccc
Confidence              0                                                    0000       0    001111111


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      +++...    ....|..+|..||+++|.||.++|..|    +|++|||+.||||..+|+.+++||+++||+.+...
T Consensus       112 ~~e~~~----~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  179 (188)
T PRK12517        112 SSEEEM----EQEWLRRQIAKLDPEYREPLLLQVIGG----FSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP  179 (188)
T ss_pred             ChhHHH----HHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            333322    235689999999999999999999988    99999999999999999999999999999998753

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=8.7e-18  Score=160.32  Aligned_cols=160  Identities=14%  Similarity=0.156  Sum_probs=127.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 009803          285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  364 (525)
Q Consensus       285 ~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP  364 (525)
                      .++..++..|.+.++.+|.++.++..+++|++||+|+.+|+..++|++..  .|.+|++..++|.+.++++++.+.... 
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~~-   81 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVED-   81 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccccc-
Confidence            57889999999999999999999999999999999999999999998653  699999999999999998876531000 


Q ss_pred             cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHH
Q 009803          365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED  444 (525)
Q Consensus       365 ~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee  444 (525)
                                                                           .+.        ...+... +   .++.
T Consensus        82 -----------------------------------------------------~~~--------~~~~~~~-~---~~~~   96 (182)
T PRK12540         82 -----------------------------------------------------ADG--------SYAKTLK-S---QPGQ   96 (182)
T ss_pred             -----------------------------------------------------ccc--------ccccccc-C---CCch
Confidence                                                                 000        0000000 0   1111


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 009803          445 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  518 (525)
Q Consensus       445 ~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L  518 (525)
                      ..  ......|..+|+.||+++|+||.|+|..+    +|++|||+.||+|..+|+++++||+++||+.+.....
T Consensus        97 ~~--~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~  164 (182)
T PRK12540         97 NA--HLEFEEFRAALDKLPQDQREALILVGASG----FSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA  164 (182)
T ss_pred             HH--HHHHHHHHHHHHhCCHHHHHHhhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            11  11234689999999999999999999887    9999999999999999999999999999999986553

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.78  E-value=1e-17  Score=164.58  Aligned_cols=115  Identities=16%  Similarity=0.187  Sum_probs=104.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc-
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAG--MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS-  358 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g--~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~-  358 (525)
                      |+.. +++||..|.|+|.++|++|.++.  .+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++++.. 
T Consensus         7 gd~~-~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k   85 (218)
T TIGR02895         7 GNEE-REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQK   85 (218)
T ss_pred             CChH-HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhccc
Confidence            3455 99999999999999999998764  5899999999999999999999999999999999999999999999887 


Q ss_pred             --cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Q 009803          359 --RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA  397 (525)
Q Consensus       359 --r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~  397 (525)
                        +.+++|....+....+..+...+..+.++.|+.+||+..
T Consensus        86 ~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~  126 (218)
T TIGR02895        86 YQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY  126 (218)
T ss_pred             ccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence              788999877666778888888999999999999999854

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).

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.78  E-value=1.3e-17  Score=158.97  Aligned_cols=154  Identities=14%  Similarity=0.110  Sum_probs=126.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (525)
Q Consensus       287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~  366 (525)
                      ++.|+..|.+.|+.++.++.++..+++|++||+++.+|+.+..|++.  .+|.+|++..+++.+.++++++.+...++  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~--   78 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP--   78 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence            67899999999999999999999999999999999999999999853  47999999999999999998765411000  


Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  446 (525)
Q Consensus       367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~  446 (525)
                                                                               .+      +...+    ++++..
T Consensus        79 ---------------------------------------------------------~~------~~~~~----~~~~~~   91 (181)
T PRK09637         79 ---------------------------------------------------------DD------LLFED----EEREEN   91 (181)
T ss_pred             ---------------------------------------------------------hh------hhccC----CChhHH
Confidence                                                                     00      00000    111222


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      ...+....+..+|+.||+++|.||.|+|..|    ++++|||++||+|..+|+.++.||+++||+.+..
T Consensus        92 ~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  156 (181)
T PRK09637         92 AKKELAPCLRPFIDALPEKYAEALRLTELEG----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG  156 (181)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            3344567799999999999999999999988    9999999999999999999999999999998764

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.77  E-value=1.3e-17  Score=157.16  Aligned_cols=162  Identities=13%  Similarity=0.096  Sum_probs=126.5

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccccee
Q 009803          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  362 (525)
Q Consensus       283 g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iR  362 (525)
                      +..|+..++..|.+.++.++.++.++..+++|++||.|+.+|+. ..|++..  .|.+|++..+++.+.++++++.+.. 
T Consensus         8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~-   83 (172)
T PRK09651          8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEK-   83 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHh-
Confidence            46799999999999999999999999999999999999999998 3565432  5899999999999999988653200 


Q ss_pred             cccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCH
Q 009803          363 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA  442 (525)
Q Consensus       363 iP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~p  442 (525)
                                       ..                                  .  + .+.     .    +.+....+|
T Consensus        84 -----------------~~----------------------------------~--~-~~~-----~----~~~~~~~~~  100 (172)
T PRK09651         84 -----------------AY----------------------------------L--E-MLA-----L----MPEGGAPSP  100 (172)
T ss_pred             -----------------hh----------------------------------h--h-HHh-----h----ccccCCCCh
Confidence                             00                                  0  0 000     0    000011134


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          443 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       443 ee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      +......+....|..+|+.||+++|+||.++|+.|    +|++|||+.||+|.++|+..++||+++|+.....
T Consensus       101 ~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~  169 (172)
T PRK09651        101 EERESQLETLQLLDSMLDGLNGKTREAFLLSQLDG----LTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLE  169 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhhccC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            44444445556799999999999999999999988    9999999999999999999999999999986543

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=2.5e-17  Score=158.11  Aligned_cols=157  Identities=12%  Similarity=0.146  Sum_probs=122.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi  363 (525)
                      ..+++.|+. |.+.|+++|+.+.++..+++|++||+|+.+|+.+..|+..  ..|.+|++..++|.+.++++++.+... 
T Consensus         7 ~~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~-   82 (188)
T PRK12546          7 RDPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVP-   82 (188)
T ss_pred             hhHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccccc-
Confidence            456777766 7799999999999999999999999999999999999863  469999999999999999887653100 


Q ss_pred             ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  443 (525)
Q Consensus       364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe  443 (525)
                                                                           ..+.        ...+...+..  ..+
T Consensus        83 -----------------------------------------------------~~~~--------~~~~~~~~~~--~~~   99 (188)
T PRK12546         83 -----------------------------------------------------DPEG--------VHAASLAVKP--AHD   99 (188)
T ss_pred             -----------------------------------------------------Cccc--------ccccccccCC--cch
Confidence                                                                 0000        0000000000  111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      .    ......+..+|+.||+++|+||.|+|..+    +|.+|||+.||||..+|+++++||+++||+.+..
T Consensus       100 ~----~~~~~~l~~~L~~Lp~~~r~v~~L~~~~g----~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~  163 (188)
T PRK12546        100 G----RLAMSDFRAAFAQLPDEQREALILVGASG----FSYEEAAEMCGVAVGTVKSRANRARARLAELLQL  163 (188)
T ss_pred             h----HHHHHHHHHHHHhCCHHHhHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            1    11234688999999999999999999987    9999999999999999999999999999998864

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.76  E-value=2.6e-17  Score=155.01  Aligned_cols=149  Identities=18%  Similarity=0.210  Sum_probs=121.3

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHH
Q 009803          292 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT  371 (525)
Q Consensus       292 ~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~  371 (525)
                      ..|.+.++.++.++.++..+++|++||+++.+|+++.+|++.  .+|.+|++..+++.+.+++++..+...++       
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~-------   72 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP-------   72 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence            458899999999999999999999999999999999999863  58999999999999999998875411100       


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHH
Q 009803          372 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM  451 (525)
Q Consensus       372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~  451 (525)
                                                                     +     +       .... .  ++++.....+.
T Consensus        73 -----------------------------------------------~-----~-------~~~~-~--~~~~~~~~~e~   90 (170)
T TIGR02959        73 -----------------------------------------------E-----S-------LLAA-D--SAREETFVKEL   90 (170)
T ss_pred             -----------------------------------------------h-----h-------hccc-C--CccHHHHHHHH
Confidence                                                           0     0       0000 0  11222333445


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      ...|..+|+.||+++|.||.++|..+    +|++|||+.||+|..+|++.++||+++||..+..
T Consensus        91 ~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  150 (170)
T TIGR02959        91 SQCIPPMIKELPDEYREAIRLTELEG----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET  150 (170)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            56789999999999999999999988    9999999999999999999999999999998763

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=3.1e-17  Score=156.66  Aligned_cols=156  Identities=14%  Similarity=0.138  Sum_probs=122.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (525)
Q Consensus       287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~  366 (525)
                      .+..+..+++.|+.+|.++.++..+++|++||.|+.+|+....|++.  .+|.+|++..+++.+.++++++.+.....  
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~--   81 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA--   81 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc--
Confidence            44557789999999999999998999999999999999999999864  37999999999999999998765411000  


Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  446 (525)
Q Consensus       367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~  446 (525)
                                               ++                        +.            +. .+.....+..  
T Consensus        82 -------------------------~~------------------------~~------------~~-~~~~~~~~~~--   97 (182)
T PRK12511         82 -------------------------DE------------------------LA------------VL-ADASLPAAQE--   97 (182)
T ss_pred             -------------------------cc------------------------hh------------hc-cccCCCcchH--
Confidence                                     00                        00            00 0000001111  


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                       .......|..+|..||+++|+||.|+|..|    +|++|||+.||||.++|+++++||+++||+.+..
T Consensus        98 -~~~~~~~l~~~l~~Lp~~~R~v~~L~~~eg----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~  161 (182)
T PRK12511         98 -HAVRLAQIRDAFFDLPEEQRAALHLVAIEG----LSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEG  161 (182)
T ss_pred             -HHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence             112345688999999999999999999987    9999999999999999999999999999998864

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=6.7e-17  Score=151.65  Aligned_cols=159  Identities=16%  Similarity=0.118  Sum_probs=127.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceec
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  363 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRi  363 (525)
                      ..++.+++..|.+.++.+|.+|.++..+++|++||+|+.+|+....++.   ..|.+|++..++|.+.+++++....   
T Consensus         8 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~~---   81 (168)
T PRK12525          8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDLE---   81 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHHH---
Confidence            5689999999999999999999999999999999999999987665542   3699999999999999988754210   


Q ss_pred             ccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHH
Q 009803          364 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  443 (525)
Q Consensus       364 P~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pe  443 (525)
                                     +....                                 ++      .      + .+.+...+|+
T Consensus        82 ---------------~~~~~---------------------------------~~------~------~-~~~~~~~~~~  100 (168)
T PRK12525         82 ---------------RAYLQ---------------------------------SL------A------E-APEAVQPSPE  100 (168)
T ss_pred             ---------------HHHHH---------------------------------HH------h------c-ccccccCChH
Confidence                           00000                                 00      0      0 0001123566


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       444 e~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      +..........|..+|+.||+++|.||.|+|..|    +|++|||+.||+|..+|+..+.||+++||..+
T Consensus       101 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~eg----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~  166 (168)
T PRK12525        101 EQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEG----LTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF  166 (168)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence            6666666678899999999999999999999988    99999999999999999999999999999865

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.73  E-value=9.5e-17  Score=164.06  Aligned_cols=160  Identities=15%  Similarity=0.124  Sum_probs=124.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 009803          285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  364 (525)
Q Consensus       285 ~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP  364 (525)
                      ..+.+++..|.+.++.+|+++.++..+++|++||+|+. |.....|+   ...|.+|++..++|.+.++++++.+.... 
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~~~-   78 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRRET-   78 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence            34778999999999999999999989999999999999 66667776   34799999999999999999875430000 


Q ss_pred             cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHH
Q 009803          365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED  444 (525)
Q Consensus       365 ~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee  444 (525)
                                                                          ....        .+.+...+.. .+|++
T Consensus        79 ----------------------------------------------------~~~~--------~~~e~~~~~~-~~~~~   97 (293)
T PRK09636         79 ----------------------------------------------------YVGP--------WLPEPVVEEL-DDPLE   97 (293)
T ss_pred             ----------------------------------------------------ccCC--------cCCcCCCCCC-CChHH
Confidence                                                                0000        0000011111 13443


Q ss_pred             H-HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          445 L-LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       445 ~-~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      . .........+..+|+.|||++|.||.|+|..+    +|++|||+.||+|..+|+++++||+++||+...
T Consensus        98 ~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~~~g----~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~  164 (293)
T PRK09636         98 AVVAAEDLSLALMLALERLSPLERAAFLLHDVFG----VPFDEIASTLGRSPAACRQLASRARKHVRAARP  164 (293)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence            3 33445556789999999999999999999988    999999999999999999999999999999754

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.72  E-value=1.1e-16  Score=148.13  Aligned_cols=155  Identities=16%  Similarity=0.180  Sum_probs=112.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcC
Q 009803          307 GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENG  386 (525)
Q Consensus       307 ~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lg  386 (525)
                      ++..+++|++||+|+.+|+....+ +  +..|.+|++..++|.+.++++++.+..+....                    
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~--------------------   58 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL--------------------   58 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence            344578999999999999998863 3  45799999999999999999876531110000                    


Q ss_pred             CCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCC--CCCHHHHHHHHHHHHHHHHHHhcCCH
Q 009803          387 RHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE--AETAEDLLIKKFMKEDLEKVLDTLNP  464 (525)
Q Consensus       387 r~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~--~~~pee~~~~~~~~~~L~~aL~~L~~  464 (525)
                                                  ..++..... +++....+.+.+..  ..+|++.+...+....|..+|+.||+
T Consensus        59 ----------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~  109 (161)
T PRK09047         59 ----------------------------FSSFSDDDD-DDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA  109 (161)
T ss_pred             ----------------------------ccccccccc-cccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence                                        000000000 00011111111111  23677777777788889999999999


Q ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      ++|+||.|+|+.|    +|++|||+.||||.++|+.+++||+++||+++...+
T Consensus       110 ~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  158 (161)
T PRK09047        110 RQREAFLLRYWED----MDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG  158 (161)
T ss_pred             HHHHHHHHHHHhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999988    999999999999999999999999999999887654

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=99.69  E-value=7.2e-16  Score=156.92  Aligned_cols=156  Identities=18%  Similarity=0.161  Sum_probs=120.0

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchH
Q 009803          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  368 (525)
Q Consensus       289 ~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~  368 (525)
                      +++..|.+.++.+|+++.++..+++|++||+++.+++.  .|+.  ...|.+|++.+++|.+.+++++..+.-..     
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~-----   71 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREV-----   71 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence            47899999999999999999999999999999998775  4543  23699999999999999999865420000     


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHH
Q 009803          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  448 (525)
Q Consensus       369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~  448 (525)
                                                                      ...        ..+.+...+. ..+|++....
T Consensus        72 ------------------------------------------------~~~--------~~~~e~~~~~-~~~~~~~~~~   94 (281)
T TIGR02957        72 ------------------------------------------------YVG--------PWLPEPLLTT-SADPAESVEL   94 (281)
T ss_pred             ------------------------------------------------cCC--------CCCCcccCCC-CCChHHHHHH
Confidence                                                            000        0000001111 1245554433


Q ss_pred             -HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          449 -KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       449 -~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                       +.+...+..+|+.|||+||.||.|+|..+    +|++|||+.||+|..+|+++.+||+++||+...
T Consensus        95 ~e~~~~~l~~~l~~L~~~~R~v~~L~~~~g----~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~  157 (281)
T TIGR02957        95 AESLSMAYLLLLERLSPLERAVFVLREVFD----YPYEEIASIVGKSEANCRQLVSRARRHLDARRP  157 (281)
T ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence             34556788999999999999999999988    999999999999999999999999999998653

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.

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.69  E-value=7.6e-16  Score=152.46  Aligned_cols=159  Identities=12%  Similarity=0.130  Sum_probs=124.9

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHH
Q 009803          275 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  354 (525)
Q Consensus       275 ~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~i  354 (525)
                      .|.+.+.++..+++.++..| +.++.++.++.++..+++||+||+|+.+|+.   |+..  ..|.+|++.+++|.+.+++
T Consensus         8 ~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~id~~   81 (228)
T PRK06704          8 ILKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWLDQI   81 (228)
T ss_pred             HHhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHHHHH
Confidence            45566667788999888888 7899999999999999999999999999986   5543  2599999999999999998


Q ss_pred             HhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCccc
Q 009803          355 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  434 (525)
Q Consensus       355 r~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  434 (525)
                      +++.+.-.+                                                       .     + ...    .
T Consensus        82 Rk~k~~~~~-------------------------------------------------------~-----~-~~~----~   96 (228)
T PRK06704         82 KSKSVHEKI-------------------------------------------------------R-----D-QIT----F   96 (228)
T ss_pred             hcccccccc-------------------------------------------------------c-----c-ccc----c
Confidence            876431000                                                       0     0 000    0


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          435 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       435 ~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      .     .+.+..  ......+..+|+.||+++|.||.|+|..+    +|++|||+.||+|.++|+++++||+++||+.+.
T Consensus        97 ~-----~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg----~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~  165 (228)
T PRK06704         97 E-----EPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDVFQ----YSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE  165 (228)
T ss_pred             C-----ChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHhhC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            0     111111  12335688999999999999999999987    999999999999999999999999999999876


Q ss_pred             h
Q 009803          515 T  515 (525)
Q Consensus       515 ~  515 (525)
                      .
T Consensus       166 ~  166 (228)
T PRK06704        166 E  166 (228)
T ss_pred             h
Confidence            4

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.69  E-value=1.1e-15  Score=156.42  Aligned_cols=161  Identities=16%  Similarity=0.133  Sum_probs=124.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecc
Q 009803          285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  364 (525)
Q Consensus       285 ~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP  364 (525)
                      ..+..++..|.+.++.+|+++.++..+++|++||.|+.+|++...+ .   ..|.+|++...+|.+.+++++..+.-.. 
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~-   79 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRER-   79 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcC-
Confidence            4688999999999999999999999999999999999999987653 1   3699999999999999999875320000 


Q ss_pred             cchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHH
Q 009803          365 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED  444 (525)
Q Consensus       365 ~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee  444 (525)
                                                                        ....+...       ..+...+  ..+|++
T Consensus        80 --------------------------------------------------~~~~~~~~-------~~~~~~~--~~~~~~  100 (290)
T PRK09635         80 --------------------------------------------------PQDIAAWH-------DGDASVS--SVDPAD  100 (290)
T ss_pred             --------------------------------------------------cccccccC-------ccccCCC--CCCcHH
Confidence                                                              00000000       0000111  113333


Q ss_pred             -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          445 -LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       445 -~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                       .....+....+..+|+.|||++|.||.|+|..+    +|++|||+.||+|..+|+++.+||+++||+..
T Consensus       101 ~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~~~g----~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~  166 (290)
T PRK09635        101 RVTLDDEVRLALLIMLERLGPAERVVFVLHEIFG----LPYQQIATTIGSQASTCRQLAHRARRKINESR  166 (290)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHHhC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence             344555667899999999999999999999998    99999999999999999999999999999854

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.55  E-value=6.5e-14  Score=127.59  Aligned_cols=136  Identities=12%  Similarity=0.187  Sum_probs=100.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhh-----cCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK-----FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiek-----FDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++.++..|.++++.+|++|...    +| +||.++.+|..+.+     |++.  ..|.||++..++|.+.++++++.+..
T Consensus         1 f~~~~~~y~~~l~~~~~~~~~~----~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~   73 (142)
T TIGR03209         1 FEEIYMNFKNTIDIFTRKYNLY----YD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK   73 (142)
T ss_pred             ChHHHHHHHHHHHHHHHHhcch----hh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            4679999999999999999662    34 49999999999875     5432  47999999999999999998764310


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                      +.                 ..                                    +.    +        ..+.. ..
T Consensus        74 ~~-----------------~~------------------------------------~~----~--------~~~~~-~~   87 (142)
T TIGR03209        74 KI-----------------IY------------------------------------NS----E--------ITDIK-LS   87 (142)
T ss_pred             hh-----------------hh------------------------------------hh----h--------hhccc-cc
Confidence            00                 00                                    00    0        00000 01


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHH
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIR  499 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVR  499 (525)
                      +.+.....+....+..+|+.||+++|+||.|+|..|    +|++|||++||+|.+||+
T Consensus        88 ~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~~~~----~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        88 LINVYSSNDLEFEFNDLISILPNKQKKIIYMKFFED----MKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             hhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHhhc
Confidence            122233334456788999999999999999999988    999999999999999997

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=99.53  E-value=1.1e-13  Score=136.86  Aligned_cols=136  Identities=13%  Similarity=0.112  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceeccc
Q 009803          286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  365 (525)
Q Consensus       286 A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~  365 (525)
                      ++.+|+..|.+.++++|.++.++..+++|++||+|+.+|+...+|++.  ..|.+|++.++++....    ..       
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~----~~-------   68 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSS----AG-------   68 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhcc----cc-------
Confidence            578999999999999999999999999999999999999999999864  46899999876543210    00       


Q ss_pred             chHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803          366 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  445 (525)
Q Consensus       366 ~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~  445 (525)
                                                                              .  . ..      .. .  .+.. 
T Consensus        69 --------------------------------------------------------~--~-~~------~~-~--~~~~-   79 (261)
T PRK09191         69 --------------------------------------------------------A--N-DP------EP-G--SPFE-   79 (261)
T ss_pred             --------------------------------------------------------c--c-CC------CC-C--CCch-
Confidence                                                                    0  0 00      00 0  0110 


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          446 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       446 ~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                             ..+..+|+.||+++|+||.|+|..+    +|++|||+.||+|.++|+.+.++|+++||..+.
T Consensus        80 -------~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~  137 (261)
T PRK09191         80 -------ARAERRLAGLTPLPRQAFLLTALEG----FSVEEAAEILGVDPAEAEALLDDARAEIARQVA  137 (261)
T ss_pred             -------HHHHHHHHhCCHHHhHHHHHHHHhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence                   1688999999999999999999887    999999999999999999999999999998765

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.39  E-value=1.9e-11  Score=121.95  Aligned_cols=82  Identities=16%  Similarity=0.227  Sum_probs=74.7

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          279 RLNYGILCKDKMITSNIRLVISIAKNYQGAGM--NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       279 ~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~--~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      ...++..|++.|+..|.++|+++|.+|+++..  +.+|++|||++++|+++++|++.+|..|.+|++.+|++.+.+++++
T Consensus        12 ~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDylRk   91 (237)
T PRK08311         12 IKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRK   91 (237)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            33456889999999999999999999998765  5899999999999999999999988889999999999999999998


Q ss_pred             cccc
Q 009803          357 QSRT  360 (525)
Q Consensus       357 ~~r~  360 (525)
                      +.+-
T Consensus        92 ~~~~   95 (237)
T PRK08311         92 ESKH   95 (237)
T ss_pred             hhcc
Confidence            7663

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.39  E-value=2.9e-11  Score=115.91  Aligned_cols=172  Identities=25%  Similarity=0.318  Sum_probs=118.8

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCC---CCCHHH--HHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHH
Q 009803          276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGA---GMNLQD--LVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV  350 (525)
Q Consensus       276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~---g~~~eD--LIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI  350 (525)
                      |.+..+||..|.++|+..|++.++.+|+++.+.   +.+.+|  |++|.|+.+++.-...++.....|-.|+...+++.+
T Consensus         8 l~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~l   87 (185)
T PF07638_consen    8 LDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRKL   87 (185)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHHH
Confidence            444555679999999999999999999987643   345555  577888877774333233333468899999999999


Q ss_pred             HHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCC
Q 009803          351 RKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP  430 (525)
Q Consensus       351 ~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l  430 (525)
                      .++.+.+....|-                      |..                         ...+|+...        
T Consensus        88 id~~R~~~a~KRg----------------------~~~-------------------------~~~~l~~~~--------  112 (185)
T PF07638_consen   88 IDHARRRQAQKRG----------------------GDQ-------------------------VRVELDERA--------  112 (185)
T ss_pred             HHHHHHHHHHhcC----------------------CCC-------------------------cccchhhhh--------
Confidence            9988766532111                      000                         011122111        


Q ss_pred             CcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          431 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       431 ~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                          .+...+.|++.+.   +.+.+..+.. |+|+++++|.++|..|    +|.+|||+.||||..+|+.....|..+|+
T Consensus       113 ----~~~~~~~~~~~~~---l~e~l~~L~~-l~~~~~~~v~l~~~~G----ls~~EIA~~lgiS~~tV~r~l~~aR~~l~  180 (185)
T PF07638_consen  113 ----DSGDEPSPEELLE---LEEALERLLA-LDPRQRRVVELRFFEG----LSVEEIAERLGISERTVRRRLRRARAWLR  180 (185)
T ss_pred             ----ccccCCCHHHHHH---HHHHHHHHHc-cCHHHHHHHHHHHHCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence                1111234555433   3344555445 9999999999999877    99999999999999999999999999999


Q ss_pred             hHHh
Q 009803          511 NKKR  514 (525)
Q Consensus       511 ~~l~  514 (525)
                      ..+.
T Consensus       181 ~~l~  184 (185)
T PF07638_consen  181 RELR  184 (185)
T ss_pred             HHhc
Confidence            8764

>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=99.28  E-value=1.2e-11  Score=98.69  Aligned_cols=70  Identities=23%  Similarity=0.377  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccc
Q 009803          290 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  359 (525)
Q Consensus       290 Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r  359 (525)
                      |++.|.++|++++++|.+++.+.+|++||++++||+++++||++++..|.+|++..+++.+.++++++.|
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            6899999999999999999999999999999999999999999999899999999999999999998765

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.25  E-value=1.7e-11  Score=92.83  Aligned_cols=50  Identities=46%  Similarity=0.726  Sum_probs=46.0

Q ss_pred             HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       458 aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +|+.||++|++||.++|+.+    +|+.|||+.||+|+++|++++.+|++|||+
T Consensus         1 Al~~L~~~er~vi~~~y~~~----~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen    1 ALDQLPPREREVIRLRYFEG----LTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             HHCTS-HHHHHHHHHHHTST-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             ChhhCCHHHHHHHHHHhcCC----CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            58899999999999999877    999999999999999999999999999995

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.11  E-value=1e-10  Score=96.33  Aligned_cols=77  Identities=31%  Similarity=0.538  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHH
Q 009803          369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  445 (525)
Q Consensus       369 ~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~  445 (525)
                      +.+++|.++.+.|.+++||.||.+|||+.||+++++|..++.+...++||+.+++.+++.++.+++.|+...+|++.
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~   77 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE   77 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence            46789999999999999999999999999999999999999999999999999998888899999999988888875

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=98.94  E-value=2.5e-09  Score=81.96  Aligned_cols=53  Identities=28%  Similarity=0.457  Sum_probs=46.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL  509 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL  509 (525)
                      +.|..+|..||+++|.||.++|..|    +|+.|||+.+|+|.++|++.+.||+++|
T Consensus         2 ~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIa~~l~~s~~~v~~~l~ra~~~L   54 (54)
T PF08281_consen    2 EALQQALAQLPERQREIFLLRYFQG----MSYAEIAEILGISESTVKRRLRRARKKL   54 (54)
T ss_dssp             HHHHHHHHCS-HHHHHHHHHHHTS-------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHC----cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence            5688999999999999999999988    9999999999999999999999999987

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PRK06930 positive control sigma-like factor; Validated

Probab=98.69  E-value=9e-08  Score=91.00  Aligned_cols=70  Identities=19%  Similarity=0.332  Sum_probs=61.8

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          443 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       443 ee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      .+..........|..+++.||+++|.||.++|+.|    +|++|||+.||+|.++|++++.||+++|+..+...
T Consensus        96 ~~~~~~~e~~~~l~~al~~L~~rer~V~~L~~~eg----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~  165 (170)
T PRK06930         96 PESVISEWDKIRIEDALSVLTEREKEVYLMHRGYG----LSYSEIADYLNIKKSTVQSMIERAEKKIARQINES  165 (170)
T ss_pred             hhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            33344455667899999999999999999999888    99999999999999999999999999999988754

>PRK00118 putative DNA-binding protein; Validated

Probab=98.48  E-value=8e-07  Score=77.81  Aligned_cols=61  Identities=18%  Similarity=0.163  Sum_probs=54.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      ..+.-....||+++++|+.++|..+    +|..|||+.+|+|+.+|+.++.||+++||+++..-+
T Consensus         9 ~l~d~~~~~L~ekqRevl~L~y~eg----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~   69 (104)
T PRK00118          9 LLFDFYGSLLTEKQRNYMELYYLDD----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLH   69 (104)
T ss_pred             HHHHHHhccCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence            3445567899999999999999987    999999999999999999999999999999987643

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

Probab=98.30  E-value=2.2e-06  Score=63.69  Aligned_cols=54  Identities=44%  Similarity=0.701  Sum_probs=49.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      ..+..++..||+.++.++.++|..+    +|..+||+.+|+|..+|+++.+++..+||
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~~~----~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            3577889999999999999999866    99999999999999999999999988874

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

>PRK04217 hypothetical protein; Provisional

Probab=98.12  E-value=6.3e-06  Score=72.92  Aligned_cols=57  Identities=23%  Similarity=0.116  Sum_probs=51.6

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhh
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLM  519 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~  519 (525)
                      ...|++.++++|.++|..+    +|++|||+.||||+.+|++++.+|+++|++.+......
T Consensus        40 ~~~Lt~eereai~l~~~eG----lS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~   96 (110)
T PRK04217         40 PIFMTYEEFEALRLVDYEG----LTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGREL   96 (110)
T ss_pred             cccCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccce
Confidence            3579999999999999877    99999999999999999999999999999998765543

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.10  E-value=8.7e-06  Score=74.72  Aligned_cols=58  Identities=19%  Similarity=0.330  Sum_probs=49.8

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA  522 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl  522 (525)
                      .-||++|++||.+++ .|    +|++|||+.||+|+.+|++++++|+++|+.......+-.++
T Consensus         5 ~~Lte~qr~VL~Lr~-~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~   62 (137)
T TIGR00721         5 TFLTERQIKVLELRE-KG----LSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFI   62 (137)
T ss_pred             CCCCHHHHHHHHHHH-cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHh
Confidence            359999999999964 44    99999999999999999999999999999876665555444

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=98.03  E-value=1.5e-05  Score=73.56  Aligned_cols=51  Identities=31%  Similarity=0.444  Sum_probs=46.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      ..|+++|++||.+++ .+    +|++|||+.||+|+.+|++++++|+++||+....
T Consensus         5 ~~Lt~rqreVL~lr~-~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t   55 (141)
T PRK03975          5 SFLTERQIEVLRLRE-RG----LTQQEIADILGTSRANVSSIEKRARENIEKARET   55 (141)
T ss_pred             cCCCHHHHHHHHHHH-cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999954 55    9999999999999999999999999999987764

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.03  E-value=2.4e-06  Score=61.01  Aligned_cols=31  Identities=42%  Similarity=0.553  Sum_probs=28.0

Q ss_pred             CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHH
Q 009803          212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLL  243 (525)
Q Consensus       212 d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~  243 (525)
                      |+++ ||++| +++||||++||++|+++|+.+.
T Consensus         2 D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g~   33 (37)
T PF00140_consen    2 DSLRLYLKEI-GRYPLLTAEEEIELARRIRKGD   33 (37)
T ss_dssp             HHHHHHHHHH-HHS-EETTHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHhH
Confidence            7899 99999 9999999999999999999854

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 ....

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=97.98  E-value=3.4e-05  Score=67.18  Aligned_cols=57  Identities=23%  Similarity=0.379  Sum_probs=45.0

Q ss_pred             HHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          455 LEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       455 L~~aL-~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      |.+.. .-|+++|+.++.++|..|    +|+.|||+.+|||+..|...++||.++|...-..
T Consensus        10 L~d~Yg~LLT~kQ~~~l~lyy~eD----lSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~k   67 (101)
T PF04297_consen   10 LFDFYGELLTEKQREILELYYEED----LSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEK   67 (101)
T ss_dssp             HHHHHGGGS-HHHHHHHHHHCTS-------HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCHHHHHHHHHHHccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            44444 349999999999999888    9999999999999999999999999999876544

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=97.90  E-value=5e-05  Score=69.46  Aligned_cols=62  Identities=11%  Similarity=0.205  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       450 ~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      .....|..+|+.|++.+|.||.++|+..  .++|..+||..||+|+.+|+++..+++.+|+..+
T Consensus        71 ~~~~~I~~~l~~Ld~~er~II~~rY~~~--~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l  132 (134)
T TIGR01636        71 RNRDAIENCLNEADEQTRVIIQELYMKK--RPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL  132 (134)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHccC--CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            4556789999999999999999999754  3379999999999999999999999999998764

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.80  E-value=4.9e-05  Score=57.41  Aligned_cols=47  Identities=36%  Similarity=0.525  Sum_probs=41.2

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|+.|+.+ +..+    +|..|||+.||+|+.+|+++..++++||+.
T Consensus         2 ~~l~~~e~~i~~~-~~~g----~s~~eia~~l~is~~tv~~~~~~~~~kl~~   48 (58)
T smart00421        2 ASLTPREREVLRL-LAEG----LTNKEIAERLGISEKTVKTHLSNIMRKLGV   48 (58)
T ss_pred             CCCCHHHHHHHHH-HHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            4689999998877 4444    899999999999999999999999998864

lux regulon (activates the bioluminescence operon

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.78  E-value=8.8e-05  Score=60.87  Aligned_cols=47  Identities=19%  Similarity=0.196  Sum_probs=41.1

Q ss_pred             HHHHHHhcCCHHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          454 DLEKVLDTLNPRERQVVRWRF-GLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       454 ~L~~aL~~L~~rER~VL~lRy-gl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .+.+-|+.||++.++++.|.+ ..+    +|++|||+.||+|..+|++++++
T Consensus         8 ~~~~~l~~l~~~~r~af~L~R~~eG----lS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879         8 KLAERLTWVDSLAEAAAALAREEAG----KTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             hHHHHHhcCCHHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHhc
Confidence            466778999999999999964 455    99999999999999999998775

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.

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=97.68  E-value=0.0046  Score=70.16  Aligned_cols=32  Identities=34%  Similarity=0.583  Sum_probs=30.3

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL  242 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~  242 (525)
                      ..||++ ||+++ |++||||+|+|+++|++|..+
T Consensus       102 t~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G  134 (619)
T PRK05658        102 TDDPVRMYLREM-GTVELLTREGEIEIAKRIEAG  134 (619)
T ss_pred             CCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHH
Confidence            479999 99999 999999999999999999975

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=97.66  E-value=0.00026  Score=61.57  Aligned_cols=55  Identities=27%  Similarity=0.491  Sum_probs=49.4

Q ss_pred             HHHHHHHHHhcCC-HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803          451 MKEDLEKVLDTLN-PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL  509 (525)
Q Consensus       451 ~~~~L~~aL~~L~-~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL  509 (525)
                      .+..+..+++.|+ +.+|.||.++|..+    ++..+|++.||+|+.++..+..+|++.|
T Consensus        44 ~k~ei~~~I~~l~d~~~r~iL~~~Yi~~----~~~~~I~~~l~~S~~t~yr~~~~Al~~L   99 (100)
T PF07374_consen   44 EKLEIRRAINKLEDPDERLILRMRYINK----LTWEQIAEELNISRRTYYRIHKKALKEL   99 (100)
T ss_pred             HHHHHHHHHHHccChhHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            3456888888886 78999999999976    9999999999999999999999999876

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=97.66  E-value=0.00019  Score=55.38  Aligned_cols=48  Identities=31%  Similarity=0.465  Sum_probs=42.7

Q ss_pred             CCHHHHHHHHHHHhcC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLE---DGRMKTLQEIGELMGVSRERIRQIESSAFRKL  509 (525)
Q Consensus       462 L~~rER~VL~lRygl~---~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL  509 (525)
                      |+++|+++|..-|-.|   -.+..|+.|||+.||||+.++..++.+|.+||
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl   51 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL   51 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            7899999999988664   23568999999999999999999999999987

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.57  E-value=0.00019  Score=54.26  Aligned_cols=46  Identities=37%  Similarity=0.571  Sum_probs=40.2

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      |+++|+.|+.+. ..+    +|.+|||+.+|+|+.+|+++.++++++|+..
T Consensus         1 l~~~e~~i~~~~-~~~----~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~   46 (57)
T cd06170           1 LTPREREVLRLL-AEG----KTNKEIADILGISEKTVKTHLRNIMRKLGVK   46 (57)
T ss_pred             CCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence            689999998874 344    8999999999999999999999999988763

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=97.40  E-value=0.00041  Score=53.95  Aligned_cols=47  Identities=26%  Similarity=0.354  Sum_probs=39.5

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|.+|+.+.. .|    +|.+|||+.+|||..+|+.+..+.++||.-
T Consensus         2 ~~LT~~E~~vl~~l~-~G----~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~   48 (58)
T PF00196_consen    2 PSLTERELEVLRLLA-QG----MSNKEIAEELGISEKTVKSHRRRIMKKLGV   48 (58)
T ss_dssp             GSS-HHHHHHHHHHH-TT----S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred             CccCHHHHHHHHHHH-hc----CCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence            479999999998754 44    899999999999999999999999999864

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.16  E-value=0.00074  Score=58.06  Aligned_cols=49  Identities=24%  Similarity=0.284  Sum_probs=41.7

Q ss_pred             HHHHHHH-hcCCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHHHH
Q 009803          453 EDLEKVL-DTLNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIRQI  501 (525)
Q Consensus       453 ~~L~~aL-~~L~~rER~VL~lRygl~~---g~~~Tl~EIAe~LgIS~erVRqi  501 (525)
                      +.+..+| ..|+|+|+.+|.+||++-+   ..++|++|||+.+|||+.+|...
T Consensus        23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~   75 (94)
T TIGR01321        23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRG   75 (94)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence            4566777 4599999999999999875   45699999999999999999843

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.10  E-value=0.00094  Score=65.72  Aligned_cols=51  Identities=8%  Similarity=0.067  Sum_probs=45.7

Q ss_pred             HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          456 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       456 ~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .++...|+++|++|+.+. ..|    +|.+|||+.|++|..||+....+.++||.-
T Consensus       138 ~~~~~~LS~RE~eVL~Li-a~G----~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv  188 (217)
T PRK13719        138 LEAKNKVTKYQNDVFILY-SFG----FSHEYIAQLLNITVGSSKNKISEILKFFGI  188 (217)
T ss_pred             hhccCCCCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            556789999999999985 455    999999999999999999999999999964

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.08  E-value=0.00094  Score=66.40  Aligned_cols=51  Identities=29%  Similarity=0.490  Sum_probs=44.8

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ...|+++|++||.+. ..|    +|..|||++||||..||+.++.++++||+..-+
T Consensus       169 ~~~Lt~re~evl~~~-a~G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~  219 (232)
T TIGR03541       169 AGVLSEREREVLAWT-ALG----RRQADIAAILGISERTVENHLRSARRKLGVATT  219 (232)
T ss_pred             hccCCHHHHHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence            347999999999996 444    999999999999999999999999999985433

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.05  E-value=0.0011  Score=64.81  Aligned_cols=46  Identities=17%  Similarity=0.258  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|++||++||.+. ..|    +|.+|||+.||+|..||+.+..+.++||.-
T Consensus       137 ~LT~RE~eVL~ll-a~G----~snkeIA~~L~iS~~TVk~h~~~I~~KL~v  182 (207)
T PRK15411        137 SLSRTESSMLRMW-MAG----QGTIQISDQMNIKAKTVSSHKGNIKRKIKT  182 (207)
T ss_pred             cCCHHHHHHHHHH-HcC----CCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            5999999999985 344    999999999999999999999999999974

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=97.05  E-value=0.0013  Score=62.59  Aligned_cols=47  Identities=23%  Similarity=0.364  Sum_probs=42.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|++|+.+. ..|    +|.+|||+.|++|..||+....+.++||.-
T Consensus       132 ~~LSpRErEVLrLL-AqG----kTnKEIAe~L~IS~rTVkth~srImkKLgV  178 (198)
T PRK15201        132 RHFSVTERHLLKLI-ASG----YHLSETAALLSLSEEQTKSLRRSIMRKLHV  178 (198)
T ss_pred             CCCCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            36999999999985 344    999999999999999999999999999965

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.04  E-value=0.0011  Score=66.76  Aligned_cols=49  Identities=24%  Similarity=0.440  Sum_probs=44.0

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      +..|+++|++|+.+.. .|    +|.+|||++||||..||+....++++||.-.
T Consensus       188 ~~~LT~RE~evl~l~a-~G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~  236 (247)
T TIGR03020       188 AGLITAREAEILAWVR-DG----KTNEEIAAILGISSLTVKNHLQHIFKKLDVR  236 (247)
T ss_pred             ccCCCHHHHHHHHHHH-CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            4579999999999854 55    9999999999999999999999999999753

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.01  E-value=0.0012  Score=63.69  Aligned_cols=46  Identities=28%  Similarity=0.299  Sum_probs=41.7

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      ..|++||++|+.+.- .|    +|.+|||+.|+||..||+.+..+.++||-
T Consensus       149 ~~Lt~rE~evl~~~~-~G----~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~  194 (216)
T PRK10840        149 KRLSPKESEVLRLFA-EG----FLVTEIAKKLNRSIKTISSQKKSAMMKLG  194 (216)
T ss_pred             ccCCHHHHHHHHHHH-CC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            459999999999863 34    99999999999999999999999999995

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=96.99  E-value=0.0014  Score=64.24  Aligned_cols=47  Identities=23%  Similarity=0.341  Sum_probs=42.3

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      ...|++||++||.+.- .|    +|.+|||+.|+||..||+.+..+.++||.
T Consensus       132 ~~~LT~RE~eVL~ll~-~G----~snkeIA~~L~iS~~TV~~h~~~I~~KLg  178 (207)
T PRK11475        132 SRMLSPTEREILRFMS-RG----YSMPQIAEQLERNIKTIRAHKFNVMSKLG  178 (207)
T ss_pred             cCCCCHHHHHHHHHHH-CC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            3469999999999853 44    99999999999999999999999999995

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=96.96  E-value=0.0021  Score=56.49  Aligned_cols=53  Identities=26%  Similarity=0.225  Sum_probs=48.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      .|+..|-+.|+|-+.++    +|.+|-|+.||||+.|+..++..|.+|+-..+-...
T Consensus        41 ~L~~dElEAiRL~D~eg----l~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk   93 (106)
T PF02001_consen   41 VLTVDELEAIRLVDYEG----LSQEEAAERMGVSRPTFQRILESARKKIADALVEGK   93 (106)
T ss_pred             EeeHHHHHHHHHHHHcC----CCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence            58888999999999988    999999999999999999999999999999886544

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=96.94  E-value=0.0015  Score=64.33  Aligned_cols=48  Identities=17%  Similarity=0.171  Sum_probs=43.7

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +..|+++|++|+.+.+. |    +|.+|||+.|++|..||+.+..++++||.-
T Consensus       153 ~~~Lt~rE~~Vl~l~~~-G----~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v  200 (216)
T PRK10100        153 SALLTHREKEILNKLRI-G----ASNNEIARSLFISENTVKTHLYNLFKKIAV  200 (216)
T ss_pred             cCCCCHHHHHHHHHHHc-C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            34699999999999874 5    999999999999999999999999999975

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=96.90  E-value=0.0018  Score=64.86  Aligned_cols=47  Identities=19%  Similarity=0.439  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .|++||++||.+- ..|    +|..|||++||||..||+.++.++++||--.
T Consensus       179 ~LT~rE~evl~~~-a~G----~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~  225 (240)
T PRK10188        179 NFSKREKEILKWT-AEG----KTSAEIAMILSISENTVNFHQKNMQKKFNAP  225 (240)
T ss_pred             CCCHHHHHHHHHH-HcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            5999999999987 344    9999999999999999999999999999643

>PRK13870 transcriptional regulator TraR; Provisional

Probab=96.90  E-value=0.0017  Score=64.81  Aligned_cols=47  Identities=28%  Similarity=0.556  Sum_probs=41.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .|++||++||.+- ..|    +|..|||.+||||..||..++.+|++||--.
T Consensus       173 ~LT~RE~E~L~W~-A~G----KT~~EIa~ILgISe~TV~~Hl~na~~KLga~  219 (234)
T PRK13870        173 WLDPKEATYLRWI-AVG----KTMEEIADVEGVKYNSVRVKLREAMKRFDVR  219 (234)
T ss_pred             CCCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            5999999999875 333    9999999999999999999999999999543

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=96.87  E-value=0.0017  Score=63.67  Aligned_cols=47  Identities=30%  Similarity=0.393  Sum_probs=42.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|++||++|+++- ..|    +|.+|||+.|++|..||+.+.++.++||.-
T Consensus       147 ~~LT~RE~eVL~ll-a~G----~snkeIA~~L~iS~~TVk~h~~~i~~KL~v  193 (211)
T COG2197         147 ELLTPRELEVLRLL-AEG----LSNKEIAEELNLSEKTVKTHVSNILRKLGV  193 (211)
T ss_pred             CCCCHHHHHHHHHH-HCC----CCHHHHHHHHCCCHhHHHHHHHHHHHHcCC
Confidence            47999999999884 444    999999999999999999999999999964

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=96.83  E-value=0.0015  Score=48.36  Aligned_cols=41  Identities=22%  Similarity=0.337  Sum_probs=23.6

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      ..|++.||..|...+-.|    +|..+||+.||+|++||...+.|
T Consensus         3 ~~Lt~~eR~~I~~l~~~G----~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALLEQG----MSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHHCS-------HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHHHcC----CCHHHHHHHHCcCcHHHHHHHhc
Confidence            468999999998777555    99999999999999999987765

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.79  E-value=0.0031  Score=61.98  Aligned_cols=53  Identities=23%  Similarity=0.351  Sum_probs=46.3

Q ss_pred             cCCHHHHHHHHHHHhcC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          461 TLNPRERQVVRWRFGLE---DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~---~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      .|+++|++||+.-|-.|   -.+..|++|||+.||||+.++.+++++|.+||=..+
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~  210 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY  210 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            69999999999998765   235589999999999999999999999999996543

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=96.71  E-value=0.0081  Score=57.97  Aligned_cols=64  Identities=20%  Similarity=0.288  Sum_probs=54.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhh
Q 009803          451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLM  519 (525)
Q Consensus       451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~  519 (525)
                      ....+...+++|++|||+|+..-- .|    +..++||..||||.-||..+..+.++|++...-..-++
T Consensus       132 ~~~~~~~~l~tLT~RERqVl~~vV-~G----~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr  195 (202)
T COG4566         132 RQAAIRARLATLTPRERQVLDLVV-RG----LMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVR  195 (202)
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHH-cC----cccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHH
Confidence            446788899999999999998764 45    89999999999999999999999999998755444443

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.70  E-value=0.0034  Score=54.33  Aligned_cols=49  Identities=20%  Similarity=0.239  Sum_probs=44.1

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .-|+.+|+..+.++|..|    +|+.|||+.++||+..|...+.|+-+.|-..
T Consensus        16 sLLT~KQ~~Y~~lyy~dD----lSl~EIAee~~VSRqAIyDnIKr~~~~L~~Y   64 (105)
T COG2739          16 SLLTKKQKNYLELYYLDD----LSLSEIAEEFNVSRQAIYDNIKRTEKILEDY   64 (105)
T ss_pred             HHHhHHHHHHHHHHHHhh----ccHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence            458999999999999988    9999999999999999999999987776543

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.70  E-value=0.0037  Score=57.95  Aligned_cols=47  Identities=28%  Similarity=0.397  Sum_probs=42.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|++||.+ +..+    +|.+|||+.+++|..||+.+..++++||.-
T Consensus       148 ~~lt~~e~~vl~l-~~~g----~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~  194 (211)
T PRK15369        148 PLLTPRERQILKL-ITEG----YTNRDIAEQLSISIKTVETHRLNMMRKLDV  194 (211)
T ss_pred             cCCCHHHHHHHHH-HHCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            4599999999998 5555    899999999999999999999999999963

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.66  E-value=0.012  Score=53.41  Aligned_cols=63  Identities=16%  Similarity=0.142  Sum_probs=54.1

Q ss_pred             HHHHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          450 FMKEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       450 ~~~~~L~~aL-~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      .....+..++ +.|++.+|+||.++|...++  ++..+|+..||+|+.+...+..+|+.++-..+.
T Consensus        67 ~~~~~i~~ai~~~l~~~~r~Il~~~Yl~~~~--~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~  130 (132)
T TIGR01637        67 QEARAIVNAIVNQLDEISRQILYDKYLEPDQ--KYDYQIMMELGYSHRQYYRIKKRALLRFATLYG  130 (132)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHcCccc--cchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence            3445677777 99999999999999987333  899999999999999999999999999987654

This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.

>PRK09483 response regulator; Provisional

Probab=96.62  E-value=0.0037  Score=59.31  Aligned_cols=46  Identities=24%  Similarity=0.336  Sum_probs=41.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      ..|+++|++||.+. ..|    +|.+|||+.|++|..||+.+.++.++||-
T Consensus       147 ~~Lt~rE~~vl~~~-~~G----~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~  192 (217)
T PRK09483        147 ASLSERELQIMLMI-TKG----QKVNEISEQLNLSPKTVNSYRYRMFSKLN  192 (217)
T ss_pred             cccCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            46999999999874 344    99999999999999999999999999994

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=96.60  E-value=0.007  Score=47.11  Aligned_cols=50  Identities=34%  Similarity=0.566  Sum_probs=42.7

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ..|+++|.+|+.+.- .+    +|..|||..+|+|..+|+....+.++||.-.-+
T Consensus         3 ~~Lt~rE~~v~~l~~-~G----~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r   52 (65)
T COG2771           3 ADLTPREREILRLVA-QG----KSNKEIARILGISEETVKTHLRNIYRKLGVKNR   52 (65)
T ss_pred             ccCCHHHHHHHHHHH-CC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence            368999999997753 33    899999999999999999999999999975443

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=96.46  E-value=0.068  Score=55.82  Aligned_cols=159  Identities=11%  Similarity=0.057  Sum_probs=99.0

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccch
Q 009803          288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM  367 (525)
Q Consensus       288 e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~  367 (525)
                      +..+..-.+-++.---+|+++-.-.|+.+||+|+..++.-.+=-|-+.  -..|.+..-|+.-++.++++.+.-..|.+.
T Consensus         8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~--PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el   85 (415)
T COG4941           8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRN--PAAWLIAVGRNRAIDRVRRRARRDAAPPEL   85 (415)
T ss_pred             HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCC--hHHHHHHHHhhhHHHHHHHHHHhccCChhh
Confidence            344444444444444556666556899999999877666655444332  467888888999999888776532222110


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHH
Q 009803          368 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI  447 (525)
Q Consensus       368 ~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~  447 (525)
                                                                     .++.+     |......+.        +++...
T Consensus        86 -----------------------------------------------~~~~e-----~~e~~~a~~--------~~d~~i  105 (415)
T COG4941          86 -----------------------------------------------LLSDE-----DEEMEEAEA--------LDDEHI  105 (415)
T ss_pred             -----------------------------------------------ccccc-----chhhhcccc--------cccccc
Confidence                                                           00000     000000000        011111


Q ss_pred             HHHHHHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          448 KKFMKEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       448 ~~~~~~~L~~aL-~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .++....|--|- -.|++.+|--|.+|...|    +|..|||..|=|+..++-|++.||.++++..
T Consensus       106 ~Dd~LRLiFvccHPal~~~~riALtLR~v~G----Ls~~eIArAFLv~e~am~QRivRAK~ri~~a  167 (415)
T COG4941         106 RDDRLRLIFVCCHPALPPEQRIALTLRLVGG----LSTAEIARAFLVPEAAMAQRIVRAKARIREA  167 (415)
T ss_pred             chhhHHhhhhhcCCCCChhhHHHHHHHHHcC----CcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc
Confidence            111122222222 469999999999998876    9999999999999999999999999999873

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=96.34  E-value=0.0048  Score=42.72  Aligned_cols=27  Identities=30%  Similarity=0.559  Sum_probs=21.4

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      |+|.+|||+.+|+|+++|+    |++++|++
T Consensus         2 ~mtr~diA~~lG~t~ETVS----R~l~~l~~   28 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVS----RILKKLER   28 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence            4899999999999999999    77888875

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.27  E-value=0.012  Score=54.22  Aligned_cols=56  Identities=18%  Similarity=0.243  Sum_probs=47.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       454 ~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      .+...+..|+++|++|+.+ +..+    ++.++||+.+|+|..+|+....++++||+..-.
T Consensus       134 ~~~~~~~~l~~~e~~vl~~-~~~~----~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~  189 (202)
T PRK09390        134 DIRARIASLSERERQVMDG-LVAG----LSNKVIARDLDISPRTVEVYRANVMTKMQAGSL  189 (202)
T ss_pred             HHHHHHHhhhhhHHHHHHH-HHcc----CchHHHHHHcCCCHHHHHHHHHHHHHHHccccH
Confidence            3556678899999999996 4444    899999999999999999999999999975443

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.20  E-value=0.0088  Score=56.11  Aligned_cols=47  Identities=17%  Similarity=0.329  Sum_probs=41.8

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|++|+.+. ..+    ++.++||+.+++|..||+.+..+.++||.-
T Consensus       154 ~~Lt~rE~~vl~~l-~~g----~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~  200 (216)
T PRK10651        154 NQLTPRERDILKLI-AQG----LPNKMIARRLDITESTVKVHVKHMLKKMKL  200 (216)
T ss_pred             ccCCHHHHHHHHHH-HcC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence            45999999999984 344    899999999999999999999999999964

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=96.09  E-value=0.017  Score=49.63  Aligned_cols=53  Identities=23%  Similarity=0.166  Sum_probs=47.5

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      .|+..|-+.|+|...++    +|.+|-|..||||+.|+-..+..|++|+-.++-...
T Consensus        33 ~lt~eElEAlRLvD~~~----l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveGk   85 (99)
T COG1342          33 ILTIEELEALRLVDYEG----LTQEEAALRMGISRQTFWRLLTSARKKVADALVEGK   85 (99)
T ss_pred             eecHHHHHHHHHHhHhh----ccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence            46777888999999988    999999999999999999999999999998886543

>PRK01381 Trp operon repressor; Provisional

Probab=96.02  E-value=0.0088  Score=51.91  Aligned_cols=48  Identities=23%  Similarity=0.285  Sum_probs=39.7

Q ss_pred             HHHHHHHHhc-CCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHH
Q 009803          452 KEDLEKVLDT-LNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIR  499 (525)
Q Consensus       452 ~~~L~~aL~~-L~~rER~VL~lRygl~~---g~~~Tl~EIAe~LgIS~erVR  499 (525)
                      ...+..+|.. |+|+|+..|..||+.-.   ...+|+.||++.+|||..+|.
T Consensus        22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT   73 (99)
T PRK01381         22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT   73 (99)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence            3456667765 99999999999998753   234999999999999999887

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.46  E-value=0.028  Score=63.67  Aligned_cols=53  Identities=26%  Similarity=0.228  Sum_probs=45.7

Q ss_pred             HhcCCHHHHHHHHHHHhcC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          459 LDTLNPRERQVVRWRFGLE---DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~---~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ...|+++|+++|..-|..|   -.+.-|++|||+.||||+.|+.+++++|.+||=.
T Consensus       605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~  660 (665)
T PRK13558        605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVG  660 (665)
T ss_pred             hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            4689999999999999876   1122399999999999999999999999999854

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=95.32  E-value=0.017  Score=51.97  Aligned_cols=50  Identities=22%  Similarity=0.326  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      -|+++|-.||.||- .|    .|.+|||++||-|+..|+-++.+|+.++.+.-+.
T Consensus         8 flte~qikvl~lRe-kG----~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT   57 (143)
T COG1356           8 FLTEQQIKVLVLRE-KG----LTQSEIARILKTTRANVSAIEKRALENIEKARNT   57 (143)
T ss_pred             eeehhheeeeehhh-cc----ccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHH
Confidence            38889999999994 23    8999999999999999999999999999876543

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=95.12  E-value=0.034  Score=44.71  Aligned_cols=45  Identities=22%  Similarity=0.457  Sum_probs=30.0

Q ss_pred             HhcCCHHHHHHHHH--HHhcCCCCCCCHHHHHHHHCCC-HHHHHHHHH
Q 009803          459 LDTLNPRERQVVRW--RFGLEDGRMKTLQEIGELMGVS-RERIRQIES  503 (525)
Q Consensus       459 L~~L~~rER~VL~l--Rygl~~g~~~Tl~EIAe~LgIS-~erVRqie~  503 (525)
                      |..|+++|++||..  .|....|-|-|+.|||+.||++ ..+|.+.+.
T Consensus         1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen    1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            46799999999875  3555567778999999999996 999986543

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.

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=95.11  E-value=0.058  Score=41.33  Aligned_cols=49  Identities=14%  Similarity=0.176  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      +|+..++-++.+.|.-.+   .|++.||..+|||+++|.++.+..+.-|...
T Consensus         2 kLs~~d~lll~L~~LR~~---~~~~~La~~FgIs~stvsri~~~~~~~L~~~   50 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYLRLN---LTFQDLAYRFGISQSTVSRIFHEWIPLLYQV   50 (53)
T ss_pred             CCCHHHHHHHHHHHHHcC---CcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence            588888888888776654   8999999999999999999999888877654

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.05  E-value=0.046  Score=50.92  Aligned_cols=49  Identities=27%  Similarity=0.323  Sum_probs=42.5

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      ..|+++|++|+.+.. .+    +|.++||+.+++|..+|+.+..+.++||.-.-
T Consensus       136 ~~Lt~~E~~il~~l~-~g----~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~  184 (196)
T PRK10360        136 DPLTKRERQVAEKLA-QG----MAVKEIAAELGLSPKTVHVHRANLMEKLGVSN  184 (196)
T ss_pred             cCCCHHHHHHHHHHH-CC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence            469999999999854 34    89999999999999999999999999986433

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.05  E-value=0.048  Score=51.06  Aligned_cols=46  Identities=22%  Similarity=0.304  Sum_probs=39.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|..|+.+ +..+    +|.+|||+.|++|..||+.+..++++||.-
T Consensus       149 ~lt~re~~vl~~-l~~g----~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~  194 (210)
T PRK09935        149 VLSNREVTILRY-LVSG----LSNKEIADQLLLSNKTVSAHKSNIYGKLGL  194 (210)
T ss_pred             cCCHHHHHHHHH-HHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence            488888888764 3344    999999999999999999999999999953

>PRK10403 transcriptional regulator NarP; Provisional

Probab=94.99  E-value=0.047  Score=50.99  Aligned_cols=49  Identities=18%  Similarity=0.271  Sum_probs=42.2

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      ..|+++|.+|+.+. ..+    +|.++||+.+|+|..||+.+..+.++||.-.-
T Consensus       152 ~~Lt~~e~~vl~~~-~~g----~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~  200 (215)
T PRK10403        152 SVLTERELDVLHEL-AQG----LSNKQIASVLNISEQTVKVHIRNLLRKLNVRS  200 (215)
T ss_pred             ccCCHHHHHHHHHH-HCC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence            35999999999865 344    99999999999999999999999999995433

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=94.95  E-value=0.081  Score=39.24  Aligned_cols=40  Identities=20%  Similarity=0.343  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      |++.++.||..-+-.+   ..|..|||+.+|+|..+|++++.+
T Consensus         1 l~~~~~~Il~~l~~~~---~~t~~ela~~~~is~~tv~~~l~~   40 (48)
T PF13412_consen    1 LDETQRKILNYLRENP---RITQKELAEKLGISRSTVNRYLKK   40 (48)
T ss_dssp             --HHHHHHHHHHHHCT---TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcC---CCCHHHHHHHhCCCHHHHHHHHHH
Confidence            5778888887665422   399999999999999999965543

...

>PRK15320 transcriptional activator SprB; Provisional

Probab=94.90  E-value=0.053  Score=52.78  Aligned_cols=66  Identities=11%  Similarity=0.088  Sum_probs=48.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ++|++.+..-.. -....+--.|+++|.+|+.+-- .|    +|.+|||+.|++|..||+....+.+.||.-
T Consensus       144 ~~~~~~~~~~~~-~~~~~~~~~LSdREIEVL~LLA-kG----~SNKEIAekL~LS~KTVSTYKnRLLeKLgA  209 (251)
T PRK15320        144 ETPEEVLFNINQ-YAWWNLPPGVTQAKYALLILLS-SG----HPAIELAKKFGLGTKTVSIYRKKVMYRLGM  209 (251)
T ss_pred             CChHHHhhhccc-eeeecCCCCCCHHHHHHHHHHH-cC----CCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence            466665433111 1122233578999999988752 33    999999999999999999999999999863

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=94.81  E-value=0.16  Score=46.39  Aligned_cols=51  Identities=22%  Similarity=0.433  Sum_probs=43.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      +..|..+++.|.+.++.||.+||+...+  +|..+||..|+||..+++.....
T Consensus        72 k~~id~~~~~l~de~k~Ii~lry~~r~~--~TW~~IA~~l~i~erta~r~~~~  122 (130)
T PF05263_consen   72 KEAIDRWLETLIDEEKRIIKLRYDRRSR--RTWYQIAQKLHISERTARRWRDR  122 (130)
T ss_pred             HHHHHHHHHhhCHHHHHHHHHHHccccc--chHHHHHHHhCccHHHHHHHHHH
Confidence            4567778899999999999999986644  99999999999999999865544

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=94.41  E-value=0.046  Score=40.79  Aligned_cols=32  Identities=22%  Similarity=0.276  Sum_probs=21.8

Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      ||.+.. .+    +|..+||+.||||+.+|+++..+-
T Consensus        10 ii~l~~-~G----~s~~~ia~~lgvs~~Tv~~w~kr~   41 (50)
T PF13384_consen   10 IIRLLR-EG----WSIREIAKRLGVSRSTVYRWIKRY   41 (50)
T ss_dssp             HHHHHH-HT------HHHHHHHHTS-HHHHHHHHT--
T ss_pred             HHHHHH-CC----CCHHHHHHHHCcCHHHHHHHHHHc
Confidence            555544 34    999999999999999999887653

>PRK04841 transcriptional regulator MalT; Provisional

Probab=94.32  E-value=0.071  Score=62.42  Aligned_cols=47  Identities=21%  Similarity=0.257  Sum_probs=42.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|++|+.+.. .|    +|.+|||+.|+||..||+.++++.++||.-
T Consensus       837 ~~lt~~e~~v~~~~~-~g----~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v  883 (903)
T PRK04841        837 SPLTQREWQVLGLIY-SG----YSNEQIAGELDVAATTIKTHIRNLYQKLGI  883 (903)
T ss_pred             CCCCHHHHHHHHHHH-cC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            359999999999854 44    999999999999999999999999999964

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=94.31  E-value=0.095  Score=49.08  Aligned_cols=47  Identities=30%  Similarity=0.398  Sum_probs=41.2

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      +..|+++|++|+.+.. .+    .|.++||+.+++|..||+....+.++||.
T Consensus       141 ~~~lt~~E~~vl~~l~-~g----~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~  187 (204)
T PRK09958        141 LDSLSKQEISVMRYIL-DG----KDNNDIAEKMFISNKTVSTYKSRLMEKLE  187 (204)
T ss_pred             cccCCHHHHHHHHHHH-cC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            3569999999998754 33    79999999999999999999999999994

>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein

Probab=94.22  E-value=0.19  Score=40.39  Aligned_cols=56  Identities=14%  Similarity=0.132  Sum_probs=46.0

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhh----C--CCCCHHHHHHHHHHHHHHhhhhcC
Q 009803          276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQ----G--AGMNLQDLVQEGCRGLVRGAEKFD  331 (525)
Q Consensus       276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~----~--~g~~~eDLIQEG~lGLirAiekFD  331 (525)
                      +.++.+||..|.++++..|.+++.+.+.+-.    +  ++.-=+|+-|+-...|++++.+|+
T Consensus         4 I~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen    4 IKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            4556678899999999999999999988722    2  233338999999999999999996

Some proteins with this domain are annotated as conjugative transposon proteins.

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=93.98  E-value=0.32  Score=43.99  Aligned_cols=52  Identities=15%  Similarity=0.136  Sum_probs=47.6

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      |..-.+.+-.+|.++|..+    +|...||..+++|...||+...+|-..+..++.
T Consensus        60 L~~~~~~~~~ll~~~Yv~g----~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~  111 (125)
T PF06530_consen   60 LKKRDPEEYDLLILYYVYG----WSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLS  111 (125)
T ss_pred             HHccCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhH
Confidence            4557889999999999988    999999999999999999999999999988764

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=93.91  E-value=0.19  Score=36.90  Aligned_cols=40  Identities=20%  Similarity=0.321  Sum_probs=26.9

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      |++-.+.||..--..   ...|+.+||+.+|+|..+|.+++.+
T Consensus         1 lD~~D~~Il~~Lq~d---~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    1 LDELDRKILRLLQED---GRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHc---CCccHHHHHHHHCcCHHHHHHHHHH
Confidence            355667777765432   2399999999999999999976654

...

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=93.87  E-value=0.087  Score=55.12  Aligned_cols=36  Identities=19%  Similarity=0.364  Sum_probs=32.0

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803          468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR  507 (525)
Q Consensus       468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk  507 (525)
                      +|-.|+|..+    +|.+|||++|||||.+|.+++.+|++
T Consensus        20 ~vA~lYY~~g----~tQ~eIA~~lgiSR~~VsRlL~~Ar~   55 (318)
T PRK15418         20 RIAWFYYHDG----LTQSEIGERLGLTRLKVSRLLEKGRQ   55 (318)
T ss_pred             HHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4667888776    99999999999999999999999876

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=93.66  E-value=0.14  Score=40.64  Aligned_cols=35  Identities=26%  Similarity=0.301  Sum_probs=26.7

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      ..+.++.-.+|.  +++.+||+.||||..+||....+
T Consensus        11 kA~e~y~~~~g~--i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   11 KAFEIYKESNGK--IKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             HHHHHHHHhCCC--ccHHHHHHHHCCCHHHHHHHhhh
Confidence            455555444433  99999999999999999987554

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=93.61  E-value=0.17  Score=33.29  Aligned_cols=36  Identities=25%  Similarity=0.420  Sum_probs=27.4

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  501 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqi  501 (525)
                      +++.++..+...|..+    .|..+|++.+|+|+.+|..+
T Consensus         6 ~~~~~~~~i~~~~~~~----~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLLAAG----ESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHh
Confidence            4555666565555443    79999999999999999865

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=93.37  E-value=0.24  Score=44.19  Aligned_cols=49  Identities=20%  Similarity=0.337  Sum_probs=41.3

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +..|++.+..-|... ....|   +++|+++.||||..|||.++.+.+++|.-
T Consensus        31 ~~~L~~E~~~Fi~~F-i~~rG---nlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   31 FARLSPEQLEFIKLF-IKNRG---NLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hhcCCHHHHHHHHHH-HHhcC---CHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            678998887776654 44444   99999999999999999999999999975

>PF13730 HTH_36: Helix-turn-helix domain

Probab=93.33  E-value=0.34  Score=36.78  Aligned_cols=47  Identities=21%  Similarity=0.435  Sum_probs=33.5

Q ss_pred             cCCHHHHHHHHHHHhc--CCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGL--EDGRM-KTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl--~~g~~-~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|++.++.|+..-.-.  +++.. .|.+.||+.+|+|+.||+    ++++.|.+
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~~   51 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELEE   51 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            5788888776543322  22223 389999999999999999    67777764

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=93.32  E-value=0.18  Score=43.01  Aligned_cols=38  Identities=26%  Similarity=0.351  Sum_probs=29.8

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ++.|++| ..|+.+. ..+    +|..+||+.+|||+.||..+.
T Consensus        34 ~~~Ls~R-~~I~~ll-~~G----~S~~eIA~~LgISrsTIyRi~   71 (88)
T TIGR02531        34 IQSLAQR-LQVAKML-KQG----KTYSDIEAETGASTATISRVK   71 (88)
T ss_pred             HHhhhHH-HHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHH
Confidence            3468888 7777763 222    899999999999999999733

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=93.10  E-value=0.13  Score=38.06  Aligned_cols=32  Identities=19%  Similarity=0.250  Sum_probs=22.0

Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       466 ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ..+|+.|+ -.+    +|..+||+.+|||+.||..++
T Consensus        11 ~~~i~~l~-~~G----~si~~IA~~~gvsr~TvyR~l   42 (45)
T PF02796_consen   11 IEEIKELY-AEG----MSIAEIAKQFGVSRSTVYRYL   42 (45)
T ss_dssp             HHHHHHHH-HTT------HHHHHHHTTS-HHHHHHHH
T ss_pred             HHHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHH
Confidence            34566654 333    999999999999999999765

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=93.05  E-value=1  Score=48.10  Aligned_cols=126  Identities=21%  Similarity=0.188  Sum_probs=70.6

Q ss_pred             HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH-HHH
Q 009803          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEG-CRG  322 (525)
Q Consensus       244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG-~lG  322 (525)
                      ++.+...+|...+|+.||..+.|...|++...+...+...                   ..    ..++++.+.++ -..
T Consensus       217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~-------------------~~----~~SLd~~~~~~~~~~  273 (367)
T PRK09210        217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIA-------------------QE----PVSLETPIGEEDDSH  273 (367)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHh-------------------cC----CCCcCCCCCCCCcch
Confidence            3455667788889999999999999999987665432211                   10    11111111100 001


Q ss_pred             HHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHc----CCCCCHHHHHHHc
Q 009803          323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT  398 (525)
Q Consensus       323 LirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~l----gr~Pt~eEIA~~l  398 (525)
                      |..-+.  |+.............++..+.+++..      +|..-..          -+....    |.+-|.+|||+.+
T Consensus       274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~------L~~rEr~----------Vl~lrygl~~~~~~tl~EIa~~l  335 (367)
T PRK09210        274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLDT------LTDREEN----------VLRLRFGLDDGRTRTLEEVGKVF  335 (367)
T ss_pred             hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh------CCHHHHH----------HHHHHhccCCCCCccHHHHHHHH
Confidence            111111  11222234445566667777766642      3322111          112222    3677999999999


Q ss_pred             CCCHHHHHHHHh
Q 009803          399 GLSMKRLHAVLL  410 (525)
Q Consensus       399 gis~~~v~~~l~  410 (525)
                      |+|.++|+++..
T Consensus       336 gvs~erVrQi~~  347 (367)
T PRK09210        336 GVTRERIRQIEA  347 (367)
T ss_pred             CCCHHHHHHHHH
Confidence            999999998853

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

Probab=92.90  E-value=1.4  Score=43.70  Aligned_cols=34  Identities=24%  Similarity=0.332  Sum_probs=27.5

Q ss_pred             HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803          245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (525)
Q Consensus       245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~  278 (525)
                      +.+....|....|++||..+.|...|++.+.+..
T Consensus        89 ~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~  122 (238)
T TIGR02393        89 LIKAERQLTQELGREPTDEELAERMGMPAEKVRE  122 (238)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            4455677788899999999999999999876543

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.

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=92.84  E-value=0.26  Score=37.41  Aligned_cols=41  Identities=29%  Similarity=0.501  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      |++.||.+-+-.  +.+.|.+|||+.||||+.||+    +-++.|+.
T Consensus         1 R~~~il~~L~~~--~~~it~~eLa~~l~vS~rTi~----~~i~~L~~   41 (55)
T PF08279_consen    1 RQKQILKLLLES--KEPITAKELAEELGVSRRTIR----RDIKELRE   41 (55)
T ss_dssp             HHHHHHHHHHHT--TTSBEHHHHHHHCTS-HHHHH----HHHHHHHH
T ss_pred             CHHHHHHHHHHc--CCCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence            456677664333  334999999999999999999    45555554

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=92.84  E-value=1.2  Score=49.57  Aligned_cols=126  Identities=16%  Similarity=0.219  Sum_probs=69.0

Q ss_pred             HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHH-HHHH
Q 009803          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQE-GCRG  322 (525)
Q Consensus       244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQE-G~lG  322 (525)
                      ++.+.+.+|...+|+.||..+.|...|++.+.+...+..                       ....+++++.+.+ +...
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~-----------------------~~~~~SLD~~i~~d~~~~  415 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKY-----------------------NREPISLDKTIGKEGDSQ  415 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh-----------------------cCCCcccccccccCCccc
Confidence            455667888888999999999999999987665433211                       1111222222211 1111


Q ss_pred             HHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHc----CCCCCHHHHHHHc
Q 009803          323 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT  398 (525)
Q Consensus       323 LirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~l----gr~Pt~eEIA~~l  398 (525)
                      +...+.  |+........+..+..+..+..++..      +|..-.          .-+....    +.+-|..|||+.+
T Consensus       416 l~d~l~--D~~~~~p~~~~~~~~l~~~L~~aL~~------L~eREr----------~VI~lRyGL~~~e~~TL~EIa~~l  477 (509)
T PRK05901        416 FGDFIE--DSEAVSPVDAVSFTLLQDQLQEVLET------LSEREA----------GVIRMRFGLTDGQPKTLDEIGQVY  477 (509)
T ss_pred             HHHhcc--CCCCCCHHHHHHHHHHHHHHHHHHhh------CCHHHH----------HHHHHHhhccCCCCCCHHHHHHHH
Confidence            111111  11111223334444555555555532      222211          1112223    4567999999999


Q ss_pred             CCCHHHHHHHHh
Q 009803          399 GLSMKRLHAVLL  410 (525)
Q Consensus       399 gis~~~v~~~l~  410 (525)
                      |+|.++|+++..
T Consensus       478 GVSrERVRQIe~  489 (509)
T PRK05901        478 GVTRERIRQIES  489 (509)
T ss_pred             CCCHHHHHHHHH
Confidence            999999999853

>PHA00675 hypothetical protein

Probab=92.44  E-value=0.28  Score=40.60  Aligned_cols=40  Identities=18%  Similarity=0.085  Sum_probs=32.0

Q ss_pred             hcCCHHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          460 DTLNPRERQVVRWRF-GLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       460 ~~L~~rER~VL~lRy-gl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      ..|++.+-+.|+.++ -.+    .|+.+||..||||+++|.+|..
T Consensus        21 AKLt~~qV~~IR~l~~r~G----~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         21 AKLTDAEVERIRELHEVEG----MSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             cccCHHHHHHHHHHHHhcC----ccHHHHHHHhCCCHHHHHHHHc
Confidence            467777777677666 444    7999999999999999998864

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=92.02  E-value=2.1  Score=44.96  Aligned_cols=35  Identities=20%  Similarity=0.368  Sum_probs=28.7

Q ss_pred             HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (525)
Q Consensus       244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~  278 (525)
                      ++.+.+..|...+|++||..+.|...|++...+..
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~  208 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD  208 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            45566778888899999999999999999866543

>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=91.85  E-value=0.31  Score=39.70  Aligned_cols=37  Identities=30%  Similarity=0.390  Sum_probs=28.4

Q ss_pred             HHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHH
Q 009803          243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR  279 (525)
Q Consensus       243 ~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~  279 (525)
                      .++.+.+.+|...+||.||..+.|..+|++...+...
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            3456778899999999999999999999998776544

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 ....

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=91.71  E-value=1.4  Score=47.96  Aligned_cols=39  Identities=33%  Similarity=0.463  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHH
Q 009803          371 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL  409 (525)
Q Consensus       371 ~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l  409 (525)
                      +..+.+.+..|..++|+.||..|.|..+|+++..++..+
T Consensus       110 ~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l  148 (415)
T PRK07598        110 YLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL  148 (415)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence            345667788999999999999999988887776666555

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=91.65  E-value=0.39  Score=47.25  Aligned_cols=47  Identities=13%  Similarity=0.105  Sum_probs=34.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR  507 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk  507 (525)
                      .|+++|.+++........+..+|.+|||+.||+|..||+....++..
T Consensus       158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~  204 (239)
T PRK10430        158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN  204 (239)
T ss_pred             CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence            48889887765433211123399999999999999999998887744

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=91.13  E-value=0.55  Score=37.05  Aligned_cols=46  Identities=22%  Similarity=0.400  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          462 LNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       462 L~~rER~VL~lRygl~-~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      |++....-|..-|.+. ++.+.+..+||+.||||+.+|.    .+++||.+
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt----~ml~~L~~   48 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVT----EMLKRLAE   48 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHH----HHHHHHHH
Confidence            3443333333333332 5667999999999999999999    56666654

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PF13518 HTH_28: Helix-turn-helix domain

Probab=91.10  E-value=0.43  Score=35.47  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=21.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIESSAF  506 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~RAL  506 (525)
                      .|+.+||..+|||+.+|+++..+-.
T Consensus        13 ~s~~~~a~~~gis~~tv~~w~~~y~   37 (52)
T PF13518_consen   13 ESVREIAREFGISRSTVYRWIKRYR   37 (52)
T ss_pred             CCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            6999999999999999998776543

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=90.89  E-value=0.52  Score=37.04  Aligned_cols=29  Identities=21%  Similarity=0.280  Sum_probs=24.7

Q ss_pred             HHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          473 RFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       473 Rygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      -|..|    ++..|||+.||+++.+|.+...+-
T Consensus         9 LY~~G----~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen    9 LYLQG----WSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             HHHcC----CCHHHHHHHHCCChHHHHHHHHhh
Confidence            34555    999999999999999999987764

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=90.62  E-value=0.36  Score=37.12  Aligned_cols=40  Identities=23%  Similarity=0.309  Sum_probs=26.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .|+..|+.=|.-+|-.|    .+..+||..|||+++||+.|...
T Consensus         6 ~LTl~eK~~iI~~~e~g----~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    6 SLTLEEKLEIIKRLEEG----ESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             S--HHHHHHHHHHHHCT----T-HHHHHHHHT--CCHHHHHHHC
T ss_pred             cCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHh
Confidence            46666666555555444    69999999999999999998765

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=90.59  E-value=0.71  Score=35.56  Aligned_cols=43  Identities=23%  Similarity=0.303  Sum_probs=32.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .|++.+..||..-+..+ +..+|..|||+.+|+++.+|.++..+
T Consensus         2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v~~   44 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIVKR   44 (62)
T ss_dssp             TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            36788888887766554 33489999999999999999955443

...

>smart00351 PAX Paired Box domain

Probab=90.49  E-value=0.74  Score=41.57  Aligned_cols=41  Identities=20%  Similarity=0.094  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  506 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL  506 (525)
                      ++..+|.=|...|-.+    .|..+||+.||||+.+|..++.+..
T Consensus        18 ~s~~~R~riv~~~~~G----~s~~~iA~~~gvs~~tV~kwi~r~~   58 (125)
T smart00351       18 LPDEERQRIVELAQNG----VRPCDISRQLCVSHGCVSKILGRYY   58 (125)
T ss_pred             CCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            5555555555555443    8999999999999999999988864

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

Probab=89.97  E-value=3.7  Score=41.56  Aligned_cols=144  Identities=18%  Similarity=0.189  Sum_probs=78.8

Q ss_pred             HHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHhccHHHHHHHHHHH
Q 009803          215 RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSN  294 (525)
Q Consensus       215 ~yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~~g~~A~e~Lv~~n  294 (525)
                      .|||+- .  +.--|--=.+++.++      +.+..+|+..+|++||..+.|...|++.+++..          .+...+
T Consensus        91 d~LR~~-~--~v~vpR~~~~~~~~i------~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~----------~~~~~~  151 (247)
T COG1191          91 DYLRKN-D--SVKVPRSLRELGRRI------EEAIDELEQELGREPTDEEIAEELGIDKEEYIE----------ALLAIN  151 (247)
T ss_pred             HHHHhC-C--CccCcHHHHHHHHHH------HHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHH----------HHHHhc
Confidence            377776 4  222233334444444      456778889999999999999999999866543          333333


Q ss_pred             HHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHH
Q 009803          295 IRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRV  374 (525)
Q Consensus       295 lrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki  374 (525)
                      ....+++--.....+...                 -+...+..+..+-.|-..+.+..++..      +|..-..     
T Consensus       152 ~~~~~sld~~~~~~~d~~-----------------~~~~~~~~~~~~~~~~~~~~l~~ai~~------L~EREk~-----  203 (247)
T COG1191         152 GSQLLSLDEDVLKDDDDD-----------------VDDQIENPDDGVEKEELLEILKEAIEP------LPEREKL-----  203 (247)
T ss_pred             cccccchhhhhccccccc-----------------hhhccccchhHHHHHHHHHHHHHHHHc------cCHHHHH-----
Confidence            222222222221111110                 011122344555566666666666541      2221110     


Q ss_pred             HHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHh
Q 009803          375 KEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL  410 (525)
Q Consensus       375 ~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~  410 (525)
                           -+.-....+-|..|||+.||+|..+|..+.+
T Consensus       204 -----Vl~l~y~eelt~kEI~~~LgISes~VSql~k  234 (247)
T COG1191         204 -----VLVLRYKEELTQKEIAEVLGISESRVSRLHK  234 (247)
T ss_pred             -----HHHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence                 1111223456789999999999999988753

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=89.97  E-value=0.44  Score=50.02  Aligned_cols=36  Identities=22%  Similarity=0.267  Sum_probs=30.7

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803          468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR  507 (525)
Q Consensus       468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk  507 (525)
                      .+-.+||..+    +|..|||++||||+.+|+..+.+|.+
T Consensus        17 ~~A~lYY~~g----ltQ~eIA~~LgiSR~~v~rlL~~Ar~   52 (321)
T COG2390          17 RAAWLYYVEG----LTQSEIAERLGISRATVSRLLAKARE   52 (321)
T ss_pred             HHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3556777766    99999999999999999988888865

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=89.82  E-value=1.2  Score=40.45  Aligned_cols=53  Identities=21%  Similarity=0.265  Sum_probs=41.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .++..++=.|++.+-+|+..-.-.+  .|+|..|||+.+|++++||.    ||+++|=.
T Consensus        16 ~dvl~c~~GLs~~Dv~v~~~LL~~~--~~~tvdelae~lnr~rStv~----rsl~~L~~   68 (126)
T COG3355          16 EDVLKCVYGLSELDVEVYKALLEEN--GPLTVDELAEILNRSRSTVY----RSLQNLLE   68 (126)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHhhc--CCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence            4566777789999999887654223  35999999999999999998    77777743

>PHA02591 hypothetical protein; Provisional

Probab=89.33  E-value=0.81  Score=38.06  Aligned_cols=22  Identities=32%  Similarity=0.527  Sum_probs=20.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      +|.++||+.||+|.++||+..+
T Consensus        60 lSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         60 FTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHh
Confidence            9999999999999999998865

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=88.86  E-value=0.93  Score=38.47  Aligned_cols=43  Identities=28%  Similarity=0.463  Sum_probs=32.2

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH--CCCHHHHHHHHHH
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELM--GVSRERIRQIESS  504 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L--gIS~erVRqie~R  504 (525)
                      ++.||+..+++..+|--.-+   .|+.|+|+.|  .||++.|.-+..+
T Consensus        35 ~~~l~~~l~~~a~lRl~~Pd---~SL~EL~~~~~~~iSKSgvnhrlrK   79 (85)
T PF02650_consen   35 LDKLPEKLREFAELRLENPD---ASLKELGELLEPPISKSGVNHRLRK   79 (85)
T ss_dssp             GGGS-HHHHHHHHHHHH-TT---S-HHHHHHTT--T--HHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHCcc---ccHHHHHHHHcCcCcHHHHHHHHHH
Confidence            57899999999999975543   9999999999  9999999866543

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=88.66  E-value=0.67  Score=35.06  Aligned_cols=36  Identities=22%  Similarity=0.302  Sum_probs=25.9

Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          467 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       467 R~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      |-+-.+.+.-..+.++|+.||++.+|+++.+|..+.
T Consensus         4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L   39 (52)
T PF09339_consen    4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLL   39 (52)
T ss_dssp             HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            333444555555666999999999999999998554

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=88.62  E-value=1  Score=37.57  Aligned_cols=41  Identities=27%  Similarity=0.341  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHHHH---HhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          461 TLNPRERQVVRWR---FGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~lR---ygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .|++++++||..-   |. ..|+|..-++||+.+|+|..|||+..
T Consensus         1 ~Lt~rq~~IL~alV~~Y~-~~~~PVgSk~ia~~l~~s~aTIRN~M   44 (78)
T PF03444_consen    1 MLTERQREILKALVELYI-ETGEPVGSKTIAEELGRSPATIRNEM   44 (78)
T ss_pred             CCCHHHHHHHHHHHHHHH-hcCCCcCHHHHHHHHCCChHHHHHHH
Confidence            3889999987654   33 36889999999999999999999654

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=88.62  E-value=1.3  Score=37.98  Aligned_cols=49  Identities=29%  Similarity=0.342  Sum_probs=36.8

Q ss_pred             HhcCCHHHHHHHHHH----HhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          459 LDTLNPRERQVVRWR----FGLE-DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       459 L~~L~~rER~VL~lR----ygl~-~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ...+++++..+|..-    ||.+ ...++|..|||+.+|+++++|+    |++++|.+
T Consensus        20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~   73 (95)
T TIGR01610        20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR   73 (95)
T ss_pred             hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            357899999877643    3321 2346999999999999999998    67777754

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=88.57  E-value=1.2  Score=35.77  Aligned_cols=41  Identities=10%  Similarity=0.306  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       466 ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +..||.+-.. .+++.+|..|||+.+||++.+|+    +.|.+|.+
T Consensus         8 ~~~IL~~L~~-~g~~~~ta~eLa~~lgl~~~~v~----r~L~~L~~   48 (68)
T smart00550        8 EEKILEFLEN-SGDETSTALQLAKNLGLPKKEVN----RVLYSLEK   48 (68)
T ss_pred             HHHHHHHHHH-CCCCCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            3445444332 23334999999999999999999    45555544

Helix-turn-helix-containing domain. Also known as Zab.

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=88.24  E-value=0.79  Score=43.10  Aligned_cols=49  Identities=27%  Similarity=0.246  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLK  510 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR  510 (525)
                      .|+++|.+|+.+.. .+-|.++|.++|++.+.     +|..+|+....+.++||.
T Consensus       148 ~Lt~~E~~il~~l~-~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~  201 (221)
T PRK15479        148 ALTPREQALLTVLM-YRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ  201 (221)
T ss_pred             ecCHHHHHHHHHHH-hCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence            59999999998764 44467789999999986     999999999999999985

>PRK12423 LexA repressor; Provisional

Probab=88.18  E-value=0.94  Score=44.14  Aligned_cols=48  Identities=27%  Similarity=0.424  Sum_probs=36.4

Q ss_pred             hcCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWR--FGLEDGRMKTLQEIGELMG-VSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lR--ygl~~g~~~Tl~EIAe~Lg-IS~erVRqie~RALkKLR~  511 (525)
                      ..|++++++|+..-  |...+|-+.|..|||+.|| +|+.+|+    ++|++|++
T Consensus         2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~----~~l~~L~~   52 (202)
T PRK12423          2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVAR----KHVQALAE   52 (202)
T ss_pred             CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence            35899999988753  3334555679999999999 5999999    46666665

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=88.16  E-value=1.8  Score=43.72  Aligned_cols=35  Identities=23%  Similarity=0.315  Sum_probs=28.3

Q ss_pred             HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (525)
Q Consensus       244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~  278 (525)
                      ++.+...+|...+|++||..+.|...|++...+..
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~  148 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE  148 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence            34556778888899999999999999999876543

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=88.00  E-value=0.6  Score=37.16  Aligned_cols=44  Identities=27%  Similarity=0.323  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|++.|..|+..-.-.+   ++|..|||+.+|+++.+|+    +++++|.+
T Consensus         5 gLs~~E~~vy~~Ll~~~---~~t~~eIa~~l~i~~~~v~----~~L~~L~~   48 (68)
T PF01978_consen    5 GLSENEAKVYLALLKNG---PATAEEIAEELGISRSTVY----RALKSLEE   48 (68)
T ss_dssp             CHHHHHHHHHHHHHHHC---HEEHHHHHHHHTSSHHHHH----HHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHcC---CCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            36777777776543222   3999999999999999999    56666643

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=87.96  E-value=1.8  Score=41.25  Aligned_cols=63  Identities=14%  Similarity=0.259  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHh
Q 009803          294 NIRLVISIAKNYQGAGMN---LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  356 (525)
Q Consensus       294 nlrLV~~IA~~y~~~g~~---~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~  356 (525)
                      -+..+..++++|.-+|..   -+|.|.+|.-.+++.+..|||++...+-.|.+..+-++..+.|..
T Consensus        46 imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~k  111 (179)
T PHA02547         46 IMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKK  111 (179)
T ss_pred             HHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHH
Confidence            444555555555444544   589999999999999999999998777777777666666655543

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=87.94  E-value=1.8  Score=36.61  Aligned_cols=42  Identities=19%  Similarity=0.120  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHH
Q 009803          465 RERQVVRWRFGLEDGRMKTLQEIGELMG-VSRERIRQIESSAFRKLK  510 (525)
Q Consensus       465 rER~VL~lRygl~~g~~~Tl~EIAe~Lg-IS~erVRqie~RALkKLR  510 (525)
                      |+--+...+...+    +|+.+||+.|| .+..+|.....+.-+++.
T Consensus        32 R~ia~yl~~~~~~----~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~   74 (90)
T cd06571          32 RQIAMYLARELTG----LSLPEIGRAFGGRDHSTVLHAVRKIEELLE   74 (90)
T ss_pred             HHHHHHHHHHHhC----CCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence            3333444444445    99999999999 999999955554444443

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=87.79  E-value=1.3  Score=33.85  Aligned_cols=40  Identities=25%  Similarity=0.422  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      |+..|-.||..-+-.++   .|..+||+.+++++.+|.++..+
T Consensus         1 lt~~q~~iL~~l~~~~~---~~~~~la~~~~~~~~~~t~~i~~   40 (59)
T PF01047_consen    1 LTPSQFRILRILYENGG---ITQSELAEKLGISRSTVTRIIKR   40 (59)
T ss_dssp             STHHHHHHHHHHHHHSS---EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCC---CCHHHHHHHHCCChhHHHHHHHH
Confidence            56667777777765543   99999999999999999955443

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=87.69  E-value=0.93  Score=34.18  Aligned_cols=29  Identities=31%  Similarity=0.547  Sum_probs=24.1

Q ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          479 GRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       479 g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      |..+ |..|||+.+|+|+.+|+    +++++|.+
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~----~~l~~L~~   46 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVR----EALSRLEA   46 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            3346 99999999999999999    67777765

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=87.63  E-value=0.84  Score=43.14  Aligned_cols=50  Identities=16%  Similarity=0.129  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVS-----RERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS-----~erVRqie~RALkKLR~  511 (525)
                      .|+++|.+|+.+-.- +.|..+|.+||++.++.+     ..+|+.+..+.++||..
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (228)
T PRK11083        154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA  208 (228)
T ss_pred             ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence            599999999987653 456679999999999986     78999999999999974

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=87.59  E-value=1.8  Score=36.92  Aligned_cols=45  Identities=31%  Similarity=0.436  Sum_probs=31.3

Q ss_pred             cCCHHHHHHHHHHHh-----cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFG-----LEDGRMKTLQEIGELMGVSRERIRQIESSAFRK  508 (525)
Q Consensus       461 ~L~~rER~VL~lRyg-----l~~g~~~Tl~EIAe~LgIS~erVRqie~RALkK  508 (525)
                      -++|.|+.-|..|+-     +.+|  +|+.||++.+|+|..||. +.+|+|+.
T Consensus        26 L~T~~E~~~l~~R~~va~~lL~~g--~syreIa~~tgvS~aTIt-Rvsr~Lk~   75 (87)
T PF01371_consen   26 LCTPDELEALAQRWQVAKELLDEG--KSYREIAEETGVSIATIT-RVSRCLKY   75 (87)
T ss_dssp             HSSHHHHHHHHHHHHHHHHHHHTT--SSHHHHHHHHTSTHHHHH-HHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHhCCCHHHHH-HHHHHHHc
Confidence            467777766655542     2233  999999999999999997 33444443

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=87.11  E-value=1.2  Score=34.91  Aligned_cols=43  Identities=23%  Similarity=0.338  Sum_probs=26.2

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      |+..|..||..-.  ..+.++|..+|++.+|+++.+|.    +++++|.
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs----~~i~~L~   43 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVS----RIIKKLE   43 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHH----HHHHHHH
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHH----HHHHHHH
Confidence            4556666655443  34456999999999999999999    4555554

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=87.08  E-value=0.75  Score=53.46  Aligned_cols=48  Identities=19%  Similarity=0.184  Sum_probs=42.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      -|+.||++|+.+-| .|    +|.+|||+.+.||-.||+.+.++-..||.-.-
T Consensus       831 ~Ls~RE~eVL~Lia-~G----~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~  878 (894)
T COG2909         831 PLSQRELEVLGLIA-QG----LSNEEIAQELFISLTTVKTHIRNIYQKLGVAN  878 (894)
T ss_pred             CccHHHHHHHHHHH-cc----CCHHHHHHHHHHHHHHHHHHHHHHHHHhCcch
Confidence            48999999999998 33    89999999999999999999999999996443

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=87.03  E-value=0.96  Score=43.07  Aligned_cols=50  Identities=18%  Similarity=0.129  Sum_probs=42.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHH--HHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEI--GELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EI--Ae~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|.+||.+-. .+.|..+|.++|  +..++++..+|+.+..+.++||..
T Consensus       156 ~Lt~~E~~il~~l~-~~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~  207 (227)
T TIGR03787       156 DLTVTEFWMVHALA-KHPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA  207 (227)
T ss_pred             cCCHHHHHHHHHHH-hCCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence            49999999998754 344667899999  888999999999999999999963

This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=87.02  E-value=1  Score=43.16  Aligned_cols=50  Identities=20%  Similarity=0.226  Sum_probs=44.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR~  511 (525)
                      .|+++|++|+.+... +.|+..|.++|++.+.     ++..+|+....+.++||..
T Consensus       160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~  214 (240)
T PRK10710        160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES  214 (240)
T ss_pred             ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence            599999999998765 4566799999999998     9999999999999999963

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=86.80  E-value=3.8  Score=41.34  Aligned_cols=32  Identities=22%  Similarity=0.285  Sum_probs=25.4

Q ss_pred             hHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803          247 GLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (525)
Q Consensus       247 ~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~  278 (525)
                      .....|...+|++|+..+.|+..|++...+..
T Consensus       114 ~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~  145 (257)
T PRK05911        114 DAMDSLRQSLGKEPTDGELCEYLNISQQELSG  145 (257)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence            34456777889999999999999998876543

>cd00131 PAX Paired Box domain

Probab=86.80  E-value=1.8  Score=39.26  Aligned_cols=41  Identities=17%  Similarity=0.054  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  506 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL  506 (525)
                      |+...|.=|...|-.+    +|..+||+.||||+.+|..+.++-.
T Consensus        18 lS~d~R~rIv~~~~~G----~s~~~iA~~~~Vs~~tV~r~i~r~~   58 (128)
T cd00131          18 LPDSIRQRIVELAQSG----IRPCDISRQLRVSHGCVSKILNRYY   58 (128)
T ss_pred             CCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            5554444444445444    9999999999999999998877754

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=86.66  E-value=2.2  Score=41.92  Aligned_cols=31  Identities=35%  Similarity=0.493  Sum_probs=25.0

Q ss_pred             hHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803          247 GLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (525)
Q Consensus       247 ~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~  277 (525)
                      +....|...+|+.||..+.|+..|++...+.
T Consensus       101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~  131 (231)
T TIGR02885       101 YMKEELSKELGREPTINELAEALGVSPEEIV  131 (231)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHH
Confidence            3455677778999999999999999876654

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.

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=86.59  E-value=1  Score=42.29  Aligned_cols=49  Identities=24%  Similarity=0.230  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLK  510 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR  510 (525)
                      .|+++|.+|+.+. ..+.|..+|.++|++.+.     ++..+|+....+.++||.
T Consensus       149 ~Lt~~E~~il~~l-~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~  202 (219)
T PRK10336        149 TLKPKEFALLELL-MRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG  202 (219)
T ss_pred             ecCHHHHHHHHHH-HhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence            4999999999865 345567799999999996     999999999999999985

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=86.57  E-value=7.7  Score=41.65  Aligned_cols=35  Identities=26%  Similarity=0.362  Sum_probs=28.0

Q ss_pred             HHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803          243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (525)
Q Consensus       243 ~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~  277 (525)
                      .++.+....|...+|+.||..+.|...|++...+.
T Consensus       223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~  257 (373)
T PRK07406        223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLR  257 (373)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHH
Confidence            34455667778888999999999999999976653

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=86.57  E-value=1.7  Score=37.49  Aligned_cols=39  Identities=15%  Similarity=0.245  Sum_probs=29.8

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      |++.++.||..-.- +  .+.|+.+||+.+|+|+.+|+.+..
T Consensus         1 ld~~D~~il~~L~~-~--~~~~~~~la~~l~~s~~tv~~~l~   39 (108)
T smart00344        1 LDEIDRKILEELQK-D--ARISLAELAKKVGLSPSTVHNRVK   39 (108)
T ss_pred             CCHHHHHHHHHHHH-h--CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            46677888876543 2  249999999999999999995443

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=86.50  E-value=1.9  Score=33.03  Aligned_cols=38  Identities=32%  Similarity=0.351  Sum_probs=26.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .|++-||.-|....-++    +++.|||..+|-|+..|+..+
T Consensus         4 ~Lt~~Eqaqid~m~qlG----~s~~~isr~i~RSr~~Ir~yl   41 (50)
T PF11427_consen    4 TLTDAEQAQIDVMHQLG----MSLREISRRIGRSRTCIRRYL   41 (50)
T ss_dssp             ---HHHHHHHHHHHHTT------HHHHHHHHT--HHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhc----hhHHHHHHHhCccHHHHHHHh
Confidence            47888888888777777    999999999999999999664

>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=86.50  E-value=2  Score=34.55  Aligned_cols=39  Identities=33%  Similarity=0.393  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHcCCC-HHHHHHHHh
Q 009803          372 YRVKEARKQLYSENGRHPNNEEVAEATGLS-MKRLHAVLL  410 (525)
Q Consensus       372 ~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis-~~~v~~~l~  410 (525)
                      .++-..-..+..++|..||..|||+.+|++ ...|...+.
T Consensus         9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen    9 KEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             HHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            344455566778899999999999999997 888887764

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.

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=86.49  E-value=8.2  Score=39.18  Aligned_cols=34  Identities=35%  Similarity=0.479  Sum_probs=27.2

Q ss_pred             HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803          245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (525)
Q Consensus       245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~  278 (525)
                      +.+...+|...+|+.||..+.|...|++.+.+..
T Consensus       129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~  162 (264)
T PRK07122        129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE  162 (264)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            3445667777889999999999999999876543

>PRK05949 RNA polymerase sigma factor; Validated

Probab=86.45  E-value=5.2  Score=42.04  Aligned_cols=34  Identities=24%  Similarity=0.330  Sum_probs=26.8

Q ss_pred             HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803          245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (525)
Q Consensus       245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~  278 (525)
                      +.+.+..+...+|++||..+.|...|++...+..
T Consensus       180 l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~  213 (327)
T PRK05949        180 IKKTQRELSQKLGRSATPAEIAKELELEPSQIRE  213 (327)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            4445566777889999999999999999766543

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=86.16  E-value=12  Score=38.53  Aligned_cols=98  Identities=19%  Similarity=0.200  Sum_probs=52.2

Q ss_pred             CCCCCHHHHHHHcC--CCHHHHHHHHhCCCCCCCcccccccccCCCC---CcccCCCCCCCHHH-HHHHHHHHHHHHHHH
Q 009803          386 GRHPNNEEVAEATG--LSMKRLHAVLLSPKAPRSLDQKIGINQNLKP---SEVIADPEAETAED-LLIKKFMKEDLEKVL  459 (525)
Q Consensus       386 gr~Pt~eEIA~~lg--is~~~v~~~l~~~~~~~SLD~~i~~d~~~~l---~d~l~d~~~~~pee-~~~~~~~~~~L~~aL  459 (525)
                      +..+++++||+.++  ||.++|++.+......-=+..    +++..+   ...+..+....+.. .-.+.++.+.-.++|
T Consensus       135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk----~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al  210 (271)
T TIGR02147       135 PFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKK----NEDGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEAL  210 (271)
T ss_pred             CCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeE----CCCCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHH
Confidence            34567889999999  999999998864321111110    111111   11122222112221 112233445556778


Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGEL  490 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~  490 (525)
                      +..|+.+|.+=.+-++.+.   -++++|.+.
T Consensus       211 ~~~p~~eR~~S~lT~~i~~---~~~~~i~~~  238 (271)
T TIGR02147       211 DALPPSERDVSTVTFGISE---EAYKEIVKK  238 (271)
T ss_pred             HhCCccccccceeeEecCH---HHHHHHHHH
Confidence            8999999997766665542   345555444

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

>TIGR00498 lexA SOS regulatory protein LexA

Probab=86.08  E-value=1.4  Score=42.45  Aligned_cols=48  Identities=17%  Similarity=0.270  Sum_probs=36.7

Q ss_pred             hcCCHHHHHHHHHHH--hcCCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRF--GLEDGRMKTLQEIGELMGVS-RERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRy--gl~~g~~~Tl~EIAe~LgIS-~erVRqie~RALkKLR~  511 (525)
                      ..|+++|++||..-.  ...++.+.|..|||+.+|++ +.+|+    +.+++|.+
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~----~~l~~L~~   52 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAE----EHLKALER   52 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHH----HHHHHHHH
Confidence            358999999987764  23356778999999999998 99999    44555543

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=85.77  E-value=1.8  Score=40.19  Aligned_cols=40  Identities=15%  Similarity=0.227  Sum_probs=31.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      .|++.++.||..---  || ..|+.+||+.+|+|+.+|+.+..
T Consensus         6 ~lD~~D~~Il~~Lq~--d~-R~s~~eiA~~lglS~~tV~~Ri~   45 (153)
T PRK11179          6 QIDNLDRGILEALME--NA-RTPYAELAKQFGVSPGTIHVRVE   45 (153)
T ss_pred             ccCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHHHHH
Confidence            477888888876533  22 38999999999999999995543

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=85.39  E-value=10  Score=38.00  Aligned_cols=35  Identities=23%  Similarity=0.186  Sum_probs=27.4

Q ss_pred             HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHH
Q 009803          245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR  279 (525)
Q Consensus       245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~  279 (525)
                      +.+...++...+|++||..+.|...|++.+.+...
T Consensus       122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~  156 (254)
T TIGR02850       122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA  156 (254)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            33455677778899999999999999998766543

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.

>PF12728 HTH_17: Helix-turn-helix domain

Probab=85.36  E-value=0.92  Score=33.91  Aligned_cols=24  Identities=29%  Similarity=0.457  Sum_probs=21.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      +|.+|+|+.||||+.+|+++..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g   25 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQG   25 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            799999999999999999887643

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=85.33  E-value=14  Score=37.34  Aligned_cols=34  Identities=24%  Similarity=0.371  Sum_probs=27.4

Q ss_pred             HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (525)
Q Consensus       244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~  277 (525)
                      .+.+....|+..+|+.||..+.|...|++...+.
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~  152 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYN  152 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence            4555667788889999999999999999876543

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=85.24  E-value=2.4  Score=36.07  Aligned_cols=44  Identities=20%  Similarity=0.148  Sum_probs=36.8

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  506 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL  506 (525)
                      ..|++.-|..|..+...+|   .++.++|+.||||+.|++.+..|=.
T Consensus         7 A~Lt~~gR~~lv~~vv~~g---~~~a~aA~~~gVS~~Ta~kW~~Ryr   50 (85)
T PF13011_consen    7 ARLTPRGRLRLVRRVVEQG---WPVAHAAAEFGVSRRTAYKWLARYR   50 (85)
T ss_pred             CCCCHHHHHHHHHHHHHcC---CcHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3589999998888876543   8999999999999999998877643

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=85.15  E-value=1.4  Score=40.20  Aligned_cols=42  Identities=24%  Similarity=0.317  Sum_probs=33.0

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      ..|++.++.||..--  .|++ .|+.|||+.+|+|+.+|+.+..+
T Consensus         4 ~~lD~~D~~IL~~L~--~d~r-~~~~eia~~lglS~~~v~~Ri~~   45 (154)
T COG1522           4 MKLDDIDRRILRLLQ--EDAR-ISNAELAERVGLSPSTVLRRIKR   45 (154)
T ss_pred             ccccHHHHHHHHHHH--HhCC-CCHHHHHHHHCCCHHHHHHHHHH
Confidence            468888889988753  2333 99999999999999999965443

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=84.91  E-value=2.6  Score=31.19  Aligned_cols=23  Identities=22%  Similarity=0.317  Sum_probs=19.4

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Q 009803          481 MKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       481 ~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      +++..||++.+|+|+.+|++.+.
T Consensus        15 ~~~~~el~~~l~~s~~~vs~hL~   37 (47)
T PF01022_consen   15 PLTVSELAEELGLSQSTVSHHLK   37 (47)
T ss_dssp             SEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCchhhHHHhccccchHHHHHHH
Confidence            59999999999999999996543

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=84.71  E-value=0.96  Score=33.86  Aligned_cols=22  Identities=23%  Similarity=0.483  Sum_probs=19.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q 009803          483 TLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       483 Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      |+++||+..|||..||+..++.
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~   22 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNG   22 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTT
T ss_pred             CHHHHHHHHCcCHHHHHHHHhC
Confidence            7899999999999999977653

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=84.59  E-value=1.3  Score=35.50  Aligned_cols=28  Identities=36%  Similarity=0.611  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      -++|.++||..+|+|+++|.    +.+++|++
T Consensus        27 ~~lt~~~iA~~~g~sr~tv~----r~l~~l~~   54 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSRETVS----RILKRLKD   54 (76)
T ss_dssp             EESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             ecCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            35899999999999999998    66777765

...

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=84.46  E-value=7.9  Score=34.50  Aligned_cols=27  Identities=37%  Similarity=0.522  Sum_probs=22.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          482 KTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .|+.|||+.||||..+|.    ++|++|.-.
T Consensus        72 ~tl~Ela~~l~Vs~~ti~----~~Lkrlg~t   98 (119)
T PF01710_consen   72 ATLRELAERLGVSPSTIW----RALKRLGIT   98 (119)
T ss_pred             cCHHHHHHHcCCCHHHHH----HHHHHcCch
Confidence            899999999999999998    666666543

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK00215 LexA repressor; Validated

Probab=84.34  E-value=1.9  Score=41.73  Aligned_cols=43  Identities=19%  Similarity=0.322  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHCC-CHHHHHHHHHH
Q 009803          462 LNPRERQVVRWR--FGLEDGRMKTLQEIGELMGV-SRERIRQIESS  504 (525)
Q Consensus       462 L~~rER~VL~lR--ygl~~g~~~Tl~EIAe~LgI-S~erVRqie~R  504 (525)
                      |+++|++||.+-  |....+.+.|+.|||+.+|+ |+.+|..++.+
T Consensus         2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~   47 (205)
T PRK00215          2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKA   47 (205)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            788899988644  33345667899999999999 99999955443

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=84.20  E-value=1.1  Score=43.68  Aligned_cols=39  Identities=21%  Similarity=0.232  Sum_probs=27.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      .|+++  +|+.+--  .|...+|.+|||+.||||+.||+....
T Consensus       161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~  199 (225)
T PRK10046        161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE  199 (225)
T ss_pred             HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence            35554  5665432  222238999999999999999998764

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=84.15  E-value=1.9  Score=31.25  Aligned_cols=38  Identities=18%  Similarity=0.288  Sum_probs=26.2

Q ss_pred             CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          463 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       463 ~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      .+-|+.+|.-..-..+   -+..+.|+.||||+.+++..+.
T Consensus         3 ~~~E~~~i~~aL~~~~---gn~~~aA~~Lgisr~tL~~klk   40 (42)
T PF02954_consen    3 EEFEKQLIRQALERCG---GNVSKAARLLGISRRTLYRKLK   40 (42)
T ss_dssp             HHHHHHHHHHHHHHTT---T-HHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhC---CCHHHHHHHHCCCHHHHHHHHH
Confidence            3456677766655544   3889999999999999985543

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=84.08  E-value=1.7  Score=31.41  Aligned_cols=27  Identities=37%  Similarity=0.639  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ++|..+||+.+|+|+.+|+    +++++|.+
T Consensus         8 ~~s~~~la~~l~~s~~tv~----~~l~~L~~   34 (48)
T smart00419        8 PLTRQEIAELLGLTRETVS----RTLKRLEK   34 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4899999999999999997    56666654

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

Probab=84.04  E-value=13  Score=38.23  Aligned_cols=34  Identities=24%  Similarity=0.437  Sum_probs=26.9

Q ss_pred             HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803          245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (525)
Q Consensus       245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~  278 (525)
                      +.+.+..+...+|+.||..+.|...|++...+..
T Consensus       163 ~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~  196 (298)
T TIGR02997       163 IKKVQRELSQKLGRTPSEAEIAEALELEPEQVRE  196 (298)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            3445566777889999999999999999876543

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).

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=83.68  E-value=5.6  Score=40.16  Aligned_cols=55  Identities=27%  Similarity=0.417  Sum_probs=41.6

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDG--RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g--~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..++-++++|+--|.+.+...+-.=++  --.+..+||+.+|||+..|+    +|+++|-.
T Consensus       168 a~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~  224 (251)
T TIGR02787       168 AAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES  224 (251)
T ss_pred             HHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            457778999998887766655433222  34899999999999999999    67777754

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=83.56  E-value=1.3  Score=41.62  Aligned_cols=29  Identities=28%  Similarity=0.346  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      -|+|.+|||..+|+|+++|.    |++++|++.
T Consensus       142 ~~~t~~~iA~~lG~tretvs----R~l~~l~~~  170 (193)
T TIGR03697       142 LRLSHQAIAEAIGSTRVTIT----RLLGDLRKK  170 (193)
T ss_pred             CCCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence            46899999999999999999    788888763

Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=83.52  E-value=5.2  Score=31.09  Aligned_cols=36  Identities=19%  Similarity=0.299  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      |.-+.||.+-..   +.++|..|||+.+|++..+|+..+
T Consensus        10 p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL   45 (61)
T PF12840_consen   10 PTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHL   45 (61)
T ss_dssp             HHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHH
Confidence            455556655422   235999999999999999999543

...

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=83.49  E-value=1.7  Score=40.83  Aligned_cols=40  Identities=18%  Similarity=0.199  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      |++.+++||..-  ..|| ..|+.|||+.+|+|+.+|+.+..|
T Consensus        12 lD~~D~~IL~~L--q~d~-R~s~~eiA~~lglS~~tv~~Ri~r   51 (164)
T PRK11169         12 LDRIDRNILNEL--QKDG-RISNVELSKRVGLSPTPCLERVRR   51 (164)
T ss_pred             HHHHHHHHHHHh--ccCC-CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            666778888753  2233 399999999999999999955443

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=83.36  E-value=2.6  Score=40.04  Aligned_cols=42  Identities=21%  Similarity=0.272  Sum_probs=35.0

Q ss_pred             CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803          463 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR  507 (525)
Q Consensus       463 ~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk  507 (525)
                      |+.-|.-++..|..++   +|++.+|..+|||..|+|.+..+|..
T Consensus         4 ~~e~R~~~R~~YV~~~---~sLe~aA~~~gVs~~TarrWK~~Ak~   45 (165)
T PF08822_consen    4 PQETRDAVRRAYVFDR---LSLEQAAAKCGVSYATARRWKREAKA   45 (165)
T ss_pred             cHHHHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3455677788887654   99999999999999999999998854

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=83.34  E-value=2.3  Score=39.31  Aligned_cols=34  Identities=21%  Similarity=0.104  Sum_probs=27.3

Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803          469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  506 (525)
Q Consensus       469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL  506 (525)
                      ++...++.|    +|..|||++||||..||.....+--
T Consensus        13 ~~~~~~~~G----~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415          13 VVDAVVGEG----LSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             HHHHHHHcC----ccHHHHHHHhCccHHHHHHHHHHhc
Confidence            444444555    9999999999999999998887754

>TIGR01764 excise DNA binding domain, excisionase family

Probab=83.27  E-value=1.4  Score=31.89  Aligned_cols=24  Identities=25%  Similarity=0.479  Sum_probs=21.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      +|.+|+|+.||||+.+|+++....
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            689999999999999999987654

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=83.22  E-value=14  Score=29.04  Aligned_cols=23  Identities=30%  Similarity=0.408  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHcCCCHHHHHHHHh
Q 009803          388 HPNNEEVAEATGLSMKRLHAVLL  410 (525)
Q Consensus       388 ~Pt~eEIA~~lgis~~~v~~~l~  410 (525)
                      +++.++||+.+|++...+..+..
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f~   23 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFK   23 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Confidence            36889999999999999988764

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=82.89  E-value=0.97  Score=42.57  Aligned_cols=50  Identities=14%  Similarity=0.212  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEI-----GELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EI-----Ae~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|.+|+.+-.. +-|..+|.++|     |..+++|..+|+....+.++||..
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (226)
T TIGR02154       154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP  208 (226)
T ss_pred             EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence            599999999987654 34556888888     778999999999999999999963

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=82.82  E-value=6.6  Score=36.40  Aligned_cols=65  Identities=26%  Similarity=0.379  Sum_probs=36.7

Q ss_pred             HHHHHhcCCHHHHHHHHHH----HhcCCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHhHHhhchhh
Q 009803          455 LEKVLDTLNPRERQVVRWR----FGLEDGRMKTLQEIGELMGVSRERIRQIES--SAFRKLKNKKRTKHLM  519 (525)
Q Consensus       455 L~~aL~~L~~rER~VL~lR----ygl~~g~~~Tl~EIAe~LgIS~erVRqie~--RALkKLR~~l~~~~L~  519 (525)
                      +..+=.+|++.|+....+-    |...+|..+|+.|||+.+|||+.+.-++.+  +++....+.+....+.
T Consensus         4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~   74 (142)
T PF13022_consen    4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLS   74 (142)
T ss_dssp             HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence            4445578999888833322    222244669999999999999999998874  4444444444433333

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=82.76  E-value=1.5  Score=31.45  Aligned_cols=25  Identities=32%  Similarity=0.380  Sum_probs=22.3

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIESSAF  506 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~RAL  506 (525)
                      +|..|+|+.||||+.+|+.+.....
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~   25 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGK   25 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence            5889999999999999999987754

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=82.73  E-value=2.9  Score=32.39  Aligned_cols=39  Identities=26%  Similarity=0.371  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       466 ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +..|+.+-.-   ....|.+|+|+.||||..|||    |=|..|-+
T Consensus         2 ~~~Il~~l~~---~~~~s~~ela~~~~VS~~TiR----RDl~~L~~   40 (57)
T PF08220_consen    2 QQQILELLKE---KGKVSVKELAEEFGVSEMTIR----RDLNKLEK   40 (57)
T ss_pred             HHHHHHHHHH---cCCEEHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            3455554322   234899999999999999999    44445543

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=82.52  E-value=14  Score=38.56  Aligned_cols=34  Identities=21%  Similarity=0.375  Sum_probs=27.0

Q ss_pred             HHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHH
Q 009803          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  277 (525)
Q Consensus       244 ~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~  277 (525)
                      ++.+.+..+...+|+.||..+.|...|++...+.
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~  202 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVR  202 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHH
Confidence            3455667777788999999999999999876543

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=82.48  E-value=4.2  Score=31.53  Aligned_cols=28  Identities=29%  Similarity=0.515  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .++|..|||+.+|+|+.+|+    +.+++|++
T Consensus        24 ~~~s~~ela~~~g~s~~tv~----r~l~~L~~   51 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVS----RTLKELEE   51 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            45999999999999999998    56666655

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=82.40  E-value=3.6  Score=34.44  Aligned_cols=32  Identities=22%  Similarity=0.451  Sum_probs=26.9

Q ss_pred             cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          476 LEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       476 l~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +.++.+.|-++||+.||+|+.+|-    +.+++||+
T Consensus        14 ~~~~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~   45 (79)
T COG1654          14 LLTGNFVSGEKLAEELGISRTAVW----KHIQQLRE   45 (79)
T ss_pred             HcCCCcccHHHHHHHHCccHHHHH----HHHHHHHH
Confidence            345677999999999999999998    67778875

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=81.29  E-value=3  Score=34.27  Aligned_cols=50  Identities=20%  Similarity=0.373  Sum_probs=33.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHH
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQI  501 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~-~g~~~Tl~EIAe~LgIS~erVRqi  501 (525)
                      ...|......|++.|+.|...-.-.- .-..+|..|||+..|||..+|-..
T Consensus         4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf   54 (77)
T PF01418_consen    4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRF   54 (77)
T ss_dssp             HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHH
T ss_pred             HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHH
Confidence            45677778899999999876432211 113499999999999999999743

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>COG1510 Predicted transcriptional regulators [Transcription]

Probab=81.18  E-value=1.5  Score=41.83  Aligned_cols=30  Identities=30%  Similarity=0.552  Sum_probs=25.4

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          478 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       478 ~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..+|+|+.||++.+|+|+++|+    -++++|..
T Consensus        38 s~~Pmtl~Ei~E~lg~Sks~vS----~~lkkL~~   67 (177)
T COG1510          38 SRKPLTLDEIAEALGMSKSNVS----MGLKKLQD   67 (177)
T ss_pred             cCCCccHHHHHHHHCCCcchHH----HHHHHHHh
Confidence            3578999999999999999999    56777754

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=81.01  E-value=18  Score=36.16  Aligned_cols=34  Identities=26%  Similarity=0.251  Sum_probs=26.7

Q ss_pred             HHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHH
Q 009803          245 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  278 (525)
Q Consensus       245 le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~  278 (525)
                      +++....+...+|+.|+..++|...|++...+..
T Consensus       111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~  144 (251)
T PRK07670        111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEA  144 (251)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHH
Confidence            3444566777889999999999999998866544

>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities

Probab=80.26  E-value=2.4  Score=33.27  Aligned_cols=30  Identities=37%  Similarity=0.572  Sum_probs=22.9

Q ss_pred             CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          478 DGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       478 ~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|..+ |..+||+.||||+.+||    +|+..|..
T Consensus        20 ~g~~lps~~~la~~~~vsr~tvr----~al~~L~~   50 (64)
T PF00392_consen   20 PGDRLPSERELAERYGVSRTTVR----EALRRLEA   50 (64)
T ss_dssp             TTSBE--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred             CCCEeCCHHHHHHHhccCCcHHH----HHHHHHHH
Confidence            34557 99999999999999999    77777754

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=80.11  E-value=4.7  Score=30.01  Aligned_cols=24  Identities=21%  Similarity=0.452  Sum_probs=21.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      .|+++||+.+|||..+|+.+..+.
T Consensus        28 ~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   28 RSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHhh
Confidence            599999999999999999887764

>PF00046 Homeobox: Homeobox domain not present here

Probab=80.07  E-value=4.3  Score=30.82  Aligned_cols=51  Identities=14%  Similarity=0.188  Sum_probs=40.5

Q ss_pred             cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g-~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .+++.+..+|.-.|..+.. ......+||..+||+...|......-..+.|+
T Consensus         6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            4678888999999887532 12467899999999999999999887777663

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	525
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		4e-55
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		3e-54
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		8e-53
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		8e-53
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		9e-53
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		9e-48
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		1e-47
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		1e-34
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		1e-34
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		3e-21
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		1e-19
4g6d_A	73	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		8e-18
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		9e-17
1tty_A	87	Solution Structure Of Sigma A Region 4 From Thermot		1e-16
4g94_A	62	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		3e-16
3n97_A	72	Rna Polymerase Alpha C-Terminal Domain (E. Coli) An		1e-11
1ku3_A	73	Crystal Structure Of Thermus Aquaticus Rna Polymera		2e-11
1rio_H	73	Structure Of Bacteriophage Lambda Ci-Ntd In Complex		2e-11
1rp3_A	239	Cocrystal Structure Of The Flagellar SigmaANTI-Sigm		1e-09
1tlh_B	81	T4 Asia Bound To Sigma70 Region 4 Length = 81		3e-08
3t72_q	99	Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna		4e-08
2p7v_B	68	Crystal Structure Of The Escherichia Coli Regulator		6e-08

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score =  212 bits (540), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 128/329 (38%), Positives = 189/329 (57%), Gaps = 18/329 (5%)
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--GLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 433
              +QL  E GR P+ EE+AEA   G   KR+   L   + P SL+  IG  ++    + 
Sbjct: 182 RTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDF 241
Query: 434 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGV 493
           I D    +  +   +  + E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV
Sbjct: 242 IPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGV 301
Query: 494 SRERIRQIESSAFRKLK-NKKRTKHLMQY 521
           +RERIRQIE+ A RKLK ++ RT+ L  +
Sbjct: 302 TRERIRQIENKALRKLKYHESRTRKLRDF 330

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score =  209 bits (532), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 131/347 (37%), Positives = 194/347 (55%), Gaps = 33/347 (9%)
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 RSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFG 475
            SL+  IG  ++    + I D    +  +   +  + E+LEK L  L+ RE  V++ R G
Sbjct: 330 VSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKG 389
Query: 476 LEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLMQY 521
           L DGR  TL+E+G   GV+RERIRQIE+ A RKLK ++ RT+ L  +
Sbjct: 390 LIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDF 436

>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423

Iteration: 1
 Score =  204 bits (520), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 107/242 (44%), Positives = 152/242 (62%), Gaps = 3/242 (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 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 460
             KR+   L   + P SL+  IG  ++    + I D    +  D   +  + E+LEK L 
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLM 519
            L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK ++ RT+ L 
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLR 419
Query: 520 QY 521
            +
Sbjct: 420 DF 421

>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423

Iteration: 1
 Score =  204 bits (520), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 107/242 (44%), Positives = 152/242 (62%), Gaps = 3/242 (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 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 460
             KR+   L   + P SL+  IG  ++    + I D    +  D   +  + E+LEK L 
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLM 519
            L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK ++ RT+ L 
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLR 419
Query: 520 QY 521
            +
Sbjct: 420 DF 421

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score =  204 bits (519), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 107/242 (44%), Positives = 152/242 (62%), Gaps = 3/242 (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 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 460
             KR+   L   + P SL+  IG  ++    + I D    +  D   +  + E+LEK L 
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 379
Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLM 519
            L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK ++ RT+ L 
Sbjct: 380 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLR 439
Query: 520 QY 521
            +
Sbjct: 440 DF 441

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score =  187 bits (476), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 97/252 (38%), Positives = 153/252 (60%), Gaps = 4/252 (1%)
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 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 449
             EE+AE   +   ++  VL   K P S++  IG +++    + I D   E   D    +
Sbjct: 479 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTE 538
Query: 450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509
            ++     VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL
Sbjct: 539 SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 598
Query: 510 KNKKRTKHLMQY 521
           ++  R++ L  +
Sbjct: 599 RHPSRSEVLRSF 610

>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613

Iteration: 1
 Score =  187 bits (476), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 97/252 (38%), Positives = 153/252 (60%), Gaps = 4/252 (1%)
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 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 449
             EE+AE   +   ++  VL   K P S++  IG +++    + I D   E   D    +
Sbjct: 479 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTE 538
Query: 450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 509
            ++     VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL
Sbjct: 539 SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKL 598
Query: 510 KNKKRTKHLMQY 521
           ++  R++ L  +
Sbjct: 599 RHPSRSEVLRSF 610

>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 =  144 bits (363), Expect = 1e-34,   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 =  144 bits (363), Expect = 1e-34,   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|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score =  100 bits (248), 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 = 94.4 bits (233), 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|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 73

Iteration: 1
 Score = 88.6 bits (218), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 42/71 (59%), Positives = 55/71 (77%)
Query: 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           MKE LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 511 NKKRTKHLMQY 521
           +  R+K L  +
Sbjct: 61  HPSRSKRLKDF 71

>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 = 85.1 bits (209), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 122/240 (50%), Gaps = 15/240 (6%)
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 EVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN--LKPSEVIADPEAETAEDLLIKKF 450
           E+A+  G+S + +     + + P S+ + +  N    +   + IAD +  +        F
Sbjct: 135 EIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASW-------F 187
Query: 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
            K  L+K ++ L+ RER +V  R+     + +T  E+   +G+S+ ++ ++E    + +K
Sbjct: 188 DKIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK 243

>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga Maritima Length = 87

Iteration: 1
 Score = 84.3 bits (207), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 56/72 (77%)
Query: 447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506
           ++  M+E+LEKVL TL+PRE  V+R R+GL DG+ KTL+E+G+   V+RERIRQIE  A 
Sbjct: 4   MRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKAL 63
Query: 507 RKLKNKKRTKHL 518
           RKL++  R+K+L
Sbjct: 64  RKLRHPSRSKYL 75

>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 62

Iteration: 1
 Score = 83.2 bits (204), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 39/61 (63%), Positives = 50/61 (81%)
Query: 451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           MKE LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 511 N 511
           +
Sbjct: 61  H 61

>pdb|3N97|A Chain A, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna Length = 72

Iteration: 1
 Score = 67.8 bits (164), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/69 (50%), Positives = 48/69 (69%)
Query: 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
           E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKL++ 
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRHP 61
Query: 513 KRTKHLMQY 521
            R++ L  +
Sbjct: 62  SRSEKLRDF 70

>pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase Sigma Subunit Fragment, Region 4 Length = 73

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/70 (52%), Positives = 49/70 (70%), Gaps = 1/70 (1%)
Query: 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-N 511
           E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK +
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61
Query: 512 KKRTKHLMQY 521
           + RT+ L  +
Sbjct: 62  ESRTRKLRDF 71

>pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With Sigma-Region4 Of Thermus Aquaticus Bound To Dna Length = 73

Iteration: 1
 Score = 67.0 bits (162), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 37/70 (52%), Positives = 49/70 (70%), Gaps = 1/70 (1%)
Query: 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-N 511
           E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK +
Sbjct: 2   EELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61
Query: 512 KKRTKHLMQY 521
           + RT+ L  +
Sbjct: 62  ESRTRKLRDF 71

>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma Complex, Sigma-28FLGM Length = 239

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/239 (25%), Positives = 113/239 (47%), Gaps = 35/239 (14%)
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 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD---------PEAETAEDLLIKKFM 451
           S + L          ++LD KI  +  L   EV  D         P +   E+ +IK+ +
Sbjct: 128 STEELF---------KTLD-KINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKREL 177
Query: 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
            E +++ +  L  RE+ V++  F  E       +E+ +++  S  R+ Q+++ A  +L+
Sbjct: 178 TEKVKEAVSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLR 232

>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4 Length = 81

Iteration: 1
 Score = 57.0 bits (136), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 43/64 (67%)
Query: 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 15  VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 74
Query: 518 LMQY 521
           L  +
Sbjct: 75  LRSF 78

>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna Transcription Activation Sub-Complex Length = 99

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 42/61 (68%)
Query: 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 16  VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 75
Query: 518 L 518
           L
Sbjct: 76  L 76

>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of Sigma 70, Rsd, In Complex With Sigma 70 Domain 4 Length = 68

Iteration: 1
 Score = 55.8 bits (133), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 43/64 (67%)
Query: 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61
Query: 518 LMQY 521
           L  +
Sbjct: 62  LRSF 65

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	525
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	2e-80
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	4e-79
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	8e-73
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	2e-69
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	4e-55
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	2e-45
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	5e-25
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	8e-25
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	9e-25
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	1e-22
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	8e-22
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	9e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07

>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 =  256 bits (656), Expect = 2e-80
 Identities = 125/406 (30%), Positives = 189/406 (46%), Gaps = 23/406 (5%)

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 SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGL 476
           SL+  IG  ++    + I D    +  D   +  + E+LEK L  L+ RE  V++ R GL
Sbjct: 316 SLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGL 375

Query: 477 EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK-KRTKHLMQY 521
            DGR  TL+E+G   GV+RERIRQIE+ A RKLK    RT+ L  +
Sbjct: 376 IDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDF 421

>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 =  253 bits (648), Expect = 4e-79
 Identities = 121/435 (27%), Positives = 196/435 (45%), Gaps = 7/435 (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--KRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 447
           + EE+AEA G     KR+   L   + P SL+  IG  ++    + I D    +  +   
Sbjct: 302 SYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAA 361

Query: 448 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507
           +  + E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A R
Sbjct: 362 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALR 421

Query: 508 KLKNK-KRTKHLMQY 521
           KLK    RT+ L  +
Sbjct: 422 KLKYHESRTRKLRDF 436

>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 =  241 bits (617), Expect = 8e-73
 Identities = 97/254 (38%), Positives = 153/254 (60%), Gaps = 4/254 (1%)

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 HPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 447
            P  EE+AE   +   ++  VL   K P S++  IG +++    + I D   E   D   
Sbjct: 477 EPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSAT 536

Query: 448 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 507
            + ++     VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A R
Sbjct: 537 TESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 508 KLKNKKRTKHLMQY 521
           KL++  R++ L  +
Sbjct: 597 KLRHPSRSEVLRSF 610

>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 =  221 bits (566), Expect = 2e-69
 Identities = 66/242 (27%), Positives = 123/242 (50%), Gaps = 15/242 (6%)

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 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGIN--QNLKPSEVIADPEAETAEDLLIK 448
             E+A+  G+S + +     + + P S+ + +  N    +   + IAD +  +  D    
Sbjct: 133 VTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASWFD---- 188

Query: 449 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 508
              K  L+K ++ L+ RER +V  R+  +    +T  E+   +G+S+ ++ ++E    + 
Sbjct: 189 ---KIALKKAIEELDERERLIVYLRYYKD----QTQSEVASRLGISQVQMSRLEKKILQH 241

Query: 509 LK 510
           +K
Sbjct: 242 IK 243

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Length = 239

 Score =  184 bits (469), Expect = 4e-55
 Identities = 52/232 (22%), Positives = 105/232 (45%), Gaps = 17/232 (7%)

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--SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 460
           + L   L         SL++                P +   E+ +IK+ + E +++ + 
Sbjct: 130 EELFKTLDKINFSYILSLEEVFRDFAR---DYSELIPSSTNVEEEVIKRELTEKVKEAVS 186

Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
            L  RE+ V++  F  E       +E+ +++  S  R+ Q+++ A  +L+  
Sbjct: 187 KLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLREM 234

>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 =  158 bits (402), Expect = 2e-45
 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

>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 =  104 bits (262), Expect = 5e-25
 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

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Length = 87

 Score = 97.1 bits (242), Expect = 8e-25
 Identities = 40/78 (51%), Positives = 56/78 (71%)

Query: 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503
              ++  M+E+LEKVL TL+PRE  V+R R+GL DG+ KTL+E+G+   V+RERIRQIE 
Sbjct: 1   KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEV 60

Query: 504 SAFRKLKNKKRTKHLMQY 521
            A RKL++  R+K+L   
Sbjct: 61  KALRKLRHPSRSKYLKSL 78

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B Length = 99

 Score = 97.5 bits (243), Expect = 9e-25
 Identities = 30/78 (38%), Positives = 46/78 (58%)

Query: 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503
           D    + ++     VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+
Sbjct: 2   DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 61

Query: 504 SAFRKLKNKKRTKHLMQY 521
            A RKL++  R++ L   
Sbjct: 62  KALRKLRHPSRSEVLRSG 79

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Length = 68

 Score = 90.4 bits (225), Expect = 1e-22
 Identities = 29/64 (45%), Positives = 43/64 (67%)

Query: 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61

Query: 518 LMQY 521
           L  +
Sbjct: 62  LRSF 65

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Length = 73

 Score = 88.2 bits (219), Expect = 8e-22
 Identities = 37/70 (52%), Positives = 47/70 (67%), Gaps = 1/70 (1%)

Query: 453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 512
           E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK  
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61

Query: 513 -KRTKHLMQY 521
             RT+ L  +
Sbjct: 62  ESRTRKLRDF 71

>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 = 56.8 bits (137), Expect = 9e-10
 Identities = 34/204 (16%), Positives = 77/204 (37%), Gaps = 49/204 (24%)

Query: 309 GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 368
           G   +DLVQEG  GL++  + +D +K   FS++A   I++ +  ++   +    +  +  
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMVLNEA 59

Query: 369 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL 428
             T  + E     + + G + NN + +E                                
Sbjct: 60  LKTNAILE-DSAYFDDEGHNINNYKSSE-------------------------------- 86

Query: 429 KPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIG 488
                 ++PE    E  L+K+ ++E  +   +  +  E++V+ +      G   + +EI 
Sbjct: 87  ------SNPE----EAYLLKEEIEEFKKFSENNFSKFEKEVLTYLI---RG--YSYREIA 131

Query: 489 ELMGVSRERIRQIESSAFRKLKNK 512
            ++  + + I        +K +  
Sbjct: 132 TILSKNLKSIDNTIQRIRKKSEEW 155

>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 = 54.1 bits (129), Expect = 1e-07
 Identities = 66/428 (15%), Positives = 131/428 (30%), Gaps = 134/428 (31%)

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  VLRINYKFLMSPIKTEQRQPSMMTRMYIEQR---------DRLYNDNQVFAKYNVSR-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 EATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP--EAETAEDLLIKKF-MK 452
            A  LS K    +LL+ +  +  D            +  +      E  + LL+K    +
Sbjct: 260 NAFNLSCK----ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV-KSLLLKYLDCR 314

Query: 453 -EDLEKVLDTLNP----------RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI 501
            +DL + + T NP          R+  +  W         K L  I   +  S   +  +
Sbjct: 315 PQDLPREVLTTNPRRLSIIAESIRDG-LATWDNWKHVNCDK-LTTI---IESS---LNVL 366

Query: 502 ESSAFRKL 509
           E + +RK+
Sbjct: 367 EPAEYRKM 374

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	525
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	100.0
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	100.0
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.97
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.89
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.89
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.87
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.7
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.67
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.58
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.55
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.32
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.29
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.26
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.23
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	99.01
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	98.95
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.91
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.84
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.7
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.64
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.54
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.46
3c57_A	95	Two component transcriptional regulatory protein;	98.45
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.38
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.36
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.19
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	97.99
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.92
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.83
2q0o_A	236	Probable transcriptional activator protein TRAR; h	97.36
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	97.35
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	97.07
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	96.98
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.94
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.47
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.06
1yio_A	208	Response regulatory protein; transcription regulat	95.93
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	95.31
3c3w_A	225	Two component transcriptional regulatory protein;	95.1
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	94.64
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	94.55
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	94.04
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	93.87
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	93.84
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	93.73
2oqr_A	230	Sensory transduction protein REGX3; response regul	93.31
2gwr_A	238	DNA-binding response regulator MTRA; two-component	93.27
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	92.91
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	92.43
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	92.31
1ys7_A	233	Transcriptional regulatory protein PRRA; response	92.22
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	91.87
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	91.04
1u78_A	141	TC3 transposase, transposable element TC3 transpos	90.92
3r0a_A	123	Putative transcriptional regulator; structural gen	90.84
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	90.67
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	90.59
2hqr_A	223	Putative transcriptional regulator; phosporylation	90.53
3r0j_A	250	Possible two component system response transcript	90.45
3q9s_A	249	DNA-binding response regulator; DNA binding protei	90.26
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	89.54
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	88.71
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	88.47
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	88.05
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	87.62
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	87.52
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	87.22
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	87.08
2w25_A	150	Probable transcriptional regulatory protein; trans	86.55
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	86.52
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	86.43
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	86.34
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	86.29
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	86.17
1ku9_A	152	Hypothetical protein MJ223; putative transcription	86.0
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	85.88
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	85.54
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	85.53
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	85.5
1sfx_A	109	Conserved hypothetical protein AF2008; structural	85.48
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	85.32
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	85.31
1y0u_A	96	Arsenical resistance operon repressor, putative; s	85.31
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	85.07
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	85.04
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	84.98
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	84.94
3sqn_A	485	Conserved domain protein; structural genomics, PSI	84.71
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	84.54
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	84.34
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	84.33
3nqo_A	189	MARR-family transcriptional regulator; structural	84.22
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	83.81
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	83.36
2k27_A	159	Paired box protein PAX-8; paired domain, solution	83.32
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	83.28
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	83.17
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	83.14
2gxg_A	146	146AA long hypothetical transcriptional regulator;	82.99
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	82.8
2nnn_A	140	Probable transcriptional regulator; structural gen	82.76
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	82.7
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	82.49
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	82.25
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	82.25
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	81.86
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	81.81
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	81.79
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	81.63
3iwf_A	107	Transcription regulator RPIR family; transcription	81.6
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	81.5
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	81.23
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	81.07
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	81.03
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	80.7
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	80.68
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	80.68
3s2w_A	159	Transcriptional regulator, MARR family; structural	80.64
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	80.49
3jth_A	98	Transcription activator HLYU; transcription factor	80.4
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	80.19
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	80.02

>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=1.6e-55  Score=469.29  Aligned_cols=313  Identities=38%  Similarity=0.625  Sum_probs=282.1

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHH------------------HHHhhcCCCCchHHhHHh--
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE------------------VLSERCGGSPTFAQWAAA--  268 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~------------------~l~~~~g~~pt~~ewa~a--  268 (525)
                      ..|+++ ||++| +++||||++||++|+++|+.++.++....                  ......|+.|+..+|+..  
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                  112235678888887432  


Q ss_pred             ----------hcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCch
Q 009803          269 ----------AGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKF  338 (525)
Q Consensus       269 ----------~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rF  338 (525)
                                .|++...|...+++|..|+++||.+|+++|++||++|.++|.+++|||||||||||+|+++|||.+|++|
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                      2456678888888999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC--CCHHHHHHHHhCCCCCC
Q 009803          339 STYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPR  416 (525)
Q Consensus       339 sTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lg--is~~~v~~~l~~~~~~~  416 (525)
                      +|||+||||+.|.++++++++++|+|.|+.+.+++++++++.+.+.+|+.|+.++||+.+|  +++++|..++.....++
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  99999999999888999


Q ss_pred             CcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHH
Q 009803          417 SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRE  496 (525)
Q Consensus       417 SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~e  496 (525)
                      |+|.+++++++..+.+.+++....+|++.+....+...|..+|+.||+++|.||.+|||++||.++|++|||+.||||++
T Consensus       331 SLd~~~~~d~d~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~ereR~VI~LRygL~~~e~~TleEIAe~LgIS~e  410 (438)
T 1l9z_H          331 SLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRE  410 (438)
T ss_pred             ccccccccccchhhhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCCCCHHHHHHHHCcCHH
Confidence            99999887766677787777655678888888888999999999999999999999999988888999999999999999


Q ss_pred             HHHHHHHHHHHHHH-hHHhhchhhhhhc
Q 009803          497 RIRQIESSAFRKLK-NKKRTKHLMQYAI  523 (525)
Q Consensus       497 rVRqie~RALkKLR-~~l~~~~L~~yl~  523 (525)
                      ||||+++||++||| +.+....|++|+.
T Consensus       411 rVRqi~~RAlkKLR~~~~~~~~l~~yl~  438 (438)
T 1l9z_H          411 RIRQIENKALRKLKYHESRTRKLRDFLE  438 (438)
T ss_pred             HHHHHHHHHHHHHHHhHhhHHHHHHhhC
Confidence            99999999999999 8888889999974

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H

Probab=100.00  E-value=1.7e-55  Score=469.13  Aligned_cols=313  Identities=39%  Similarity=0.627  Sum_probs=274.6

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHH------------------HHhhcCCCCchHHhHH---
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREV------------------LSERCGGSPTFAQWAA---  267 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~------------------l~~~~g~~pt~~ewa~---  267 (525)
                      ..|+++ ||++| +++|+||++||++|+++|+.+..+......                  .....|+.|+..+|+.   
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            357999 99999 999999999999999999987543321111                  0112345666555442   


Q ss_pred             ---------hhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCch
Q 009803          268 ---------AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKF  338 (525)
Q Consensus       268 ---------a~g~d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rF  338 (525)
                               +.+.+...|...+++|..|+++||.+|+++|++||++|.++|.+++|||||||+|||+|+++|||.+|++|
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                     23556777888888889999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC--CCHHHHHHHHhCCCCCC
Q 009803          339 STYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPR  416 (525)
Q Consensus       339 sTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lg--is~~~v~~~l~~~~~~~  416 (525)
                      +|||+||||++|.++++++++++|+|.|+.+.+++++++++.+.+.+|+.|+.++||+.+|  +++++|..++.....++
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             CcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHH
Q 009803          417 SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRE  496 (525)
Q Consensus       417 SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~e  496 (525)
                      |+|.+++++++..+.+.+++....+|++.+....+...|..+|+.||+++|.||.+|||++||.++|++|||+.||||++
T Consensus       316 Sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~L~~aL~~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS~e  395 (423)
T 2a6h_F          316 SLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRE  395 (423)
T ss_dssp             ESSCBCSSSSSCBGGGSSCCSSSCCHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTCC-----CHHHHSSSSCHH
T ss_pred             ccccccCCCCccchhhhhccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHH
Confidence            99999987766677888887766689998888888999999999999999999999999988889999999999999999


Q ss_pred             HHHHHHHHHHHHHH-hHHhhchhhhhhc
Q 009803          497 RIRQIESSAFRKLK-NKKRTKHLMQYAI  523 (525)
Q Consensus       497 rVRqie~RALkKLR-~~l~~~~L~~yl~  523 (525)
                      ||||++++|++||| +.+....|++|++
T Consensus       396 rVrqi~~rAl~kLR~~~~~~~~l~~~l~  423 (423)
T 2a6h_F          396 RIRQIENKALRKLKYHESRTRKLRDFLD  423 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSSSSCCC
T ss_pred             HHHHHHHHHHHHHHhhhhhhHHHHHhhC
Confidence            99999999999999 8888888999874

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=100.00  E-value=4e-43  Score=389.66  Aligned_cols=250  Identities=38%  Similarity=0.669  Sum_probs=232.7

Q ss_pred             HHHHHHHh-ccHHH---HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHH
Q 009803          274 RELRRRLN-YGILC---KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  349 (525)
Q Consensus       274 ~~L~~~l~-~g~~A---~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqa  349 (525)
                      ..|...++ |+..|   ++.||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+||++|||||+
T Consensus       359 ~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn~  438 (613)
T 3iyd_F          359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA  438 (613)
T ss_dssp             HHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHHH
Confidence            34444444 45666   999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCC
Q 009803          350 VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLK  429 (525)
Q Consensus       350 I~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~  429 (525)
                      |.++++++.+.+|+|.|+.+.+++++++.+.+.+++|+.||++|||+.+|+++++|..++.....++|++.+++++++..
T Consensus       439 i~~~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~~~~~~~~  518 (613)
T 3iyd_F          439 ITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSH  518 (613)
T ss_dssp             HHHHTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCCSSSSSCC
T ss_pred             HHHHHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCCCCCCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999998877778


Q ss_pred             CCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803          430 PSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL  509 (525)
Q Consensus       430 l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL  509 (525)
                      +.+.+.+....+|++.+...++...|..+|+.||+++|.||.||||+++++.+|++|||+.||||++||+++++||+++|
T Consensus       519 l~d~i~d~~~~~p~~~~~~~e~~~~l~~aL~~Lp~~er~Vl~Lr~~~~~~e~~s~~EIA~~lgis~~tVk~~~~rAl~kL  598 (613)
T 3iyd_F          519 LGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL  598 (613)
T ss_dssp             GGGSCCCSSSCCHHHHHHHHTTSSSHHHHTTSSCHHHHHHHHHHHTSSSCCCCSTTGGGTTTSSCSSHHHHHHHHHHTTT
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence            88888887777899998888888889999999999999999999997766679999999999999999999999999999


Q ss_pred             HhHHhhchhhhhhc
Q 009803          510 KNKKRTKHLMQYAI  523 (525)
Q Consensus       510 R~~l~~~~L~~yl~  523 (525)
                      |+++....|+.|++
T Consensus       599 R~~~~~~~l~~~l~  612 (613)
T 3iyd_F          599 RHPSRSEVLRSFLD  612 (613)
T ss_dssp             TSCSSSCSSTTCC-
T ss_pred             hCcchhhHHHHHhc
Confidence            99999999999986

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*

Probab=100.00  E-value=1.2e-36  Score=302.18  Aligned_cols=208  Identities=38%  Similarity=0.647  Sum_probs=130.8

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH-HHhHHHHHHh-------------------------hcCCCCch
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK-LEGLREVLSE-------------------------RCGGSPTF  262 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~-le~~~~~l~~-------------------------~~g~~pt~  262 (525)
                      ..||++ ||++| +++||||++||++|+++|+.++. .+.+......                         ..+.+|+.
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            478999 99999 99999999999999999999765 3333221100                         02467899


Q ss_pred             HHhHHhhcCC----HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCch
Q 009803          263 AQWAAAAGVD----QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKF  338 (525)
Q Consensus       263 ~ewa~a~g~d----~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rF  338 (525)
                      .+||.+.|++    ...|.+..++|..|+++||..|.++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|
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            9999998874    345667788899999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC--CCHHHHHHHHhCCCCCC
Q 009803          339 STYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPR  416 (525)
Q Consensus       339 sTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lg--is~~~v~~~l~~~~~~~  416 (525)
                      +||++||||++|.++++++.+.+++|.++.+.++++.++.+.|.+.+|+.||.+|||+.||  +|+.+|...+...+..+
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  99999999998887777


Q ss_pred             Cc
Q 009803          417 SL  418 (525)
Q Consensus       417 SL  418 (525)
                      ||
T Consensus       244 sl  245 (245)
T 3ugo_A          244 SL  245 (245)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=100.00  E-value=2.2e-32  Score=264.25  Aligned_cols=222  Identities=23%  Similarity=0.338  Sum_probs=192.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccc
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  360 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~---~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~  360 (525)
                      ..|+++|+..|.++|+++|++|.   +++.+++||+|||+++||+++++|||.+|.+|.||+++||++.|.++++++.+ 
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   67899999999999999999999999999999999999999999999998864 


Q ss_pred             eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCC--CCCCCcccccccccCCCCCcccCCCC
Q 009803          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPE  438 (525)
Q Consensus       361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~d~~  438 (525)
                        .|.+.....+++.++...+...+|+.|+.+++|..+|++++++..++...  ....|+|.++.++++.. .+. +++ 
T Consensus        90 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~-~~~-~~~-  164 (239)
T 1rp3_A           90 --GSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDY-SEL-IPS-  164 (239)
T ss_dssp             --TCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTT-GGG-
T ss_pred             --cchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccccCCCccc-ccc-cCC-
Confidence              67777788999999999999999999999999999999999998877533  22346665543322222 333 332 


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      ..+|++.+...+....|..+|+.||+++|.||.++|+.+    +|++|||+.||||.++|+++++||+++||+.+..
T Consensus       165 ~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l~~  237 (239)
T 1rp3_A          165 STNVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLREMLSN  237 (239)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHTSC----CCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            346888888888889999999999999999999999877    9999999999999999999999999999998753

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=99.97  E-value=5.4e-32  Score=261.33  Aligned_cols=217  Identities=28%  Similarity=0.449  Sum_probs=52.4

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      |+..|++.|+..|.++|+++|++|.++..+++||+|||++++|+++++|||.+|.+|.||+++|+++.+.++++++. .+
T Consensus        25 gd~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~~d~~r~~~-~~  103 (243)
T 1l0o_C           25 GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TV  103 (243)
T ss_dssp             ---------------------------------------------------------------------------CC-CC
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-Cc
Confidence            55789999999999999999999999999999999999999999999999999899999999999999999999987 78


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccC--CCCCcccCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN--LKPSEVIADPEA  439 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~--~~l~d~l~d~~~  439 (525)
                      ++|.++.....+++++...+.+..++.|+.++++..+|++.+.+...+.......|++.++.++++  .++.+.+     
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~-----  178 (243)
T 1l0o_C          104 KVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQI-----  178 (243)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC---------------------------
T ss_pred             cCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCcccchhhcc-----
Confidence            999999999999999999999999999999999999999999998887665557778776543321  2222322     


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          440 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       440 ~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                        |++.+...+....|..+|+.||+++|.||.++|+.+    +|++|||+.||||.++|++++++|+++||
T Consensus       179 --~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr  243 (243)
T 1l0o_C          179 --ADADEASWFDKIALKKAIEELDERERLIVYLRYYKD----QTQSEVASRLGISQVQMSRLEKKILQHIK  243 (243)
T ss_dssp             -----------------------------------------------------------------------
T ss_pred             --CcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence              222333445567789999999999999999999887    99999999999999999999999999997

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=99.89  E-value=5.1e-23  Score=193.19  Aligned_cols=176  Identities=16%  Similarity=0.200  Sum_probs=134.1

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803          276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  355 (525)
Q Consensus       276 L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir  355 (525)
                      +.....|+..|++.|+..|.+.|+++|++|.+ ..+++|++||+++++|+++++|++..  .|.+|++.++++.+.++++
T Consensus        14 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~d~~R   90 (194)
T 1or7_A           14 VERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAKNYLV   90 (194)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHH
Confidence            34444566999999999999999999999999 89999999999999999999999864  5999999999999999998


Q ss_pred             hcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccC
Q 009803          356 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  435 (525)
Q Consensus       356 ~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  435 (525)
                      ++.+..+.                            .++..        . ..       ..++.          .+.+.
T Consensus        91 ~~~~~~~~----------------------------~~~~~--------~-~~-------~~~~~----------~~~~~  116 (194)
T 1or7_A           91 AQGRRPPS----------------------------SDVDA--------I-EA-------ENFES----------GGALK  116 (194)
T ss_dssp             HHTTCCTH----------------------------HHHHH--------H-HH-------HSCCS----------SCC--
T ss_pred             HHhccCcc----------------------------ccccc--------c-cc-------ccccc----------ccccc
Confidence            87652111                            00000        0 00       00000          00011


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          436 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       436 d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      +.  .+|++.+...+....|..+|+.||+++|.||.|+|+.|    +|++|||+.||||..+|+++++||+++||+.+.
T Consensus       117 ~~--~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~  189 (194)
T 1or7_A          117 EI--SNPENLMLSEELRQIVFRTIESLPEDLRMAITLRELDG----LSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQ  189 (194)
T ss_dssp             --------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHTTC----CCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHC
T ss_pred             CC--CChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            11  13333333445567788999999999999999999887    999999999999999999999999999999774

>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=99.87  E-value=8.5e-22  Score=178.89  Aligned_cols=154  Identities=16%  Similarity=0.247  Sum_probs=107.3

Q ss_pred             CCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccchHHHHHHHHHHHHHHHHHcCCC
Q 009803          309 GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRH  388 (525)
Q Consensus       309 g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~  388 (525)
                      |.+++|++|||++++|+++.+||+.+ .+|.||+++++++.+.++++++.+..+.|..                      
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~----------------------   57 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLN----------------------   57 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhH----------------------
Confidence            57899999999999999999999987 7899999999999999999987543222111                      


Q ss_pred             CCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCC----cccCCCCCCCHHHHHHHHHHHHHHHHHHh-cCC
Q 009803          389 PNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS----EVIADPEAETAEDLLIKKFMKEDLEKVLD-TLN  463 (525)
Q Consensus       389 Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~----d~l~d~~~~~pee~~~~~~~~~~L~~aL~-~L~  463 (525)
                                               ..++++.+..++....+.    +.+.+ ...+|++.+...+....|..+|. .||
T Consensus        58 -------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~~L~  111 (164)
T 3mzy_A           58 -------------------------EALKTNAILEDSAYFDDEGHNINNYKS-SESNPEEAYLLKEEIEEFKKFSENNFS  111 (164)
T ss_dssp             ----------------------------------------------------------CHHHHHHHHHHHHHHHHHHHSC
T ss_pred             -------------------------HHhhhhhhhccCCCCCcccchhhhhcc-cCCCHHHHHHHHHHHHHHHHHHHhhCC
Confidence                                     011121111111111111    11222 22367777888888889999999 999


Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                      +++|.||. +|..|    +|++|||+.||||.++|+++++||+++||+.+...
T Consensus       112 ~~~r~v~~-~~~~g----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~  159 (164)
T 3mzy_A          112 KFEKEVLT-YLIRG----YSYREIATILSKNLKSIDNTIQRIRKKSEEWIKEE  159 (164)
T ss_dssp             HHHHHHHH-HHTTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH-HHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            99999999 77766    99999999999999999999999999999988754

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.70  E-value=1.2e-18  Score=160.12  Aligned_cols=142  Identities=9%  Similarity=0.111  Sum_probs=118.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccceecccc
Q 009803          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  366 (525)
Q Consensus       287 ~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~iRiP~~  366 (525)
                      ++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+++++|++.  ..|.+|++..++|.+.+++++...       
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~-------   73 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRD--VDPRLGLYRMFQGIWASANADGEA-------   73 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCS--SCTTHHHHHHHHHHHHHHTTTTSC-------
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCC--CcHHHHHHHHHHHHHHHHhhccCc-------
Confidence            56789999999999999999998999999999999999999999975  369999999999999998865310       


Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHH
Q 009803          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  446 (525)
Q Consensus       367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~  446 (525)
                                            +                                   +..  . +   ..         
T Consensus        74 ----------------------~-----------------------------------~~~--~-e---~~---------   81 (157)
T 2lfw_A           74 ----------------------Q-----------------------------------TSQ--S-D---AE---------   81 (157)
T ss_dssp             ----------------------C-----------------------------------CCC--C-S---CS---------
T ss_pred             ----------------------c-----------------------------------cCC--c-c---hH---------
Confidence                                  0                                   000  0 0   00         


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhc
Q 009803          447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  516 (525)
Q Consensus       447 ~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~  516 (525)
                         +....|..+|+.||+++|+||.|+|..|    +|++|||+.||||..+|+++++||+++||+.+...
T Consensus        82 ---~~~~~l~~~l~~Lp~~~r~vl~L~~~~g----~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~  144 (157)
T 2lfw_A           82 ---GTEAVARARLARMTPLSRQALLLTAMEG----FSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRAL  144 (157)
T ss_dssp             ---SSSSTTTTTTTTSCTTHHHHHTTTSSSC----CCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSCC
T ss_pred             ---HHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence               0112466789999999999999999887    99999999999999999999999999999977543

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=99.67  E-value=1.3e-16  Score=164.57  Aligned_cols=81  Identities=47%  Similarity=0.849  Sum_probs=74.5

Q ss_pred             HHhccH---HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHH
Q 009803          279 RLNYGI---LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  355 (525)
Q Consensus       279 ~l~~g~---~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir  355 (525)
                      ...|+.   .|++.||..|+++|+++|++|.+++.+++||+||||+|||+++++|+|.+|++|+||++|||||.|.++++
T Consensus       256 ~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~~~~~lr  335 (339)
T 1sig_A          256 MSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA  335 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHH
Confidence            334456   89999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccc
Q 009803          356 DQSR  359 (525)
Q Consensus       356 ~~~r  359 (525)
                      ++.+
T Consensus       336 ~~~r  339 (339)
T 1sig_A          336 DQAR  339 (339)
T ss_dssp             HC--
T ss_pred             HhcC
Confidence            8753

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.58  E-value=2.6e-15  Score=151.39  Aligned_cols=143  Identities=12%  Similarity=0.054  Sum_probs=118.8

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcccce
Q 009803          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  361 (525)
Q Consensus       282 ~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r~i  361 (525)
                      ++..+|++|+..|.+.++.+|++|.++..+++|++||.|+.+|+...+|++.  ..|.+|++.+++|.+.++++....  
T Consensus        18 g~~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~~~~--   93 (286)
T 3n0r_A           18 GSEMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQLEV--   93 (286)
T ss_dssp             --CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC------
T ss_pred             CCcCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhcccccc--
Confidence            4567899999999999999999999998999999999999999999999874  469999999999998876542100  


Q ss_pred             ecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCC
Q 009803          362 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  441 (525)
Q Consensus       362 RiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~  441 (525)
                                                 +                                  ..         ....   
T Consensus        94 ---------------------------~----------------------------------~~---------~~~~---  100 (286)
T 3n0r_A           94 ---------------------------G----------------------------------HD---------QGLH---  100 (286)
T ss_dssp             ---------------------------C----------------------------------CC---------CCCC---
T ss_pred             ---------------------------C----------------------------------CC---------cccc---
Confidence                                       0                                  00         0000   


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          442 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       442 pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                               ....|..+|+.||+++|+||.|+|..+    +|++|||+.+|+|..+|+....+|+++|+..+.
T Consensus       101 ---------~~~~l~~al~~Lp~~~R~v~~L~~~eg----~s~~EIA~~lgis~~tVks~l~rA~~~Lr~~l~  160 (286)
T 3n0r_A          101 ---------AGDDAAQRLMRIAPRSRQAFLLTALEG----FTPTEAAQILDCDFGEVERLIGDAQAEIDAELA  160 (286)
T ss_dssp             ---------TTSHHHHHHHHHSCHHHHHHHHHHTTC----CCHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCC
T ss_pred             ---------hHHHHHHHHHhCCHHHeeEEEEEeeCC----CCHHHHHHHhCcCHHHHHHHHHHHHhhhhccCC
Confidence                     012478899999999999999999988    999999999999999999999999999997653

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=99.55  E-value=1.7e-14  Score=123.85  Aligned_cols=80  Identities=36%  Similarity=0.530  Sum_probs=73.9

Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhcC
Q 009803          445 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT  524 (525)
Q Consensus       445 ~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~~  524 (525)
                      .+...++...|..+|+.||+++|.||.+|||++|++++|++|||+.||||++||++++.+|+++||+.+....|++|+..
T Consensus         3 ~~~~~el~~~l~~aL~~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l~~~~~~   82 (99)
T 3t72_q            3 SATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSGSSG   82 (99)
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45566778899999999999999999999998777779999999999999999999999999999999999999999865

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=99.32  E-value=1.1e-11  Score=104.14  Aligned_cols=75  Identities=13%  Similarity=0.166  Sum_probs=69.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          439 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       439 ~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      ..+|++.+...+....|..+|..||+++|+||.|+|..+    +|++|||+.||||..+|+++++||+++||+.+...+
T Consensus        15 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~   89 (92)
T 3hug_A           15 EQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSYYRG----WSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELG   89 (92)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHTSC----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCchHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            347899999999999999999999999999999999887    999999999999999999999999999999887543

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=99.29  E-value=4e-12  Score=105.88  Aligned_cols=71  Identities=55%  Similarity=0.826  Sum_probs=64.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      ..|..+|+.||+++|.||.++|+++|+..+|++|||+.||||.++|++++.+|+++||..+....++.|+.
T Consensus        10 ~~l~~~l~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l~~~~~~~~~~   80 (87)
T 1tty_A           10 EELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLS   80 (87)
T ss_dssp             SHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence            35788999999999999999999766566999999999999999999999999999999988888877764

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=99.26  E-value=1.9e-12  Score=104.07  Aligned_cols=68  Identities=53%  Similarity=0.807  Sum_probs=54.2

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-hHHhhchhhhhh
Q 009803          455 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLMQYA  522 (525)
Q Consensus       455 L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR-~~l~~~~L~~yl  522 (525)
                      |..+|+.||+++++||.++|+++|+..+|++|||+.||+|.++|++++.+|+++|| ..+....++.|+
T Consensus         4 l~~~l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   72 (73)
T 1ku3_A            4 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL   72 (73)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTC---------
T ss_pred             HHHHHHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHhhHHHHHHhh
Confidence            45678899999999999999976556699999999999999999999999999999 888888888876

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=99.23  E-value=4.9e-12  Score=100.28  Aligned_cols=66  Identities=44%  Similarity=0.674  Sum_probs=59.6

Q ss_pred             HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       458 aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      +|+.||++|++||.++||++|...+|++|||+.||+|.++|++++++|++|||..+....+..|++
T Consensus         2 ~l~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   67 (68)
T 2p7v_B            2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD   67 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTTC
T ss_pred             HHHcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            467899999999999998755455999999999999999999999999999999999888888864

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=99.01  E-value=5.6e-10  Score=87.86  Aligned_cols=64  Identities=14%  Similarity=0.141  Sum_probs=53.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 009803          451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  518 (525)
Q Consensus       451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L  518 (525)
                      ....|..+|+.||++++.||.++|..+    +|++|||+.||+|..+|+++.++|+++||+.+....+
T Consensus         5 ~~~~l~~~l~~L~~~~r~il~l~~~~g----~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l~~~~~   68 (70)
T 2o8x_A            5 DLVEVTTMIADLTTDQREALLLTQLLG----LSYADAAAVCGCPVGTIRSRVARARDALLADAEPDDL   68 (70)
T ss_dssp             HHHHHHTTTTSSCHHHHHHHHHHHTSC----CCHHHHHHHHTSCHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcccC
Confidence            446788899999999999999999877    9999999999999999999999999999998876543

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=98.95  E-value=1.9e-09  Score=92.66  Aligned_cols=79  Identities=13%  Similarity=0.042  Sum_probs=68.4

Q ss_pred             HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803          278 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  357 (525)
Q Consensus       278 ~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~  357 (525)
                      ....++..|++.|+..|.+.++.+|.++ ++..+++|++||+++.+|+.+.+|++.  ..|.+|++..+++.+.++++++
T Consensus        17 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~   93 (112)
T 2o7g_A           17 SAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRHV   93 (112)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHHHHHHTC--
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHHHHHHh
Confidence            3345668999999999999999999999 888899999999999999999999964  3799999999999999999876


Q ss_pred             cc
Q 009803          358 SR  359 (525)
Q Consensus       358 ~r  359 (525)
                      .+
T Consensus        94 ~~   95 (112)
T 2o7g_A           94 RS   95 (112)
T ss_dssp             --
T ss_pred             hc
Confidence            65

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=98.91  E-value=1.5e-09  Score=89.20  Aligned_cols=76  Identities=12%  Similarity=0.057  Sum_probs=68.2

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhcc
Q 009803          281 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  358 (525)
Q Consensus       281 ~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~  358 (525)
                      .++..+++.|+..|.+.++.+|.++.++..+++|++||+++.+|+.+++|++.  ..|.+|++.++++.+.++++++.
T Consensus         8 ~g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~   83 (87)
T 1h3l_A            8 AERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ   83 (87)
T ss_dssp             HHHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence            35688999999999999999999999998999999999999999999999975  47999999999999999887654

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=98.84  E-value=1.2e-08  Score=89.26  Aligned_cols=68  Identities=16%  Similarity=0.196  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          446 LIKKFMKEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       446 ~~~~~~~~~L~~aL-~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      +........+..++ ..||+++|.||.++|..|    +|++|||+.||+|..+|+.+.+||+++||..+....
T Consensus         9 ~e~~~~~~~l~~~l~~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~   77 (113)
T 1xsv_A            9 LVKTLRMNYLFDFYQSLLTNKQRNYLELFYLED----YSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLE   77 (113)
T ss_dssp             HHHHHHHHHHHHHHGGGSCHHHHHHHHHHHTSC----CCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            33445566788899 999999999999999887    999999999999999999999999999999886543

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=98.70  E-value=5.2e-08  Score=85.24  Aligned_cols=63  Identities=17%  Similarity=0.240  Sum_probs=56.8

Q ss_pred             HHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchh
Q 009803          452 KEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  518 (525)
Q Consensus       452 ~~~L~~aL-~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L  518 (525)
                      ...+..++ ..||++++.||.++|..|    +|++|||+.||+|..+|+.+.++|+++||..+...++
T Consensus        12 ~~~l~~~l~~~L~~~~r~vl~l~y~~g----~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   75 (113)
T 1s7o_A           12 MNALFEFYAALLTDKQMNYIELYYADD----YSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   75 (113)
T ss_dssp             HHHHHHHHGGGSCHHHHHHHHHHHHTC----CCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            45677788 899999999999999987    9999999999999999999999999999998865443

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=98.64  E-value=5.5e-11  Score=117.75  Aligned_cols=152  Identities=13%  Similarity=0.075  Sum_probs=107.9

Q ss_pred             HHHhcc-HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHH----HHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHH
Q 009803          278 RRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLV----QEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  352 (525)
Q Consensus       278 ~~l~~g-~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLI----QEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~  352 (525)
                      .+++.+ ..+++.+...+.+++..+............|+.    ||.++.+|+.+..|++..  .|.+|++..+++.+.+
T Consensus        89 ~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d  166 (258)
T 3clo_A           89 RRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTP--AGNVWLIFCLYSLSAD  166 (258)
T ss_dssp             TTBCHHHHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECT--TSCEEEEEEEEEECSC
T ss_pred             HhCChHHHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHcc
Confidence            334434 678999999999999999888777777788886    999999999999998653  5788777655554433


Q ss_pred             HHHhcccceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCc
Q 009803          353 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE  432 (525)
Q Consensus       353 ~ir~~~r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d  432 (525)
                      +.+...                                                           +...+.....   .+
T Consensus       167 ~~r~~~-----------------------------------------------------------~~~~~~~~~~---~~  184 (258)
T 3clo_A          167 QRPEQG-----------------------------------------------------------IYATITQMER---GE  184 (258)
T ss_dssp             CCCCSS-----------------------------------------------------------CCCEEEETTT---TE
T ss_pred             hhhhhH-----------------------------------------------------------HHHHHHhhcc---cc
Confidence            211000                                                           0000000000   00


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          433 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       433 ~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      ....     .           .+..++..||+++|+||.|+ ..|    +|.+|||+.||+|..||+.+.+||++|||..
T Consensus       185 ~~~~-----~-----------~~~~~~~~L~~~erevl~L~-~~G----~s~~EIA~~L~iS~~TVk~~l~ra~~kL~~~  243 (258)
T 3clo_A          185 VETL-----S-----------LSEEHRNILSEREKEILRCI-RKG----LSSKEIAATLYISVNTVNRHRQNILEKLSVG  243 (258)
T ss_dssp             EEEC-----C-----------CHHHHTTSSCHHHHHHHHHH-HTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             cccc-----h-----------hhHHHHccCCHHHHHHHHHH-HcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            0000     0           14556789999999999998 455    9999999999999999999999999999975


Q ss_pred             Hh
Q 009803          513 KR  514 (525)
Q Consensus       513 l~  514 (525)
                      ..
T Consensus       244 ~~  245 (258)
T 3clo_A          244 NS  245 (258)
T ss_dssp             SH
T ss_pred             CH
Confidence            44

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=98.54  E-value=3.6e-08  Score=82.31  Aligned_cols=60  Identities=17%  Similarity=0.209  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          450 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       450 ~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      .....+..++..||++|++||.+ |..|    +|.+|||+.||||..+|+.++.++++||+....
T Consensus        18 ~~~~~l~~~l~~Lt~~e~~vl~l-~~~g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   77 (91)
T 2rnj_A           18 SHMKKRAELYEMLTEREMEILLL-IAKG----YSNQEIASASHITIKTVKTHVSNILSKLEVQDR   77 (91)
T ss_dssp             -------CTGGGCCSHHHHHHHH-HHTT----CCTTHHHHHHTCCHHHHHHHHHHHHHHTTCCSS
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHH-HHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence            34456888999999999999999 5555    999999999999999999999999999986433

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=98.46  E-value=1.6e-07  Score=75.49  Aligned_cols=57  Identities=25%  Similarity=0.267  Sum_probs=50.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ..+..++..||++|++||.+ |..+    +|.+|||+.||+|..+|+++..++++||+....
T Consensus         8 ~~l~~~l~~L~~~e~~vl~l-~~~g----~s~~eIA~~l~is~~tV~~~~~r~~~kl~~~~~   64 (79)
T 1x3u_A            8 NDIRARLQTLSERERQVLSA-VVAG----LPNKSIAYDLDISPRTVEVHRANVMAKMKAKSL   64 (79)
T ss_dssp             HHHHHHHHHHCHHHHHHHHH-HTTT----CCHHHHHHHTTSCHHHHHHHHHHHHHHTTCCSH
T ss_pred             HHHHHHHHhCCHHHHHHHHH-HHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence            45788899999999999999 5555    999999999999999999999999999986443

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=98.45  E-value=2.4e-07  Score=78.11  Aligned_cols=58  Identities=19%  Similarity=0.253  Sum_probs=45.0

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ...|..++..|+++|++||.++ ..|    +|++|||+.||||..+|+.++.++++||+....
T Consensus        18 ~~~l~~~l~~Lt~~e~~vl~l~-~~g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   75 (95)
T 3c57_A           18 GSHMQDPLSGLTDQERTLLGLL-SEG----LTNKQIADRMFLAEKTVKNYVSRLLAKLGMERR   75 (95)
T ss_dssp             ---------CCCHHHHHHHHHH-HTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             HHHHHHHHhcCCHHHHHHHHHH-HcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence            4567889999999999999996 555    999999999999999999999999999987543

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=98.38  E-value=2.7e-07  Score=79.14  Aligned_cols=65  Identities=17%  Similarity=0.213  Sum_probs=54.7

Q ss_pred             HHHHHHHHHH-hcCCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          450 FMKEDLEKVL-DTLNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       450 ~~~~~L~~aL-~~L~~rER~VL~lRygl~~---g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      .-.+.+..++ +.|+++|+.+|.+|||+.+   +.++|+.|||+.+|+|+.+|..+ +|+|++|...++.
T Consensus        23 ~~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k~   91 (101)
T 1jhg_A           23 YQNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELRQ   91 (101)
T ss_dssp             HHTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHHH
T ss_pred             CCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHHH
Confidence            3344567777 6799999999999999853   34599999999999999999999 8999999876553

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=98.36  E-value=2.5e-07  Score=75.91  Aligned_cols=57  Identities=19%  Similarity=0.361  Sum_probs=48.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       454 ~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      .+..++..|+++|++||.+ |..|    +|.+|||+.||||..+|+.+..++++||+.....
T Consensus        14 ~~~~~~~~Lt~~e~~vl~l-~~~g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~   70 (82)
T 1je8_A           14 TTERDVNQLTPRERDILKL-IAQG----LPNKMIARRLDITESTVKVHVKHMLKKMKLKSRV   70 (82)
T ss_dssp             ---CCGGGSCHHHHHHHHH-HTTT----CCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHH
T ss_pred             HHHHHHccCCHHHHHHHHH-HHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHH
Confidence            3567789999999999999 5555    9999999999999999999999999999875543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=98.19  E-value=1.3e-06  Score=69.10  Aligned_cols=55  Identities=31%  Similarity=0.304  Sum_probs=46.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          455 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       455 L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      ....+..|+++|++||.+ |..+    +|.+|||+.||+|..+|+++..++++||+....
T Consensus         5 ~~~~~~~L~~~e~~il~~-~~~g----~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~   59 (74)
T 1fse_A            5 EFQSKPLLTKREREVFEL-LVQD----KTTKEIASELFISEKTVRNHISNAMQKLGVKGR   59 (74)
T ss_dssp             ---CCCCCCHHHHHHHHH-HTTT----CCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSH
T ss_pred             cCCCCCCCCHHHHHHHHH-HHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence            445678899999999999 5555    899999999999999999999999999987544

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=97.99  E-value=9.8e-06  Score=67.78  Aligned_cols=50  Identities=32%  Similarity=0.303  Sum_probs=43.1

Q ss_pred             HHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          457 KVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       457 ~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .....|+++|++||.+.+ .|    +|.+|||+.||||..||+....++++||.-
T Consensus        25 ~~~~~Lt~rE~~Vl~l~~-~G----~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv   74 (90)
T 3ulq_B           25 KEQDVLTPRECLILQEVE-KG----FTNQEIADALHLSKRSIEYSLTSIFNKLNV   74 (90)
T ss_dssp             ----CCCHHHHHHHHHHH-TT----CCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             ccccCCCHHHHHHHHHHH-cC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            346789999999999987 55    999999999999999999999999999964

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=97.92  E-value=8.6e-06  Score=62.14  Aligned_cols=45  Identities=29%  Similarity=0.329  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      ++|++|+.+ |..|    +|.+|||+.||+|..+|+.+..++++||+..-
T Consensus         1 ~re~~vl~l-~~~g----~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~   45 (61)
T 2jpc_A            1 LRERQVLKL-IDEG----YTNHGISEKLHISIKTVETHRMNMMRKLQVHK   45 (61)
T ss_dssp             CHHHHHHHH-HHTS----CCSHHHHHHTCSCHHHHHHHHHHHHHHHTCSS
T ss_pred             CHHHHHHHH-HHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHCCCC
Confidence            579999999 7666    99999999999999999999999999998643

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=97.83  E-value=2.6e-05  Score=66.46  Aligned_cols=47  Identities=28%  Similarity=0.277  Sum_probs=43.0

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|++||.+.+ .|    +|.+|||+.||||..+|+....++++||.-
T Consensus        33 ~~Lt~re~~Vl~l~~-~G----~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv   79 (99)
T 1p4w_A           33 KRLSPKESEVLRLFA-EG----FLVTEIAKKLNRSIKTISSQKKSAMMKLGV   79 (99)
T ss_dssp             SSCCHHHHHHHHHHH-HT----CCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHH-cC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            679999999999954 55    999999999999999999999999999965

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=97.36  E-value=0.00026  Score=68.53  Aligned_cols=47  Identities=26%  Similarity=0.392  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .|+++|++||.+. ..|    +|.+|||++||||..||+.+..++++||.-.
T Consensus       175 ~Lt~~e~~vl~~~-~~g----~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  221 (236)
T 2q0o_A          175 MLSPREMLCLVWA-SKG----KTASVTANLTGINARTVQHYLDKARAKLDAE  221 (236)
T ss_dssp             SCCHHHHHHHHHH-HTT----CCHHHHHHHHCCCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCHHHHHHHHHH-HcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            5999999999995 455    9999999999999999999999999999653

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=97.35  E-value=0.00025  Score=68.49  Aligned_cols=46  Identities=28%  Similarity=0.549  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|++||.+. ..|    +|.+|||++||||..||+.++.++++||.-
T Consensus       173 ~Lt~~e~~vl~~~-~~g----~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  218 (234)
T 1l3l_A          173 WLDPKEATYLRWI-AVG----KTMEEIADVEGVKYNSVRVKLREAMKRFDV  218 (234)
T ss_dssp             CCCHHHHHHHHHH-TTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHH-HcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            5999999999995 455    999999999999999999999999999964

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=97.07  E-value=0.00064  Score=66.06  Aligned_cols=47  Identities=28%  Similarity=0.542  Sum_probs=42.6

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|++|+.+. ..|    +|.+|||+.||||..||+....++++||.-
T Consensus       174 ~~Lt~re~~vl~~~-~~G----~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (237)
T 3szt_A          174 VRLTARETEMLKWT-AVG----KTYGEIGLILSIDQRTVKFHIVNAMRKLNS  220 (237)
T ss_dssp             CCCCHHHHHHHHHH-HTT----CCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            46999999999996 455    999999999999999999999999999864

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=96.98  E-value=0.00084  Score=66.52  Aligned_cols=46  Identities=26%  Similarity=0.416  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|++||.+.. .|    +|.+|||++||||..||+..+.++++||.-
T Consensus       197 ~Lt~re~~vl~~~~-~G----~s~~eIA~~l~is~~TV~~~~~~~~~kl~~  242 (265)
T 3qp6_A          197 PLSQREYDIFHWMS-RG----KTNWEIATILNISERTVKFHVANVIRKLNA  242 (265)
T ss_dssp             CCCHHHHHHHHHHH-TT----CCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHH-cC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            69999999999984 55    999999999999999999999999999964

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=96.94  E-value=0.0013  Score=46.71  Aligned_cols=40  Identities=25%  Similarity=0.216  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .|++.++..+...|..+    +|..+||+.||||+.+|+.++.+
T Consensus         5 ~l~~~~~~~i~~~~~~g----~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMKLLN----VSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHHHTT----CCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHhh
Confidence            57888886666666554    89999999999999999987653

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.47  E-value=0.0061  Score=52.03  Aligned_cols=46  Identities=11%  Similarity=0.172  Sum_probs=41.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      .+++.-..|-.++|..|    +|..|||+.||||+.+|.+++.+|...+-
T Consensus        18 ~~~~~~~~~A~lyYv~g----~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~   63 (101)
T 2w7n_A           18 EVGQQTIEIARGVLVDG----KPQATFATSLGLTRGAVSQAVHRVWAAFE   63 (101)
T ss_dssp             CCCHHHHHHHHHHHTTC----CCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            57888888999999877    99999999999999999999999988753

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=96.06  E-value=0.0059  Score=45.20  Aligned_cols=38  Identities=21%  Similarity=0.266  Sum_probs=28.9

Q ss_pred             CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          463 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       463 ~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      ++..+.|+.+ |..+    +|..|||+.||||+.+|+.++.+|
T Consensus        18 ~~~~~~i~~l-~~~g----~s~~eIA~~lgis~~TV~~~l~~a   55 (55)
T 2x48_A           18 DDLVSVAHEL-AKMG----YTVQQIANALGVSERKVRRYLESC   55 (55)
T ss_dssp             HHHHHHHHHH-HHTT----CCHHHHHHHHTSCHHHHHHHHTC-
T ss_pred             HHHHHHHHHH-HHcC----CCHHHHHHHHCcCHHHHHHHHHhC
Confidence            3445566666 5544    899999999999999999887654

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=95.93  E-value=0.016  Score=53.36  Aligned_cols=52  Identities=21%  Similarity=0.323  Sum_probs=44.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          455 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       455 L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +...+..|+++|++|+.+. ..+    +|.++||+.+|+|..||+.+..+.++||..
T Consensus       136 ~~~~~~~Lt~rE~~vl~~l-~~g----~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~~  187 (208)
T 1yio_A          136 LEQLFSSLTGREQQVLQLT-IRG----LMNKQIAGELGIAEVTVKVHRHNIMQKLNV  187 (208)
T ss_dssp             HHHHHHTSCHHHHHHHHHH-TTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHhcCHHHHHHHHHH-HcC----CcHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            3444568999999999875 333    899999999999999999999999999964

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=95.31  E-value=0.03  Score=51.95  Aligned_cols=47  Identities=17%  Similarity=0.309  Sum_probs=41.5

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|++|+.+-. .+    +|.+|||+.+++|..||+.+..+.++||.-
T Consensus       153 ~~Lt~rE~~vl~~l~-~g----~s~~~Ia~~l~is~~TV~~hi~~i~~Kl~~  199 (215)
T 1a04_A          153 NQLTPRERDILKLIA-QG----LPNKMIARRLDITESTVKVHVKHMLKKMKL  199 (215)
T ss_dssp             GGSCHHHHHHHHHHH-TT----CCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             cCCCHHHHHHHHHHH-cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            469999999998753 44    899999999999999999999999999953

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=95.10  E-value=0.029  Score=52.81  Aligned_cols=47  Identities=19%  Similarity=0.204  Sum_probs=41.2

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..|+++|++|+.+- ..+    +|.+|||+.+++|..||+....+.++||.-
T Consensus       148 ~~LT~rE~~vL~~l-~~g----~s~~eIa~~l~is~~TV~~hi~~l~~KL~~  194 (225)
T 3c3w_A          148 SGLTDQERTLLGLL-SEG----LTNKQIADRMFLAEKTVKNYVSRLLAKLGM  194 (225)
T ss_dssp             TTSCHHHHHHHHHH-HTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            46999999999874 334    899999999999999999999999999853

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=94.64  E-value=0.027  Score=52.84  Aligned_cols=48  Identities=23%  Similarity=0.369  Sum_probs=41.6

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ...|+++|++|+.+- ..+    +|.++||+.+++|..||+.+..+.++||.-
T Consensus       157 ~~~Lt~rE~~vL~~l-~~g----~s~~~Ia~~l~~s~~Tv~~~i~~l~~KL~~  204 (225)
T 3klo_A          157 YAKLTKREQQIIKLL-GSG----ASNIEIADKLFVSENTVKTHLHNVFKKINA  204 (225)
T ss_dssp             HHTSCHHHHHHHHHH-TTT----CCHHHHHHHTTCCHHHHHHHHHHHTTTSCC
T ss_pred             cccCCHHHHHHHHHH-HcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            346999999999873 344    999999999999999999999999999843

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=94.55  E-value=0.072  Score=43.45  Aligned_cols=43  Identities=16%  Similarity=0.431  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          465 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       465 rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .++.||.+-...+.|...|..|||+.||||+.+|+    +.|.+|.+
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~----~~L~~Le~   53 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTPKKEIN----RVLYSLAK   53 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            45667665554444667999999999999999998    56666654

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=94.04  E-value=0.14  Score=48.52  Aligned_cols=55  Identities=22%  Similarity=0.321  Sum_probs=48.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .......+..|+++++.|+.+.. .+    ++.++||..||+|..+|+....++++||.-
T Consensus       189 ~~~~~~~l~~L~~r~~~i~~~~~-~g----~~~~eia~~l~~s~~tv~~~l~~i~~kl~~  243 (258)
T 3p7n_A          189 RERAAEMLKTLSPRQLEVTTLVA-SG----LRNKEVAARLGLSEKTVKMHRGLVMEKLNL  243 (258)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHHHH-TT----CCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHhhcCHHHHHHHHHHH-cC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            45567888999999999999865 34    899999999999999999999999999864

>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=93.87  E-value=0.016  Score=64.14  Aligned_cols=32  Identities=34%  Similarity=0.624  Sum_probs=13.1

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 009803          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL  242 (525)
Q Consensus       210 ~~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~  242 (525)
                      ..||++ ||+++ |++||||+++|++|+++|..+
T Consensus        94 ~~dpvrmyl~em-g~~~ll~~~~e~~~ak~ie~g  126 (613)
T 3iyd_F           94 TTDPVRMYMREM-GTVELLTREGEIDIAKRIEDG  126 (613)
T ss_dssp             -----------C---------CSSSTTTHHHHHH
T ss_pred             CCCcHHHHHHHh-cccccCCchhHHHHHHHHHHh
Confidence            579999 99999 999999999999999999975

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=93.84  E-value=0.088  Score=42.34  Aligned_cols=44  Identities=16%  Similarity=0.452  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +.++.||.+-.-.+.|.+.|..|||+.||||+.+|+++    |.+|.+
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~----L~~L~~   57 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRV----LYSLAK   57 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHH----HHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            34567766555444456699999999999999999854    555543

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=93.73  E-value=0.085  Score=48.98  Aligned_cols=50  Identities=14%  Similarity=0.189  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG---VSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg---IS~erVRqie~RALkKLR~  511 (525)
                      .|+++|++||.+-. .+.|..+|.+|||+.++   +|..||+.+..+.++||..
T Consensus       145 ~Lt~rE~~vl~~l~-~~~~~~~s~~~Ia~~l~~~~~s~~tv~~~i~~l~~Kl~~  197 (220)
T 1p2f_A          145 HLPKKEFEILLFLA-ENAGKVVTREKLLETFWEDPVSPRVVDTVIKRIRKAIED  197 (220)
T ss_dssp             CCCHHHHHHHHHHH-HTTTSCEEHHHHHHHHCSSCCCTHHHHHHHHHHHHHHCS
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHHhCCCCCcchHHHHHHHHHHHHhc
Confidence            59999999997654 44567799999999999   9999999999999999964

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}

Probab=93.31  E-value=0.099  Score=48.77  Aligned_cols=50  Identities=14%  Similarity=0.135  Sum_probs=43.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L-----gIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|.+||.+-. .+.|+.+|.+|||+.+     ++|..||+.+..+.++||..
T Consensus       156 ~Lt~rE~~vL~~l~-~~~~~~~s~~~Ia~~lw~~~~~~s~~tv~~hi~~i~~Kl~~  210 (230)
T 2oqr_A          156 TLPLKEFDLLEYLM-RNSGRVLTRGQLIDRVWGADYVGDTKTLDVHVKRLRSKIEA  210 (230)
T ss_dssp             CCCHHHHHHHHHHH-HTTTSCEEHHHHHHHHTSSCCTTHHHHHHHHHHHHHHHHCS
T ss_pred             ecCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCcCHHHHHHHHHHHHhh
Confidence            59999999998754 4456779999999999     99999999999999999963

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=93.27  E-value=0.12  Score=48.70  Aligned_cols=50  Identities=12%  Similarity=0.012  Sum_probs=42.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L-----gIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|.+||.+-. .+-|..+|.+|||+.+     ++|..||+....+.++||..
T Consensus       153 ~LT~rE~~vL~~l~-~~~~~~~s~~eIa~~lw~~~~~~s~~tV~~hi~~lr~KL~~  207 (238)
T 2gwr_A          153 SLTPLEFDLLVALA-RKPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKVEK  207 (238)
T ss_dssp             CCCHHHHHHHHHHH-HSTTCCBCHHHHHHHHTCCC--CCTHHHHHHHHHHHHHHCS
T ss_pred             ccCHHHHHHHHHHH-HCCCceecHHHHHHHHcCCCCCCCcccHHHHHHHHHHHhcc
Confidence            59999999998754 4556779999999999     99999999999999999963

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=92.91  E-value=0.1  Score=36.99  Aligned_cols=38  Identities=16%  Similarity=0.292  Sum_probs=26.9

Q ss_pred             CCHHH-HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          462 LNPRE-RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       462 L~~rE-R~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      +++.+ +.|+.+ +..+    +|..+||+.||||+.+|..++.+
T Consensus         6 ~~~~~~~~i~~l-~~~g----~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C            6 INKHEQEQISRL-LEKG----HPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             SCTTHHHHHHHH-HHTT----CCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             CCHHHHHHHHHH-HHcC----CCHHHHHHHHCCCHHHHHHHHHH
Confidence            34333 345554 4433    89999999999999999977543

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=92.43  E-value=0.14  Score=47.43  Aligned_cols=50  Identities=20%  Similarity=0.302  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR~  511 (525)
                      .|+++|.+|+.+-. .+-|..+|.+|||+.++     +|..||+.+..+.++||..
T Consensus       151 ~Lt~rE~~vL~~l~-~~~~~~~s~~eIa~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  205 (225)
T 1kgs_A          151 DLTKKEYQILEYLV-MNKNRVVTKEELQEHLWSFDDEVFSDVLRSHIKNLRKKVDK  205 (225)
T ss_dssp             CCCHHHHHHHHHHH-HTTTSCEEHHHHHHHCC-----CHHHHHHHHHHHHHHHHHT
T ss_pred             ecCHHHHHHHHHHH-hCCCcccCHHHHHHHhcCCCCCCCcchHHHHHHHHHHHhhC
Confidence            59999999998654 44566799999999998     9999999999999999964

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=92.31  E-value=0.21  Score=38.84  Aligned_cols=44  Identities=14%  Similarity=0.229  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +++..+.||.+--  .++.++|..|||+.+|+|+.+|.    +.++.|++
T Consensus         8 m~~~~~~IL~~L~--~~~~~~s~~eLA~~lglsr~tv~----~~l~~L~~   51 (67)
T 2heo_A            8 GDNLEQKILQVLS--DDGGPVAIFQLVKKCQVPKKTLN----QVLYRLKK   51 (67)
T ss_dssp             -CHHHHHHHHHHH--HHCSCEEHHHHHHHHCSCHHHHH----HHHHHHHH
T ss_pred             ccHHHHHHHHHHH--HcCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            3444556666542  23456999999999999999998    55666664

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=92.22  E-value=0.13  Score=48.02  Aligned_cols=50  Identities=16%  Similarity=0.082  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR~  511 (525)
                      .|+++|.+||.+-. .+.|..+|.++||+.++     +|..||+.+..+.++||..
T Consensus       159 ~Lt~rE~~vL~~l~-~g~~~~~s~~~Ia~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  213 (233)
T 1ys7_A          159 DLTKREFDLLAVLA-EHKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLEA  213 (233)
T ss_dssp             CCCHHHHHHHHHHH-HTTTCCBCHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHC
T ss_pred             ccCHHHHHHHHHHH-hCCCCeEcHHHHHHHhcCcccCCCccCHHHHHHHHHHHhcc
Confidence            59999999998754 45567799999999998     9999999999999999975

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*

Probab=91.87  E-value=0.03  Score=54.86  Aligned_cols=51  Identities=24%  Similarity=0.382  Sum_probs=0.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Q 009803          455 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMG--VSRERIRQIESSAFRKLK  510 (525)
Q Consensus       455 L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg--IS~erVRqie~RALkKLR  510 (525)
                      +...+..|++.++. |...||.+    .|.+|||+.||  ||.++|+.++.+|++.|.
T Consensus       192 l~e~i~~l~~~~~~-L~~~~~~~----ps~~EIAe~Lg~~is~~tVk~~l~~ar~~ls  244 (245)
T 3ugo_A          192 MVETINKLSRTARQ-LQQELGRE----PSYEEIAEAMGPGWDAKRVEETLKIAQEPVS  244 (245)
T ss_dssp             ----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHH-HHHHhCCC----CCHHHHHHHHCCCCCHHHHHHHHHHHhhccC
Confidence            45566778777777 45566655    89999999999  999999999999988763

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=91.04  E-value=0.22  Score=46.59  Aligned_cols=42  Identities=19%  Similarity=0.247  Sum_probs=33.5

Q ss_pred             cCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          461 TLNPRERQVVRWR--FGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~lR--ygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .|+++|++|+..-  |....|.|.|..|||+.||+|..+|+.++
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l   45 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHL   45 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHH
Confidence            5899999999765  33345667999999999999999887443

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=90.92  E-value=0.3  Score=42.21  Aligned_cols=40  Identities=25%  Similarity=0.216  Sum_probs=32.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .|++.++..|...+..|    +|..+||+.||||+.+|+.+..+
T Consensus         6 ~~s~~~r~~i~~~~~~G----~s~~~ia~~lgis~~Tv~r~~~~   45 (141)
T 1u78_A            6 ALSDTERAQLDVMKLLN----VSLHEMSRKISRSRHCIRVYLKD   45 (141)
T ss_dssp             CCCHHHHHHHHHHHHTT----CCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHc
Confidence            47777777666666544    89999999999999999988764

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=90.84  E-value=0.61  Score=40.28  Aligned_cols=49  Identities=10%  Similarity=0.131  Sum_probs=38.3

Q ss_pred             HHHhcCCHHHHHHHHHHHhcCCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          457 KVLDTLNPRERQVVRWRFGLEDGRM-KTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       457 ~aL~~L~~rER~VL~lRygl~~g~~-~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ...-.|++.+..|+..-...  +.| +|..|||+.+|+|+.+|.    |.+++|.+
T Consensus        19 ~~~~gLt~~e~~il~~L~~~--~~~~~t~~eLa~~l~~s~sTV~----r~L~~L~~   68 (123)
T 3r0a_A           19 KCALNLTKADLNVMKSFLNE--PDRWIDTDALSKSLKLDVSTVQ----RSVKKLHE   68 (123)
T ss_dssp             HHHHTCCHHHHHHHHHHHHS--TTCCEEHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHC--CCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            34557999999988776543  345 899999999999999999    66666654

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=90.67  E-value=0.55  Score=38.29  Aligned_cols=46  Identities=15%  Similarity=0.255  Sum_probs=35.0

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      ...|++.+..+|...+..++  +.|..|||+.+|+|+.+|+    +.+++|.
T Consensus        16 ~~~l~~~~~~~l~~l~~~~~--~~t~~ela~~l~is~~tv~----~~l~~L~   61 (109)
T 2d1h_A           16 CYKITDTDVAVLLKMVEIEK--PITSEELADIFKLSKTTVE----NSLKKLI   61 (109)
T ss_dssp             HHTCCHHHHHHHHHHHHHCS--CEEHHHHHHHHTCCHHHHH----HHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHcCC--CCCHHHHHHHHCcCHHHHH----HHHHHHH
Confidence            45789988888766553232  4999999999999999999    5555554

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=90.59  E-value=0.45  Score=40.01  Aligned_cols=41  Identities=15%  Similarity=-0.052  Sum_probs=30.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      .+++.++.-+...|..+    +|..+||+.||||+.+|+.+..+-
T Consensus        17 ~~s~~~r~~i~~~~~~g----~s~~~ia~~lgis~~Tv~~w~~~~   57 (128)
T 1pdn_C           17 PLPNNIRLKIVEMAADG----IRPCVISRQLRVSHGCVSKILNRY   57 (128)
T ss_dssp             CCCHHHHHHHHHHHHTT----CCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45655555444445443    899999999999999999888764

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=90.53  E-value=0.11  Score=48.33  Aligned_cols=50  Identities=8%  Similarity=0.076  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~Lg-----IS~erVRqie~RALkKLR~  511 (525)
                      .|+++|++||.+-. .+.|..+|.+|||+.++     +|..+|+....+.++||..
T Consensus       143 ~Lt~rE~~vL~~l~-~~~~~~~s~~~Ia~~l~~~~~~~s~~tv~~~i~~lr~KL~~  197 (223)
T 2hqr_A          143 EVKGKPFEVLTHLA-RHRDQIVSKEQLLDAIWEEPEMVTPNVIEVAINQIRQKMDK  197 (223)
T ss_dssp             CCCSTTTHHHHHHH-HTCSEEEEHHHHHHHHCCSSCSCGGGTHHHHHHHHHHHHHT
T ss_pred             ecCHHHHHHHHHHH-hCCCCcCCHHHHHHHhcCCccCCCCcCHHHHHHHHHHHHhc
Confidence            59999999998754 34466799999999999     9999999999999999974

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=90.45  E-value=0.41  Score=45.45  Aligned_cols=50  Identities=20%  Similarity=0.299  Sum_probs=43.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L-----gIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|.+||.+-. .+.|+.+|.++|++.+     +++..+|+.+..+.++||..
T Consensus       176 ~LT~rE~~iL~~l~-~~~~~~~s~~~i~~~lw~~~~~~~~~tv~~~i~~lr~KL~~  230 (250)
T 3r0j_A          176 SLSPTEFTLLRYFV-INAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDT  230 (250)
T ss_dssp             CCCHHHHHHHHHHH-HTTTCCBCHHHHHHHHTTTSCCSCTHHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHHcCCCCCCCccCHHHHHHHHHHhhcC
Confidence            59999999998765 3457789999999999     78999999999999999964

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=90.26  E-value=0.22  Score=47.72  Aligned_cols=50  Identities=22%  Similarity=0.325  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGE-----LMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe-----~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|++||.+-. .+.|..+|.+|||+     .++++..||+....+.++||..
T Consensus       182 ~LT~rE~evL~ll~-~g~~~~~s~~eIa~~l~~~~l~~s~~TV~~hi~~lr~KL~~  236 (249)
T 3q9s_A          182 RLSPKEFDILALLI-RQPGRVYSRQEIGQEIWQGRLPEGSNVVDVHMANLRAKLRD  236 (249)
T ss_dssp             CCCHHHHHHHHHHH-HSTTCCCCHHHHHHHHHTTCSCTTCSHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhhc
Confidence            59999999999865 44567799999999     5888899999999999999864

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=89.54  E-value=0.46  Score=44.90  Aligned_cols=34  Identities=15%  Similarity=0.203  Sum_probs=27.9

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803          468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  506 (525)
Q Consensus       468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL  506 (525)
                      .+..+ |..|    +|..|||+.||||+.+|.+++..|.
T Consensus        16 ria~~-y~~g----~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           16 RLMRM-KNDG----MSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HHHHH-HHTT----CCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HHHHH-HHcC----CCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            44455 6555    9999999999999999999887764

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=88.71  E-value=0.7  Score=40.67  Aligned_cols=42  Identities=17%  Similarity=0.046  Sum_probs=31.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  506 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RAL  506 (525)
                      .++..+|.-|...+..+    +|..+||+.||||+.+|+.+..+-.
T Consensus        32 ~~s~e~r~~iv~~~~~G----~s~~~iA~~lgis~~TV~rw~~~~~   73 (149)
T 1k78_A           32 PLPDVVRQRIVELAHQG----VRPCDISRQLRVSHGCVSKILGRYY   73 (149)
T ss_dssp             CCCHHHHHHHHHHHHTT----CCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45555555554445433    8999999999999999998887643

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=88.47  E-value=0.86  Score=40.30  Aligned_cols=46  Identities=24%  Similarity=0.401  Sum_probs=33.6

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +..|++.++.||.+-.. +  .+.|..|||+.+|+|+.+|+.    .+++|.+
T Consensus         4 m~~ld~~d~~il~~L~~-~--~~~s~~ela~~lg~s~~tv~~----~l~~L~~   49 (151)
T 2dbb_A            4 MRKLDRVDMQLVKILSE-N--SRLTYRELADILNTTRQRIAR----RIDKLKK   49 (151)
T ss_dssp             --CCCHHHHHHHHHHHH-C--TTCCHHHHHHHTTSCHHHHHH----HHHHHHH
T ss_pred             hhhCCHHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            34589999998875432 2  249999999999999999984    4555543

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=88.05  E-value=1.1  Score=36.32  Aligned_cols=24  Identities=13%  Similarity=0.232  Sum_probs=21.6

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      .|..+||+.||||+.+|+++..+.
T Consensus        39 ~s~~~iA~~~gIs~sTl~rW~k~~   62 (87)
T 2elh_A           39 ESKASVARDIGVPESTLRGWCKNE   62 (87)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHH
Confidence            899999999999999999887544

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=87.62  E-value=0.95  Score=39.85  Aligned_cols=39  Identities=10%  Similarity=0.120  Sum_probs=30.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .|++.++.||.+-...   .+.|+.|||+.+|+|+.+|+.++
T Consensus         2 ~ld~~d~~il~~L~~~---~~~s~~ela~~lg~s~~tv~~~l   40 (144)
T 2cfx_A            2 KLDQIDLNIIEELKKD---SRLSMRELGRKIKLSPPSVTERV   40 (144)
T ss_dssp             CCCHHHHHHHHHHHHC---SCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHc---CCCCHHHHHHHHCcCHHHHHHHH
Confidence            3788888888765432   24999999999999999998443

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=87.52  E-value=0.42  Score=39.11  Aligned_cols=23  Identities=4%  Similarity=0.166  Sum_probs=20.6

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .|..|||+.||||+.+|++++.+
T Consensus        31 ~sa~eLAk~LgiSk~aVr~~L~~   53 (82)
T 1oyi_A           31 ATAAQLTRQLNMEKREVNKALYD   53 (82)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHH
Confidence            99999999999999999976543

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=87.22  E-value=1.1  Score=39.00  Aligned_cols=43  Identities=16%  Similarity=0.382  Sum_probs=32.0

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      |++.++.||..-. .+ + +.|+.|||+.+|+|+.+|+    +.+++|.+
T Consensus         2 ld~~~~~il~~L~-~~-~-~~~~~ela~~lg~s~~tv~----~~l~~L~~   44 (141)
T 1i1g_A            2 IDERDKIILEILE-KD-A-RTPFTEIAKKLGISETAVR----KRVKALEE   44 (141)
T ss_dssp             CCSHHHHHHHHHH-HC-T-TCCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             CCHHHHHHHHHHH-Hc-C-CCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            6778888887543 22 2 4899999999999999998    45555543

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=87.08  E-value=0.9  Score=41.00  Aligned_cols=38  Identities=16%  Similarity=0.284  Sum_probs=29.2

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      |++.++.||.+-  ..+ .+.|+.|||+.+|+|+.+|+.++
T Consensus         1 lD~~d~~il~~L--~~~-~~~s~~~la~~lg~s~~tv~~rl   38 (162)
T 3i4p_A            1 MDRLDRKILRIL--QED-STLAVADLAKKVGLSTTPCWRRI   38 (162)
T ss_dssp             CCHHHHHHHHHH--TTC-SCSCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHH--HHC-CCCCHHHHHHHHCcCHHHHHHHH
Confidence            567778887764  223 24899999999999999999443

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=86.55  E-value=1.2  Score=39.48  Aligned_cols=39  Identities=23%  Similarity=0.265  Sum_probs=31.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .|++.++.||.+-.. ++  +.|+.|||+.+|+|+.+|++++
T Consensus         4 ~ld~~~~~iL~~L~~-~~--~~s~~ela~~lg~s~~tv~~~l   42 (150)
T 2w25_A            4 ALDDIDRILVRELAA-DG--RATLSELATRAGLSVSAVQSRV   42 (150)
T ss_dssp             CCCHHHHHHHHHHHH-CT--TCCHHHHHHHHTSCHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH-cC--CCCHHHHHHHHCcCHHHHHHHH
Confidence            588889888886532 22  4999999999999999998543

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=86.52  E-value=0.97  Score=37.76  Aligned_cols=45  Identities=20%  Similarity=0.273  Sum_probs=34.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .+.+....||...+-  .|.++|..|||+.+|||+.+|+    +++++|..
T Consensus        15 ~~~~~~l~Il~~l~~--~g~~~s~~eLa~~lgvs~~tV~----~~L~~L~~   59 (110)
T 1q1h_A           15 LLGDDVIDVLRILLD--KGTEMTDEEIANQLNIKVNDVR----KKLNLLEE   59 (110)
T ss_dssp             TSCSTTHHHHHHHHH--HCSCBCHHHHHHTTTSCHHHHH----HHHHHHHH
T ss_pred             HcChHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            455666677766543  2334899999999999999999    67777765

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=86.43  E-value=1.1  Score=36.57  Aligned_cols=42  Identities=17%  Similarity=0.224  Sum_probs=28.9

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      .++.++.-+...|..++|  .|+.+||..+|||+.+|+++..+.
T Consensus         6 ys~e~k~~~v~~~~~~~g--~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            6 YSEEFKRDAVALYENSDG--ASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCHHHHHHHHHHHTTGGG--SCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCC--ChHHHHHHHHCcCHHHHHHHHHHH
Confidence            555555433333322102  899999999999999999887653

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=86.34  E-value=0.7  Score=40.36  Aligned_cols=35  Identities=26%  Similarity=0.230  Sum_probs=26.0

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQ  500 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRq  500 (525)
                      ..|+.| .+|+.+-. .+    +|+.|||+.+|+|..||..
T Consensus        60 ~aLs~R-~eV~klL~-~G----~syreIA~~~g~S~aTIsR   94 (119)
T 3kor_A           60 QSLSQR-LQVAKMIK-QG----YTYATIEQESGASTATISR   94 (119)
T ss_dssp             HHHHHH-HHHHHHHH-HT----CCHHHHHHHHCCCHHHHHH
T ss_pred             HHHHHH-HHHHHHHH-cC----CCHHHHHHHHCCCHHHHHH
Confidence            345555 56666632 33    9999999999999999984

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=86.29  E-value=1.5  Score=38.73  Aligned_cols=39  Identities=21%  Similarity=0.434  Sum_probs=30.7

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .|++.++.||.+-..  +| +.|+.|||+.+|+|+.+|++++
T Consensus         4 ~ld~~~~~il~~L~~--~~-~~s~~ela~~lg~s~~tv~~~l   42 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN--DG-KAPLREISKITGLAESTIHERI   42 (151)
T ss_dssp             CCCHHHHHHHHHHHH--CT-TCCHHHHHHHHCSCHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHHHH
Confidence            478888888875433  22 4999999999999999998543

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=86.17  E-value=1.2  Score=39.98  Aligned_cols=39  Identities=18%  Similarity=0.144  Sum_probs=31.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .|++.++.||.+-..  ++ +.|+.|||+.+|+|+.+|+.++
T Consensus         7 ~ld~~~~~il~~L~~--~~-~~s~~ela~~lg~s~~tv~~~l   45 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE--NG-RLTNVELSERVALSPSPCLRRL   45 (162)
T ss_dssp             CCCHHHHHHHHHHHH--CT-TCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHHHH
Confidence            488888888876543  22 3899999999999999999554

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=86.00  E-value=2.5  Score=36.13  Aligned_cols=48  Identities=17%  Similarity=0.142  Sum_probs=35.5

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          453 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       453 ~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ..+...+.  .|++.+..|+.+-+..+  .++|..|||+.+|+|+.+|..+.
T Consensus        13 ~~~~~~~~~~gl~~~~~~il~~L~~~~--~~~t~~ela~~l~~~~stvs~~l   62 (152)
T 1ku9_A           13 ELFSELAKIHGLNKSVGAVYAILYLSD--KPLTISDIMEELKISKGNVSMSL   62 (152)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHCS--SCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCChhHHHHHHHHHHcC--CCCCHHHHHHHHCcCHHHHHHHH
Confidence            33444443  58999998887775333  24999999999999999998443

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=85.88  E-value=1.7  Score=38.50  Aligned_cols=39  Identities=21%  Similarity=0.271  Sum_probs=30.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .|++.++.||.+-...   .+.|+.|||+.+|+|+.+|++++
T Consensus         5 ~ld~~d~~il~~L~~~---~~~s~~ela~~lg~s~~tv~~~l   43 (152)
T 2cg4_A            5 LIDNLDRGILEALMGN---ARTAYAELAKQFGVSPETIHVRV   43 (152)
T ss_dssp             CCCHHHHHHHHHHHHC---TTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHc---CCCCHHHHHHHHCcCHHHHHHHH
Confidence            4788888888764322   24899999999999999999543

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=85.54  E-value=3.8  Score=34.76  Aligned_cols=55  Identities=4%  Similarity=0.139  Sum_probs=40.1

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          451 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       451 ~~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      +...+...+.  .|++.+..||..-+..+ +.+.|..+||+.+|+++.+|..    ++++|-
T Consensus        19 ~~~~~~~~~~~~~lt~~~~~iL~~l~~~~-~~~~~~~ela~~l~~~~~tvs~----~l~~Le   75 (141)
T 3bro_A           19 MSTRFDIFAKKYDLTGTQMTIIDYLSRNK-NKEVLQRDLESEFSIKSSTATV----LLQRME   75 (141)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHTT-TSCCBHHHHHHHHTCCHHHHHH----HHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCCCcchHHH----HHHHHH
Confidence            3344555553  58999998888776543 3359999999999999999985    455554

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=85.53  E-value=1.3  Score=35.69  Aligned_cols=49  Identities=12%  Similarity=0.253  Sum_probs=32.7

Q ss_pred             HHHHHhcCC-HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          455 LEKVLDTLN-PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       455 L~~aL~~L~-~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      +..++..|. +.+..||.+-  . .+.+.|..|||+.+|+|+.+|++    .+++|.
T Consensus        14 ~~~~~~~l~~~~~~~il~~l--~-~~~~~s~~ela~~l~is~~tvs~----~l~~L~   63 (99)
T 3cuo_A           14 AAALLKAMSHPKRLLILCML--S-GSPGTSAGELTRITGLSASATSQ----HLARMR   63 (99)
T ss_dssp             HHHHHHHHCSHHHHHHHHHH--T-TCCSEEHHHHHHHHCCCHHHHHH----HHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHH--H-hCCCcCHHHHHHHHCcCHHHHHH----HHHHHH
Confidence            344444444 5555666543  2 34469999999999999999994    455554

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=85.50  E-value=1.6  Score=32.54  Aligned_cols=29  Identities=10%  Similarity=0.154  Sum_probs=23.7

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 009803          484 LQEIGELMGVSRERIRQIESSAFRKLKNKK  513 (525)
Q Consensus       484 l~EIAe~LgIS~erVRqie~RALkKLR~~l  513 (525)
                      +.+||..|||++.+|+++... ...++..+
T Consensus        28 ~~~vA~~~gIs~~tl~~W~~~-~~~~~~~~   56 (59)
T 2glo_A           28 QRATARKYNIHRRQIQKWLQC-ESNLRSSV   56 (59)
T ss_dssp             HHHHHHHTTSCHHHHHHHHTT-HHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHH-HHHHHHHH
Confidence            999999999999999999764 45555544

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=85.48  E-value=1.5  Score=35.48  Aligned_cols=43  Identities=14%  Similarity=0.232  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      .|++.+..||..-...+   +.|..|||+.+|+|+.+|+    +.+++|.
T Consensus        17 ~l~~~~~~il~~l~~~~---~~s~~ela~~l~is~~tv~----~~l~~L~   59 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLERG---GMRVSEIARELDLSARFVR----DRLKVLL   59 (109)
T ss_dssp             CCCHHHHHHHHHHHHHC---CBCHHHHHHHHTCCHHHHH----HHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcC---CCCHHHHHHHHCCCHHHHH----HHHHHHH
Confidence            47888888887654322   3999999999999999999    4455554

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=85.32  E-value=1.5  Score=37.82  Aligned_cols=48  Identities=13%  Similarity=0.170  Sum_probs=33.4

Q ss_pred             HhcCCHHHHHHHHHHHhc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          459 LDTLNPRERQVVRWRFGL-EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl-~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      +-.|++.+..+|..-+.+ ..+.+.|..+||+.+|+|+.+|+    +++++|.
T Consensus         8 ~~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~----~~l~~Le   56 (139)
T 2x4h_A            8 MSNLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVF----EEVSHLE   56 (139)
T ss_dssp             ---CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHH----HHHHHHH
T ss_pred             HhhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHH----HHHHHHH
Confidence            346888887777655432 23345999999999999999999    4555554

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=85.31  E-value=2  Score=36.97  Aligned_cols=51  Identities=20%  Similarity=0.266  Sum_probs=36.3

Q ss_pred             HHHHHHHHHhc----CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          451 MKEDLEKVLDT----LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       451 ~~~~L~~aL~~----L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      +...+...+..    |++.+..||..-+..+   +.|..|||+.+|+++.+|..+..+
T Consensus        20 ~~~~~~~~l~~~~~~lt~~~~~vL~~l~~~~---~~t~~eLa~~l~~~~~tvs~~l~~   74 (142)
T 3ech_A           20 VRTRIQSELDCQRLDLTPPDVHVLKLIDEQR---GLNLQDLGRQMCRDKALITRKIRE   74 (142)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHTT---TCCHHHHHHHHC---CHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCCHHHHHHHHHHHhCC---CcCHHHHHHHhCCCHHHHHHHHHH
Confidence            44556666654    9999999888776543   499999999999999999955443

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=85.31  E-value=5.3  Score=32.32  Aligned_cols=46  Identities=17%  Similarity=0.352  Sum_probs=31.1

Q ss_pred             HHHhcC-CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          457 KVLDTL-NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       457 ~aL~~L-~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ..+..| ++....||.+-   ++  ++|..|||+.+|+|+.+|++    .++.|.+
T Consensus        23 ~~~~~l~~~~r~~Il~~L---~~--~~~~~eLa~~l~is~~tv~~----~L~~L~~   69 (96)
T 1y0u_A           23 RYNYAVTNPVRRKILRML---DK--GRSEEEIMQTLSLSKKQLDY----HLKVLEA   69 (96)
T ss_dssp             HHHHHHSCHHHHHHHHHH---HT--TCCHHHHHHHHTCCHHHHHH----HHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHH---cC--CCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            344433 45555666654   22  39999999999999999994    4555543

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=85.07  E-value=0.85  Score=45.71  Aligned_cols=36  Identities=14%  Similarity=0.280  Sum_probs=28.2

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 009803          468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR  507 (525)
Q Consensus       468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALk  507 (525)
                      .|..++|..+    +|..|||+.||||+.|||..+..+.+
T Consensus        12 ~ia~l~~~~~----~~~~ela~~l~vS~~tIrRdL~~l~~   47 (315)
T 2w48_A           12 KIAQLYYEQD----MTQAQIARELGIYRTTISRLLKRGRE   47 (315)
T ss_dssp             HHHHHHHTSC----CCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4666666544    99999999999999999976665533

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=85.04  E-value=2.3  Score=36.23  Aligned_cols=50  Identities=18%  Similarity=0.256  Sum_probs=37.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLED-GRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~-g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ..|...+..|++.|+.|..+-...-+ -..+|..|||+..|||..+|-..-
T Consensus        10 ~~i~~~~~~ls~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~   60 (111)
T 2o3f_A           10 AIIQSMXHXLPPSERKLADYILAHPHXAIESTVNEISALANSSDAAVIRLC   60 (111)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHhccCCHHHHHHHHHHHHChHHHHhcCHHHHHHHHCCCHHHHHHHH
Confidence            45677788999999998775542200 012899999999999999998544

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=84.98  E-value=1.9  Score=34.06  Aligned_cols=27  Identities=22%  Similarity=0.183  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +.|..|||+.+|+|+.+|+    +.+++|.+
T Consensus        14 ~~s~~eLa~~lgvs~~tv~----r~L~~L~~   40 (81)
T 2htj_A           14 GGKTAEIAEALAVTDYQAR----YYLLLLEK   40 (81)
T ss_dssp             CCCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            4899999999999999998    55566654

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=84.94  E-value=2.8  Score=35.80  Aligned_cols=50  Identities=16%  Similarity=0.226  Sum_probs=36.5

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          452 KEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       452 ~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      ...+...+.  .|++.+..||..-+..+  .+.|..+||+.+|+|+.+|..+..
T Consensus        23 ~~~~~~~~~~~~l~~~~~~iL~~l~~~~--~~~t~~~la~~l~~s~~~vs~~l~   74 (146)
T 2fbh_A           23 RAELDRRLSHLGLSQARWLVLLHLARHR--DSPTQRELAQSVGVEGPTLARLLD   74 (146)
T ss_dssp             HHHHHHHTGGGCCTTTHHHHHHHHHHCS--SCCBHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHcC--CCCCHHHHHHHhCCChhhHHHHHH
Confidence            344555554  48899988887763333  349999999999999999995443

>3sqn_A Conserved domain protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MGA family; 2.31A {Enterococcus faecalis}

Probab=84.71  E-value=1.2  Score=47.69  Aligned_cols=107  Identities=11%  Similarity=0.064  Sum_probs=55.4

Q ss_pred             CCCCCHHHHHHHcCCCHHHHHHHHhCCCCCCCcccccccccCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHH
Q 009803          386 GRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPR  465 (525)
Q Consensus       386 gr~Pt~eEIA~~lgis~~~v~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~~r  465 (525)
                      +..-|..+||+.+|+|...|+.-+...+....-.-.+...+.   +-.+..+......+          +   ...+++.
T Consensus        30 ~~~it~~eLA~~L~VS~RTIr~dI~~In~~L~~~~~I~~~~~---Gy~L~~~~~~~~~~----------~---~~~~~~~   93 (485)
T 3sqn_A           30 VPQLTAKRLAAQIQTTERTVFSDLQYIRSQLPADWSIETDSS---GIRLRNQGNAQTNE----------L---WSLFLPQ   93 (485)
T ss_dssp             CCSCBCGGGHHHHTSCHHHHHHHHHHHHTTCCTTEEEEEETT---EEEEEEC---CTHH----------H---HHHHGGG
T ss_pred             CCCcCHHHHHHHhCCCHHHHHHHHHHHHHhcccCcEEEEcCC---EEEEecCcHHHHHH----------H---HHhcCHH
Confidence            344688999999999999998876432222110001110000   00111110001100          1   1123344


Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 009803          466 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL  509 (525)
Q Consensus       466 ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKL  509 (525)
                      +|....+.+.+.+ ++.|+.++|+.|.||++||.+-+.+..+.|
T Consensus        94 eR~~~Il~~LL~~-~~isi~~Lae~l~VS~sTi~~DLk~i~~~L  136 (485)
T 3sqn_A           94 SISIQLLKELLFT-KELVTTSFLSTSGVSYETLKRHIKKMNQAL  136 (485)
T ss_dssp             SHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            4443333333322 369999999999999999996554444444

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=84.34  E-value=1.1  Score=36.56  Aligned_cols=43  Identities=9%  Similarity=0.030  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHHHHHhc-CCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGL-EDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       461 ~L~~rER~VL~lRygl-~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      .|+.++..||...+.. ++|.+.|..+||+.+|+++.+|.+++.
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~   52 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIK   52 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            4788888887766543 344558999999999999999995543

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=84.33  E-value=1.5  Score=38.62  Aligned_cols=43  Identities=12%  Similarity=0.254  Sum_probs=31.1

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      |++.++.||.+-  ..+ .+.|..|||+.+|+|+.+|+.+    +++|.+
T Consensus         1 ld~~~~~il~~L--~~~-~~~~~~ela~~lg~s~~tv~~~----l~~L~~   43 (150)
T 2pn6_A            1 MDEIDLRILKIL--QYN-AKYSLDEIAREIRIPKATLSYR----IKKLEK   43 (150)
T ss_dssp             CCHHHHHHHHHH--TTC-TTSCHHHHHHHHTSCHHHHHHH----HHHHHH
T ss_pred             CChHHHHHHHHH--HHc-CCCCHHHHHHHHCcCHHHHHHH----HHHHHH
Confidence            566777777653  222 2599999999999999999944    455543

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=84.22  E-value=3.1  Score=38.02  Aligned_cols=52  Identities=21%  Similarity=0.308  Sum_probs=39.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      +...+...+..|++.+..||..-+... +.+.|..+||+.+|+++.+|..++.
T Consensus        28 ~~~~~~~~~~~lt~~q~~vL~~L~~~~-~~~~t~~eLa~~l~is~~tvs~~l~   79 (189)
T 3nqo_A           28 IQIEGDKYFGILTSRQYMTILSILHLP-EEETTLNNIARKMGTSKQNINRLVA   79 (189)
T ss_dssp             HHHHHHHHHCSSCHHHHHHHHHHHHSC-GGGCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHhcc-CCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            344555666679999999988776421 2249999999999999999995443

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=83.81  E-value=4.1  Score=34.57  Aligned_cols=53  Identities=9%  Similarity=0.230  Sum_probs=39.4

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          451 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       451 ~~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      +...+...+.  .|++.+..||..-+..+ +.+.|..|||+.+|+|+.+|..+..+
T Consensus        16 ~~~~~~~~~~~~~lt~~~~~vL~~l~~~~-~~~~t~~ela~~l~~~~~tvs~~l~~   70 (139)
T 3eco_A           16 MKQKADQKLEQFDITNEQGHTLGYLYAHQ-QDGLTQNDIAKALQRTGPTVSNLLRN   70 (139)
T ss_dssp             HHHHHHHHHGGGTCCHHHHHHHHHHHHST-TTCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHhcC-CCCcCHHHHHHHhCCCcccHHHHHHH
Confidence            4445555554  48999999988776543 23599999999999999999954433

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=83.36  E-value=4.1  Score=34.39  Aligned_cols=48  Identities=10%  Similarity=0.052  Sum_probs=36.2

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          452 KEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       452 ~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ...+...+.  .|++.+..||..-+..   .+.|..|||+.+|+|+.+|..+.
T Consensus        15 ~~~~~~~~~~~~l~~~~~~iL~~l~~~---~~~~~~ela~~l~~s~~tvs~~l   64 (138)
T 3bpv_A           15 RVFIGRELGHLNLTDAQVACLLRIHRE---PGIKQDELATFFHVDKGTIARTL   64 (138)
T ss_dssp             HHHHHHHSGGGTCCHHHHHHHHHHHHS---TTCBHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHc---CCCCHHHHHHHHCCCHHHHHHHH
Confidence            344555554  5899998888776653   24899999999999999999543

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=83.32  E-value=0.77  Score=40.99  Aligned_cols=40  Identities=18%  Similarity=0.018  Sum_probs=29.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .++..+|.-|...|-.+    +|..+||+.||||+.+|+.++.+
T Consensus        25 ~~s~e~r~~ii~l~~~G----~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           25 PLPEVVRQRIVDLAHQG----VRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             SSCHHHHHHHHHHHHHT----CCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHH
Confidence            35555555444444444    89999999999999999988764

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=83.28  E-value=4  Score=35.31  Aligned_cols=52  Identities=15%  Similarity=0.156  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          450 FMKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       450 ~~~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      .+...+...+.  .|++.+-.||..-+..+  .++|..|||+.+|+++.+|..++.
T Consensus        23 ~~~~~~~~~l~~~glt~~q~~vL~~l~~~~--~~~t~~eLa~~l~i~~~tvs~~l~   76 (150)
T 3fm5_A           23 MVLGAVNKALVPTGLRVRSYSVLVLACEQA--EGVNQRGVAATMGLDPSQIVGLVD   76 (150)
T ss_dssp             HHHHHHHHHHGGGTCCHHHHHHHHHHHHST--TCCCSHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHhCC--CCcCHHHHHHHHCCCHhHHHHHHH
Confidence            34445555554  58999988887655433  348999999999999999995543

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=83.17  E-value=4.3  Score=34.39  Aligned_cols=39  Identities=5%  Similarity=0.008  Sum_probs=32.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .|++.+..||..-+..+   +.|..+||+.+|+|+.+|..++
T Consensus        28 ~l~~~~~~iL~~l~~~~---~~~~~ela~~l~is~~~vs~~l   66 (142)
T 3bdd_A           28 GISLTRYSILQTLLKDA---PLHQLALQERLQIDRAAVTRHL   66 (142)
T ss_dssp             SSCHHHHHHHHHHHHHC---SBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCC---CCCHHHHHHHHCCCHHHHHHHH
Confidence            69999988887765433   3999999999999999999544

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=83.14  E-value=1.9  Score=39.31  Aligned_cols=40  Identities=20%  Similarity=0.194  Sum_probs=30.7

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ..|++.++.||.+-..  ++ +.|+.|||+.+|+|+.+|+.++
T Consensus        13 ~~ld~~d~~IL~~L~~--~~-~~s~~eLA~~lglS~~tv~~~l   52 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKK--DA-RLTISELSEQLKKPESTIHFRI   52 (171)
T ss_dssp             -CCCHHHHHHHHHHHH--CT-TCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHHHH
Confidence            4588888888876533  22 4899999999999999999543

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=82.99  E-value=4  Score=34.87  Aligned_cols=45  Identities=20%  Similarity=0.158  Sum_probs=34.5

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          454 DLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       454 ~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .+...+.  .|++.+..||..-+  +  .+.|..|||+.+|+|+.+|..++
T Consensus        25 ~~~~~~~~~~l~~~~~~iL~~l~--~--~~~~~~ela~~l~~s~~tvs~~l   71 (146)
T 2gxg_A           25 ELNRRLGELNLSYLDFLVLRATS--D--GPKTMAYLANRYFVTQSAITASV   71 (146)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHT--T--SCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHh--c--CCcCHHHHHHHhCCCchhHHHHH
Confidence            3444453  58999988887765  2  24999999999999999999544

>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...

Probab=82.80  E-value=5.2  Score=36.11  Aligned_cols=48  Identities=25%  Similarity=0.260  Sum_probs=33.5

Q ss_pred             hcCCHHHHHHHHHHHhcC-CC---------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          460 DTLNPRERQVVRWRFGLE-DG---------RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~-~g---------~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ...+..+|-.-.+..... .+         -++|.++||..+|+|+++|.    |++++|++
T Consensus       136 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~iA~~lg~sr~tvs----R~l~~L~~  193 (210)
T 3ryp_A          136 AFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVG----RILKMLED  193 (210)
T ss_dssp             HHSCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHHHHhcCcCCCCCceEeccCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence            456777775443332211 11         26899999999999999999    77888876

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=82.76  E-value=3.2  Score=35.14  Aligned_cols=47  Identities=11%  Similarity=0.107  Sum_probs=35.6

Q ss_pred             HHHHHHHh-cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          453 EDLEKVLD-TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       453 ~~L~~aL~-~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ..+...+. .|++.+..||..-+..+   +.|..+||+.+|+++.+|..++
T Consensus        26 ~~~~~~~~~~l~~~~~~iL~~l~~~~---~~t~~ela~~l~~~~~tvs~~l   73 (140)
T 2nnn_A           26 ALFANGIGNGLTPTQWAALVRLGETG---PCPQNQLGRLTAMDAATIKGVV   73 (140)
T ss_dssp             HHHHHHCSSCCCHHHHHHHHHHHHHS---SBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHcC---CCCHHHHHHHHCCCHHHHHHHH
Confidence            34444443 69999988887765433   4999999999999999999544

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=82.70  E-value=4.7  Score=34.91  Aligned_cols=49  Identities=18%  Similarity=0.186  Sum_probs=36.6

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          453 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       453 ~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      ..+...+.  .|++.|-.||..-+..+   +.|..|||+.+|+++.+|.++..+
T Consensus        28 ~~~~~~~~~~~lt~~q~~iL~~l~~~~---~~~~~eLa~~l~~~~~~vs~~l~~   78 (149)
T 4hbl_A           28 QFYEKKLKQFGITYSQYLVMLTLWEEN---PQTLNSIGRHLDLSSNTLTPMLKR   78 (149)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHSS---SEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHCC---CCCHHHHHHHHCCCHHHHHHHHHH
Confidence            33444443  58999988888776543   489999999999999999955443

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=82.49  E-value=3.3  Score=34.29  Aligned_cols=50  Identities=10%  Similarity=0.236  Sum_probs=34.0

Q ss_pred             HHHHHHhcCC-HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          454 DLEKVLDTLN-PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       454 ~L~~aL~~L~-~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .+..++..|. +....||.+-.  ++  ++|..|||+.+|+|+.+|++    .+++|++
T Consensus        15 ~~~~~~~~l~~~~r~~IL~~L~--~~--~~~~~ela~~l~is~stvs~----~L~~L~~   65 (106)
T 1r1u_A           15 RVTEIFKALGDYNRIRIMELLS--VS--EASVGHISHQLNLSQSNVSH----QLKLLKS   65 (106)
T ss_dssp             HHHHHHHHTCSHHHHHHHHHHH--HC--CBCHHHHHHHHTCCHHHHHH----HHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH--hC--CCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            4555566666 44455665543  22  38999999999999999994    4555553

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=82.25  E-value=4.8  Score=34.57  Aligned_cols=50  Identities=14%  Similarity=0.236  Sum_probs=37.3

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          452 KEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       452 ~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      ...+...+.  .|++.+..||..-+..+   +.|..+||+.+|+++.+|.+++.+
T Consensus        28 ~~~~~~~~~~~~l~~~~~~iL~~l~~~~---~~t~~ela~~l~~~~~tvs~~l~~   79 (150)
T 2rdp_A           28 KQRGREILTNYPITPPQFVALQWLLEEG---DLTVGELSNKMYLACSTTTDLVDR   79 (150)
T ss_dssp             HHHHHHHHTTSSSCHHHHHHHHHHHHHC---SBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHcC---CCCHHHHHHHHCCCchhHHHHHHH
Confidence            334555554  58999988887766533   499999999999999999955443

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=82.25  E-value=5.5  Score=34.76  Aligned_cols=50  Identities=10%  Similarity=0.096  Sum_probs=37.5

Q ss_pred             HHHHHHHH---hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          452 KEDLEKVL---DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       452 ~~~L~~aL---~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      ...+...+   -.|++.+..||..-+..+   +.|..|||+.+|+++.+|..++.+
T Consensus        34 ~~~~~~~l~~~~~lt~~~~~iL~~l~~~~---~~t~~ela~~l~is~~tvs~~l~~   86 (162)
T 2fa5_A           34 SGNIAKVYGDRYGMAIPEWRVITILALYP---GSSASEVSDRTAMDKVAVSRAVAR   86 (162)
T ss_dssp             HHHHHHHHHHHHCCCHHHHHHHHHHHHST---TCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHhCC---CCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34445544   369999999888776532   499999999999999999955443

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=81.86  E-value=3  Score=32.83  Aligned_cols=46  Identities=2%  Similarity=0.087  Sum_probs=34.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L-----gIS~erVRqie~RALkKLR~  511 (525)
                      .++++...||.+-... ++.+.|..||++.+     +||..||+    |.|+.|.+
T Consensus        14 ~~t~~r~~IL~~l~~~-~~~~~s~~el~~~l~~~~~~is~~TVy----R~L~~L~~   64 (83)
T 2fu4_A           14 KVTLPRLKILEVLQEP-DNHHVSAEDLYKRLIDMGEEIGLATVY----RVLNQFDD   64 (83)
T ss_dssp             CCCHHHHHHHHHHTSG-GGSSBCHHHHHHHHHHTTCCCCHHHHH----HHHHHHHH
T ss_pred             CcCHHHHHHHHHHHhC-CCCCCCHHHHHHHHHHhCCCCCHhhHH----HHHHHHHH
Confidence            4788777777654322 11469999999999     99999999    66666654

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=81.81  E-value=3.5  Score=35.27  Aligned_cols=50  Identities=14%  Similarity=0.074  Sum_probs=37.3

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          452 KEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       452 ~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      ...+...+.  .|++.+..||..-+..+   +.|..|||+.+|+++.+|.+++.+
T Consensus        23 ~~~~~~~~~~~~lt~~~~~iL~~l~~~~---~~t~~eLa~~l~~~~~~vs~~l~~   74 (143)
T 3oop_A           23 HLFLMRSIASYDVTPEQWSVLEGIEANE---PISQKEIALWTKKDTPTVNRIVDV   74 (143)
T ss_dssp             HHHHHHHTTTSSSCHHHHHHHHHHHHHS---SEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhhhCCCCHHHHHHHHHHHHcC---CcCHHHHHHHHCCCHhhHHHHHHH
Confidence            344555553  48999999888766543   399999999999999999954443

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=81.79  E-value=1.1  Score=35.96  Aligned_cols=24  Identities=21%  Similarity=0.278  Sum_probs=20.3

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          479 GRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       479 g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      |.|.|..|||+.||||..+||..+
T Consensus        22 g~~psv~EIa~~lgvS~~TVrr~L   45 (77)
T 2jt1_A           22 GAPVKTRDIADAAGLSIYQVRLYL   45 (77)
T ss_dssp             TSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHH
Confidence            346899999999999999999443

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=81.63  E-value=1.7  Score=36.16  Aligned_cols=37  Identities=19%  Similarity=0.302  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      +|...|+.+..-.+    .|+.+||+.+|||..||+..+..
T Consensus         7 ~R~~~I~~~l~~~~----~ti~dlA~~~gVS~~TVsR~L~~   43 (93)
T 2l0k_A            7 ERTIKIGKYIVETK----KTVRVIAKEFGVSKSTVHKDLTE   43 (93)
T ss_dssp             HHHHHHHHHHHHHC----CCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHcC
Confidence            35555655544333    89999999999999999987764

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=81.60  E-value=4.6  Score=34.22  Aligned_cols=51  Identities=14%  Similarity=0.182  Sum_probs=38.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~-~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ...|...+..|++.|+.|...-.-.. .-..+|..|||+..|+|..+|-..-
T Consensus         5 ~~~I~~~~~~lt~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~   56 (107)
T 3iwf_A            5 LYKIDNQYPYFTKNEKKIAQFILNYPHKVVNMTSQEIANQLETSSTSIIRLS   56 (107)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHHHCHHHHTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHhCHHHHHHCCHHHHHHHHCCCHHHHHHHH
Confidence            35677888999999999976543221 0134999999999999999987443

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=81.50  E-value=4.9  Score=34.75  Aligned_cols=48  Identities=2%  Similarity=-0.003  Sum_probs=36.1

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          454 DLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       454 ~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .+...+.  .|++.+..||..-+..+   +.|..+||+.+|+++.+|.++..+
T Consensus        29 ~~~~~~~~~~lt~~~~~iL~~l~~~~---~~t~~eLa~~l~~~~~tvs~~l~~   78 (154)
T 2qww_A           29 YADQNAASLGLTIQQLAMINVIYSTP---GISVADLTKRLIITGSSAAANVDG   78 (154)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHST---TEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHHHCC---CCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3444443  59999998888766533   399999999999999999955433

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=81.23  E-value=5.8  Score=33.52  Aligned_cols=51  Identities=12%  Similarity=0.071  Sum_probs=38.5

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          451 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       451 ~~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      +...+...+.  .|++.+..||..-+..+   +.|..+||+.+|+++.+|.++..+
T Consensus        19 ~~~~~~~~~~~~~lt~~~~~iL~~l~~~~---~~~~~~la~~l~~~~~tvs~~l~~   71 (138)
T 1jgs_A           19 KDRLLNEYLSPLDITAAQFKVLCSIRCAA---CITPVELKKVLSVDLGALTRMLDR   71 (138)
T ss_dssp             HHHHHHHHHTTTTSCHHHHHHHHHHHHHS---SBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhhhcCCCHHHHHHHHHHHhcC---CCCHHHHHHHHCCChHHHHHHHHH
Confidence            4455666664  58999998887766433   389999999999999999955443

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=81.07  E-value=2.6  Score=33.83  Aligned_cols=25  Identities=12%  Similarity=0.191  Sum_probs=19.9

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          479 GRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       479 g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      |+..|..+||..||+|+..|.+.+.
T Consensus        27 ~~~~Ta~~IAkkLg~sK~~vNr~LY   51 (75)
T 1sfu_A           27 NDYTTAISLSNRLKINKKKINQQLY   51 (75)
T ss_dssp             TCEECHHHHHHHTTCCHHHHHHHHH
T ss_pred             CcchHHHHHHHHHCCCHHHHHHHHH
Confidence            3348999999999999988874443

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=81.03  E-value=2.5  Score=36.25  Aligned_cols=39  Identities=15%  Similarity=0.215  Sum_probs=29.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      .|++.+..||..-+  .++  .|..|||+.+|+|+.+|++++.
T Consensus        35 ~lt~~~~~iL~~l~--~~~--~t~~eLa~~l~~s~~tvs~~l~   73 (146)
T 3tgn_A           35 ALTNTQEHILMLLS--EES--LTNSELARRLNVSQAAVTKAIK   73 (146)
T ss_dssp             CCCHHHHHHHHHHT--TCC--CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH--hCC--CCHHHHHHHHCCCHHHHHHHHH
Confidence            46777777776543  233  9999999999999999995443

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=80.70  E-value=4.5  Score=35.98  Aligned_cols=48  Identities=8%  Similarity=0.050  Sum_probs=36.5

Q ss_pred             HHHHHHHh----cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          453 EDLEKVLD----TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       453 ~~L~~aL~----~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      ..+...+.    .|++.+..||..-+..+   +.|..|||+.+|+++.+|.+++.
T Consensus        30 ~~~~~~l~~~~~~lt~~~~~iL~~L~~~~---~~t~~eLa~~l~is~~tvs~~l~   81 (168)
T 2nyx_A           30 AISAHSIAQVDENITIPQFRTLVILSNHG---PINLATLATLLGVQPSATGRMVD   81 (168)
T ss_dssp             HHHHHHHHHHCSSCCHHHHHHHHHHHHHC---SEEHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHHHcC---CCCHHHHHHHhCCCHHHHHHHHH
Confidence            34444554    69999999887765433   39999999999999999995443

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=80.68  E-value=2.5  Score=36.92  Aligned_cols=50  Identities=12%  Similarity=0.095  Sum_probs=37.1

Q ss_pred             HHHHHHHh---cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          453 EDLEKVLD---TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       453 ~~L~~aL~---~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      ..+...+.   .|++.+..||..-+..++  +.|..+||+.+|+++.+|.++..+
T Consensus        33 ~~~~~~l~~~~~l~~~~~~iL~~L~~~~~--~~~~~ela~~l~i~~~tvs~~l~~   85 (160)
T 3boq_A           33 GDLNRQLLDETGLSLAKFDAMAQLARNPD--GLSMGKLSGALKVTNGNVSGLVNR   85 (160)
T ss_dssp             HHHHHHHHHHHSCCHHHHHHHHHHHHCTT--CEEHHHHHHHCSSCCSCHHHHHHH
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHcCC--CCCHHHHHHHHCCChhhHHHHHHH
Confidence            34444443   599999998887754333  499999999999999999855443

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=80.68  E-value=5.2  Score=34.41  Aligned_cols=47  Identities=15%  Similarity=0.113  Sum_probs=35.3

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          453 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       453 ~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ..+...+.  .|++.+..||..-+..+   +.|..+||+.+|+++.+|..++
T Consensus        27 ~~~~~~~~~~~lt~~~~~iL~~l~~~~---~~t~~ela~~l~~~~~~vs~~l   75 (152)
T 3bj6_A           27 AAVERGTLREGVTVGQRAILEGLSLTP---GATAPQLGAALQMKRQYISRIL   75 (152)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHST---TEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHhCC---CCCHHHHHHHHCCCHHHHHHHH
Confidence            33444443  58999988887766433   4999999999999999999544

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=80.64  E-value=3.8  Score=35.94  Aligned_cols=51  Identities=2%  Similarity=0.048  Sum_probs=38.4

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          451 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       451 ~~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      +...+...+.  .|++.+..||..-+..+   +.|..|||+.+|+++.+|..+..+
T Consensus        35 ~~~~~~~~l~~~~lt~~q~~vL~~l~~~~---~~t~~eLa~~l~~~~~tvs~~l~~   87 (159)
T 3s2w_A           35 GQIYIGKKIEPYGIGSGQFPFLMRLYRED---GINQESLSDYLKIDKGTTARAIQK   87 (159)
T ss_dssp             HHHHHHHHHGGGTCCTTTHHHHHHHHHSC---SEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHCC---CCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4445555664  49999988888766543   389999999999999999955443

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=80.49  E-value=4.2  Score=35.20  Aligned_cols=48  Identities=15%  Similarity=0.150  Sum_probs=36.0

Q ss_pred             HHHHHHH--hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          453 EDLEKVL--DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       453 ~~L~~aL--~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      ..+...+  ..|++.+..||..-+..+   +.|..+||+.+|+|+.+|..++.
T Consensus        24 ~~~~~~~~~~~l~~~~~~iL~~l~~~~---~~t~~ela~~l~~s~~tvs~~l~   73 (155)
T 1s3j_A           24 PEMLESMEKQGVTPAQLFVLASLKKHG---SLKVSEIAERMEVKPSAVTLMAD   73 (155)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHS---EEEHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHHcC---CCCHHHHHHHHCCCHHHHHHHHH
Confidence            3444444  369999998887765432   48999999999999999995443

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=80.40  E-value=3  Score=33.83  Aligned_cols=50  Identities=10%  Similarity=0.120  Sum_probs=32.8

Q ss_pred             HHHHHHhcCCHH-HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          454 DLEKVLDTLNPR-ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       454 ~L~~aL~~L~~r-ER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .+..++..|... ...||.+  ..+  .++|..|||+.+|+|+.+|+    +.+++|++
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~--L~~--~~~~~~ela~~l~is~~tvs----~~L~~L~~   62 (98)
T 3jth_A           12 KAVVLLKAMANERRLQILCM--LHN--QELSVGELCAKLQLSQSALS----QHLAWLRR   62 (98)
T ss_dssp             HHHHHHHHHCSHHHHHHHHH--TTT--SCEEHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHH--Hhc--CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            345555555544 4445443  223  35999999999999999998    45555654

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=80.19  E-value=1.4  Score=34.09  Aligned_cols=23  Identities=35%  Similarity=0.450  Sum_probs=20.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      +|+.|||+.+|||+.+|+.+++.
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng   23 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVING   23 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            48999999999999999988874

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=80.02  E-value=3.8  Score=35.90  Aligned_cols=40  Identities=8%  Similarity=0.060  Sum_probs=32.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      .|++.+..||..-+..+   +.|..+||+.+|+++.+|..++.
T Consensus        49 ~lt~~~~~iL~~l~~~~---~~t~~ela~~l~is~~tvs~~l~   88 (162)
T 3cjn_A           49 GLSTAKMRALAILSAKD---GLPIGTLGIFAVVEQSTLSRALD   88 (162)
T ss_dssp             TCCHHHHHHHHHHHHSC---SEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCC---CCCHHHHHHHHCCChhHHHHHHH
Confidence            49999999888766432   48999999999999999995443

---

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	525
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	3e-27
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	2e-26
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	9e-25
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	8e-20
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	1e-19
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	8e-18
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	4e-11
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	8e-10
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	3e-08
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	7e-07
d1or7a1	68	a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escheri	2e-06
d1yioa1	70	a.4.6.2 (A:131-200) Response regulatory protein St	4e-06
d1a04a1	67	a.4.6.2 (A:150-216) Nitrate/nitrite response regul	2e-04
d1l3la1	65	a.4.6.2 (A:170-234) Quorum-sensing transcription f	7e-04
d1p4wa_	87	a.4.6.2 (A:) Transcriptional regulator RcsB {Erwin	7e-04

>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 =  110 bits (275), Expect = 3e-27
 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 =  103 bits (257), Expect = 2e-26
 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

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]} Length = 87

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

 Score = 95.6 bits (238), Expect = 9e-25
 Identities = 40/75 (53%), Positives = 56/75 (74%)

Query: 447 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 506
           ++  M+E+LEKVL TL+PRE  V+R R+GL DG+ KTL+E+G+   V+RERIRQIE  A 
Sbjct: 4   MRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKAL 63

Query: 507 RKLKNKKRTKHLMQY 521
           RKL++  R+K+L   
Sbjct: 64  RKLRHPSRSKYLKSL 78

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

 Score = 81.3 bits (201), Expect = 8e-20
 Identities = 29/64 (45%), Positives = 43/64 (67%)

Query: 458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 517
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61

Query: 518 LMQY 521
           L  +
Sbjct: 62  LRSF 65

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]} Length = 61

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

 Score = 80.5 bits (199), Expect = 1e-19
 Identities = 33/57 (57%), Positives = 41/57 (71%)

Query: 454 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 510
           +LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK
Sbjct: 1   ELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 57

>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 = 76.1 bits (187), Expect = 8e-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

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 56.4 bits (136), Expect = 4e-11
 Identities = 15/70 (21%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 443 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 502
           E+ +IK+ + E +++ +  L  RE+ V++  F          +E+ +++  S  R+ Q++
Sbjct: 3   EEEVIKRELTEKVKEAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLK 58

Query: 503 SSAFRKLKNK 512
           + A  +L+  
Sbjct: 59  AKALERLREM 68

>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 = 52.4 bits (126), Expect = 8e-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 = 47.8 bits (114), Expect = 3e-08
 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 = 44.8 bits (106), Expect = 7e-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

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

 Score = 43.1 bits (102), Expect = 2e-06
 Identities = 11/69 (15%), Positives = 29/69 (42%), Gaps = 4/69 (5%)

Query: 444 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 503
           +L++ + +++ + + +++L    R  +  R         + +EI  +M      +R    
Sbjct: 1   NLMLSEELRQIVFRTIESLPEDLRMAITLRELDG----LSYEEIAAIMDCPVGTVRSRIF 56

Query: 504 SAFRKLKNK 512
            A   + NK
Sbjct: 57  RAREAIDNK 65

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Length = 70

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

 Score = 42.4 bits (100), Expect = 4e-06
 Identities = 13/72 (18%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 511
           ++ LE++  +L  RE+QV++       G     ++I   +G++   ++    +  +KL  
Sbjct: 3   QDQLEQLFSSLTGREQQVLQL---TIRG--LMNKQIAGELGIAEVTVKVHRHNIMQKLNV 57

Query: 512 KKRTKHLMQYAI 523
           +    +L+    
Sbjct: 58  RSLA-NLVHLVE 68

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

 Score = 37.4 bits (87), Expect = 2e-04
 Identities = 11/68 (16%), Positives = 27/68 (39%), Gaps = 6/68 (8%)

Query: 456 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 515
           E+ ++ L PRER +++        +    + I   + ++   ++       +K+K K R 
Sbjct: 1   ERDVNQLTPRERDILKLI-----AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRV 55

Query: 516 KHLMQYAI 523
                +  
Sbjct: 56  -EAAVWVH 62

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

 Score = 35.9 bits (83), Expect = 7e-04
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ 520
            L+P+E   +RW   +  G  KT++EI ++ GV    +R     A ++   + +  HL  
Sbjct: 4   WLDPKEATYLRW---IAVG--KTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKA-HLTA 57

Query: 521 YAI 523
            AI
Sbjct: 58  LAI 60

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]} Length = 87

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

 Score = 36.4 bits (84), Expect = 7e-04
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 6/62 (9%)

Query: 462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 521
           L+P+E +V+R      +G    + EI + +  S + I   + SA  KL        L+ Y
Sbjct: 23  LSPKESEVLRL---FAEG--FLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDI-ALLNY 76

Query: 522 AI 523
             
Sbjct: 77  LS 78

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	525
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	100.0
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.84
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.78
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.64
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.64
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.56
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.4
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.2
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.18
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.15
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.85
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.81
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.81
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.62
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.41
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.15
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	97.89
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.76
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.7
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.26
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	95.41
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	94.34
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	93.74
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	93.0
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	92.92
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	92.84
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	92.63
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.54
d1hlva1	66	DNA-binding domain of centromere binding protein B	91.32
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	90.92
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	90.88
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	90.48
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	90.05
d1zyba1	73	Probable transcription regulator BT4300, C-termina	89.7
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	89.22
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	89.19
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	88.85
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	88.54
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	88.23
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	87.99
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	87.39
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	87.13
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	86.68
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	86.6
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	85.21
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	85.06
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	84.85
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	84.73
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	84.16
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	83.93
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	83.88
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	83.63
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	83.45
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	83.4
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	82.89
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	82.79
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	82.78
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	81.82
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	81.73
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	81.7
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	81.36
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	81.36
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	81.27
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	81.15
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	81.09
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	80.75
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	80.65
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	80.23
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	80.1
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	80.02

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=100.00  E-value=1.2e-33  Score=265.37  Aligned_cols=149  Identities=37%  Similarity=0.648  Sum_probs=123.3

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHH------------------hhcCCCCchHHhHHhhcC
Q 009803          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLS------------------ERCGGSPTFAQWAAAAGV  271 (525)
Q Consensus       211 ~d~l~-yl~~i~~~~~lLt~eEE~~L~~~iq~~~~le~~~~~l~------------------~~~g~~pt~~ewa~a~g~  271 (525)
                      +||++ ||++| +++||||++||++|+++|+.++.+.....+..                  ...+..|...+|......
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 99999999999999999998765544322221                  113444554444433221


Q ss_pred             ------------CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchh
Q 009803          272 ------------DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFS  339 (525)
Q Consensus       272 ------------d~~~L~~~l~~g~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFs  339 (525)
                                  ....+......|..|+++||.+|++||++||++|.+.|.+++||||||++|||+|+++|||++|++|+
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                        22445667778899999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHhcccc
Q 009803          340 TYAHWWIKQAVRKSLSDQSRT  360 (525)
Q Consensus       340 TYA~~wIRqaI~~~ir~~~r~  360 (525)
                      |||+||||++|.+++++++|+
T Consensus       160 tya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         160 TYATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHHhCCC
Confidence            999999999999999999874

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

Probab=99.84  E-value=1.9e-21  Score=197.06  Aligned_cols=74  Identities=50%  Similarity=0.947  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhc
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  357 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~  357 (525)
                      ..|+++||.+|+|||++||++|.++|++++||||+|++|||+|+++|||.+|++|||||+||||++|.++|++|
T Consensus       261 ~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         261 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             cchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHHHHHHhCC
Confidence            67999999999999999999999999999999999999999999999999999999999999999999999875

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.78  E-value=2.4e-19  Score=148.68  Aligned_cols=76  Identities=21%  Similarity=0.364  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHHHhccc
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGA---GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  359 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~---g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~ir~~~r  359 (525)
                      ...+++||..|++||.++|++|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|.+++|+..|
T Consensus         9 ~~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~dw   87 (87)
T d1rp3a3           9 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLDF   87 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSST
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhCCC
Confidence            3468999999999999999998764   789999999999999999999999999999999999999999999998754

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=99.64  E-value=4.5e-17  Score=134.49  Aligned_cols=74  Identities=54%  Similarity=0.818  Sum_probs=69.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhcC
Q 009803          451 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT  524 (525)
Q Consensus       451 ~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~~  524 (525)
                      +++.|..+|+.|+++|+.||.+|||++|++|+|+.|||+.||||+++|||++.+|++|||.......|+.|+++
T Consensus         8 l~~~l~~~l~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~kLr~~~~~~~L~~~l~~   81 (87)
T d1ttya_           8 MREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLSL   81 (87)
T ss_dssp             CCSHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHHHh
Confidence            34678999999999999999999999999999999999999999999999999999999999888899999864

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=99.64  E-value=3e-17  Score=129.51  Aligned_cols=66  Identities=44%  Similarity=0.674  Sum_probs=63.3

Q ss_pred             HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhchhhhhhc
Q 009803          458 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  523 (525)
Q Consensus       458 aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~L~~yl~  523 (525)
                      +|+.|+++|+.||.+|||+++++|+|++|||+.||||+++|||++.+|++|||+......|+.|++
T Consensus         2 ~L~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr~~~~~~~L~~yl~   67 (68)
T d2p7vb1           2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD   67 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTTC
T ss_pred             hhhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHhc
Confidence            478999999999999999999999999999999999999999999999999999999999999986

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=99.56  E-value=8.6e-16  Score=118.56  Aligned_cols=58  Identities=57%  Similarity=0.826  Sum_probs=54.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          455 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       455 L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      |..+|+.|+++|+.||.+|||+++++|+|+.|||+.||||+++|||++.+|++|||+.
T Consensus         2 l~~~L~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR~~   59 (61)
T d1ku3a_           2 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH   59 (61)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcC
Confidence            3457899999999999999999999999999999999999999999999999999974

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.40  E-value=5.1e-13  Score=105.05  Aligned_cols=70  Identities=23%  Similarity=0.406  Sum_probs=66.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          441 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       441 ~pee~~~~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      +|++.+...+....|..+|+.||+++|.||.++|+.+    +|++|||+.||+|.++|+++.+||+++||+.+.
T Consensus         1 d~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~L~   70 (71)
T d1rp3a2           1 NVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLREMLS   70 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHTSC----CCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHhHh----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHcc
Confidence            3678888889999999999999999999999999988    999999999999999999999999999999775

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=99.20  E-value=2.5e-11  Score=94.75  Aligned_cols=63  Identities=16%  Similarity=0.153  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 009803          448 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  514 (525)
Q Consensus       448 ~~~~~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~  514 (525)
                      .++....|..+|+.||+++|.||.++|..|    +|++|||+.||+|.++|+++.+||+++||..++
T Consensus         5 ~~e~~~~l~~~l~~Lp~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~   67 (68)
T d1or7a1           5 SEELRQIVFRTIESLPEDLRMAITLRELDG----LSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQ   67 (68)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHHHHHHHHTTC----CCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcC
Confidence            345678899999999999999999999988    999999999999999999999999999998764

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=99.15  E-value=2.8e-11  Score=92.55  Aligned_cols=58  Identities=43%  Similarity=0.661  Sum_probs=55.0

Q ss_pred             eecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC--CCHHHHHHHHhCCCCCCCc
Q 009803          361 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPRSL  418 (525)
Q Consensus       361 iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lg--is~~~v~~~l~~~~~~~SL  418 (525)
                      ||+|+|+.+.+++++++.++|.+++||+||.+|||+.+|  +++++|+.++...+.++||
T Consensus         1 IRlPvH~~e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~~~p~SL   60 (60)
T d1ku2a1           1 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL   60 (60)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGSSSCCCC
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHccCCCCC
Confidence            799999999999999999999999999999999999998  5588999999999999986

>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=98.85  E-value=1.5e-09  Score=81.89  Aligned_cols=53  Identities=21%  Similarity=0.369  Sum_probs=50.4

Q ss_pred             cceecccchHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhC
Q 009803          359 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS  411 (525)
Q Consensus       359 r~iRiP~~~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~  411 (525)
                      .+||+|.|+.+.+++++++.+.|.+++||.||.+|||+.||+|+++|..++..
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            47999999999999999999999999999999999999999999999988753

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=98.81  E-value=8.1e-09  Score=87.41  Aligned_cols=54  Identities=15%  Similarity=0.197  Sum_probs=49.2

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhch
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  517 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~~~  517 (525)
                      .-||++||.||.+||..|    +|+.|||+.||||+++|+++++||+++||+....-+
T Consensus        17 ~LLpe~QR~vl~L~~~e~----ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~ye~kL~   70 (106)
T d1xsva_          17 SLLTNKQRNYLELFYLED----YSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLE   70 (106)
T ss_dssp             GGSCHHHHHHHHHHHTSC----CCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HhCCHHHHHHHHHHHHhC----CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence            349999999999999988    999999999999999999999999999999655433

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.81  E-value=7.6e-09  Score=87.60  Aligned_cols=52  Identities=17%  Similarity=0.243  Sum_probs=48.4

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  515 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~l~~  515 (525)
                      +-||+++|.||.|+|+.|    +|++|||+.||||+++|+++++||+++||+....
T Consensus        15 ~lLp~~qR~v~~L~y~~~----ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~e~k   66 (106)
T d1s7oa_          15 ALLTDKQMNYIELYYADD----YSLAEIADEFGVSRQAVYDNIKRTEKILETYEMK   66 (106)
T ss_dssp             GGSCHHHHHHHHHHHHTC----CCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            349999999999999988    9999999999999999999999999999986544

>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=98.62  E-value=2.3e-08  Score=78.71  Aligned_cols=69  Identities=13%  Similarity=0.072  Sum_probs=64.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhhcCCcCCCchhhHHHHHHHHHHHHHH
Q 009803          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  354 (525)
Q Consensus       284 ~~A~e~Lv~~nlrLV~~IA~~y~~~g~~~eDLIQEG~lGLirAiekFDp~kG~rFsTYA~~wIRqaI~~~i  354 (525)
                      ..++++++..|.+.++.+|+++.++..+++|++||.++.+|+..++|++.  .+|.+|++..++|.+.+++
T Consensus         6 ~~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~   74 (75)
T d1h3la_           6 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSY   74 (75)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHh
Confidence            56799999999999999999999999999999999999999999999864  4799999999999998865

>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=98.41  E-value=1.2e-08  Score=81.17  Aligned_cols=69  Identities=30%  Similarity=0.322  Sum_probs=56.4

Q ss_pred             hHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcCCCHHHHHHHHhC--CCCCCCcccccccccCCCCCcccCC
Q 009803          367 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIAD  436 (525)
Q Consensus       367 ~~~~~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgis~~~v~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~d  436 (525)
                      +.+.++++.++...|.+++||.||.+|||+.||+++++|.+++..  ...++|||.++.++ +..+.+++++
T Consensus         5 ~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~d~-~~~~~e~lps   75 (77)
T d1rp3a1           5 VREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDF-ARDYSELIPS   75 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHTTTGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCccCC-CCchhccCCC
Confidence            346789999999999999999999999999999999999999864  34678999876543 3345566554

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=98.15  E-value=2.8e-06  Score=65.99  Aligned_cols=55  Identities=20%  Similarity=0.370  Sum_probs=48.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          452 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       452 ~~~L~~aL~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .+.+...++.|+|+|++|+.+.- .|    +|..|||..||||..||+....++++||.-
T Consensus         3 ~~~~~~~~~~LT~rE~~vl~~l~-~G----~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   57 (70)
T d1yioa1           3 QDQLEQLFSSLTGREQQVLQLTI-RG----LMNKQIAGELGIAEVTVKVHRHNIMQKLNV   57 (70)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHT-TT----CCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHccCCHHHHHHHHHHH-cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            45678888999999999998853 34    999999999999999999999999999853

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=97.89  E-value=1.1e-05  Score=61.91  Aligned_cols=48  Identities=17%  Similarity=0.315  Sum_probs=43.0

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          459 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       459 L~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ++.|+|+|++|+.+.- .|    +|.+|||+.||||..||++...++++||.-
T Consensus         4 l~~LT~rE~~vl~ll~-~G----~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   51 (67)
T d1a04a1           4 VNQLTPRERDILKLIA-QG----LPNKMIARRLDITESTVKVHVKHMLKKMKL   51 (67)
T ss_dssp             GGGSCHHHHHHHHHHH-TT----CCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             cccCCHHHHHHHHHHH-hC----CCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            5689999999998754 44    999999999999999999999999999853

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.76  E-value=2.5e-05  Score=59.44  Aligned_cols=46  Identities=28%  Similarity=0.549  Sum_probs=41.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|++|+.+. ..|    +|.+|||+.||+|..||+.+..++++||.-
T Consensus         4 ~Lt~rE~~vl~l~-~~G----~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   49 (65)
T d1l3la1           4 WLDPKEATYLRWI-AVG----KTMEEIADVEGVKYNSVRVKLREAMKRFDV   49 (65)
T ss_dssp             CCCHHHHHHHHHH-TTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             ccCHHHHHHHHHH-Hhc----CCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            6999999999874 344    999999999999999999999999999953

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=97.70  E-value=3.3e-05  Score=59.03  Aligned_cols=46  Identities=33%  Similarity=0.349  Sum_probs=41.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|+++|++|+.+. ..|    +|.+|||+.||+|..||+....+.++||--
T Consensus         4 ~LT~rE~~vl~l~-~~G----~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v   49 (67)
T d1fsea_           4 LLTKREREVFELL-VQD----KTTKEIASELFISEKTVRNHISNAMQKLGV   49 (67)
T ss_dssp             CCCHHHHHHHHHH-TTT----CCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHH-Hcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            4999999999873 444    999999999999999999999999999853

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=97.26  E-value=0.00024  Score=57.05  Aligned_cols=45  Identities=29%  Similarity=0.302  Sum_probs=41.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      .|+++|++|+.+.. .|    ++.+|||+.|++|..+|+....++++||.
T Consensus        22 ~LT~rE~~vl~ll~-~G----~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~   66 (87)
T d1p4wa_          22 RLSPKESEVLRLFA-EG----FLVTEIAKKLNRSIKTISSQKKSAMMKLG   66 (87)
T ss_dssp             SCCHHHHHHHHHHH-HT----CCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH-cC----CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            69999999998864 44    89999999999999999999999999985

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=95.41  E-value=0.0075  Score=46.13  Aligned_cols=42  Identities=21%  Similarity=0.234  Sum_probs=35.6

Q ss_pred             cCCHHHHHHHHH--HHhcCCCCCCCHHHHHHHHCC-CHHHHHHHH
Q 009803          461 TLNPRERQVVRW--RFGLEDGRMKTLQEIGELMGV-SRERIRQIE  502 (525)
Q Consensus       461 ~L~~rER~VL~l--Rygl~~g~~~Tl~EIAe~LgI-S~erVRqie  502 (525)
                      .|+++|++||..  .|....|-|-|++|||+.||+ |..+|+.++
T Consensus         2 ~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l   46 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHL   46 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHH
Confidence            599999999865  355667888999999999999 899999764

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=94.34  E-value=0.031  Score=39.29  Aligned_cols=37  Identities=11%  Similarity=0.251  Sum_probs=30.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  501 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqi  501 (525)
                      .|++.+.+-++-.+-.|    .|..+||..||||+.||...
T Consensus         5 ~lt~~q~~~a~~l~~~G----~s~~~iA~~~gVSr~TiYry   41 (47)
T d1ijwc_           5 AINKHEQEQISRLLEKG----HPRQQLAIIFGIGVSTLYRY   41 (47)
T ss_dssp             SSCHHHHHHHHHHHHTT----CCHHHHHHHHTCCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHCC----CCHHHHHHHHCcCHHHHHhh
Confidence            57787777777666544    89999999999999999865

>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=93.74  E-value=0.041  Score=40.02  Aligned_cols=39  Identities=21%  Similarity=0.314  Sum_probs=33.5

Q ss_pred             HHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHHh
Q 009803          243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN  281 (525)
Q Consensus       243 ~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l~  281 (525)
                      .++.+...+|...+|++||..|.|+.+|++.+.+...+.
T Consensus        15 ~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~   53 (57)
T d1l0oc_          15 NKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQE   53 (57)
T ss_dssp             HHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            455677889999999999999999999999988876654

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=93.00  E-value=0.13  Score=37.72  Aligned_cols=39  Identities=21%  Similarity=0.284  Sum_probs=31.2

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      |++.+++||..--..   ..+|+.|||+.+|+|..+|+.++.
T Consensus         3 lD~~D~~IL~~L~~~---~r~s~~eiA~~l~ls~~~v~~Ri~   41 (63)
T d2cg4a1           3 IDNLDRGILEALMGN---ARTAYAELAKQFGVSPETIHVRVE   41 (63)
T ss_dssp             CCHHHHHHHHHHHHC---TTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHc---CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            678888888876433   238999999999999999995543

>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=92.92  E-value=0.075  Score=40.59  Aligned_cols=39  Identities=28%  Similarity=0.380  Sum_probs=33.4

Q ss_pred             HHHHHhHHHHHHhhcCCCCchHHhHHhhcCCHHHHHHHH
Q 009803          242 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL  280 (525)
Q Consensus       242 ~~~le~~~~~l~~~~g~~pt~~ewa~a~g~d~~~L~~~l  280 (525)
                      ..++++....|...+||+||..|.|...|++...+...+
T Consensus         9 ~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l   47 (77)
T d1rp3a1           9 ERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTL   47 (77)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence            345778889999999999999999999999988776654

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.84  E-value=0.11  Score=38.31  Aligned_cols=42  Identities=21%  Similarity=0.473  Sum_probs=30.5

Q ss_pred             CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          463 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       463 ~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      +....+||.+-   .++...|.+|+|+.||||+.+|+.    -+++|++
T Consensus         4 ~~~~~~iL~~L---~~~~~~s~~eLa~~l~vS~~ti~r----~i~~L~~   45 (63)
T d1biaa1           4 NTVPLKLIALL---ANGEFHSGEQLGETLGMSRAAINK----HIQTLRD   45 (63)
T ss_dssp             CHHHHHHHHHH---TTSSCBCHHHHHHHHTSCHHHHHH----HHHHHHH
T ss_pred             cHHHHHHHHHH---HHCCcCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            34455565543   345679999999999999999994    4566665

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=92.63  E-value=0.13  Score=37.89  Aligned_cols=40  Identities=13%  Similarity=0.193  Sum_probs=31.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      +|++..+.||..--.  ++ ..|+.|||+.+|+|+.+|.+++.
T Consensus         2 klD~~D~~IL~~L~~--n~-r~s~~~iA~~lgis~~tv~~Ri~   41 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK--DS-RLSMRELGRKIKLSPPSVTERVR   41 (63)
T ss_dssp             CCCHHHHHHHHHHHH--CS-CCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHHHHH
Confidence            477888888876543  22 48999999999999999995543

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.54  E-value=0.14  Score=37.25  Aligned_cols=39  Identities=15%  Similarity=0.281  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      |++.++.||.+--..  + ..|+.|||+.+|+|+++|.+++.
T Consensus         1 lD~~D~kIl~~L~~n--~-r~s~~~lA~~~gls~~~v~~Ri~   39 (60)
T d1i1ga1           1 IDERDKIILEILEKD--A-RTPFTEIAKKLGISETAVRKRVK   39 (60)
T ss_dssp             CCSHHHHHHHHHHHC--T-TCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHc--C-CCCHHHHHHHHCcCHHHHHHHHH
Confidence            466778888765432  2 38999999999999999995543

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.32  E-value=0.17  Score=37.92  Aligned_cols=43  Identities=14%  Similarity=0.132  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      .|+..++.=|..+|-  .|+.++..|||..|||+++||+.|+.+-
T Consensus         7 ~LT~~eK~~ii~~~e--~g~k~sq~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           7 QLTFREKSRIIQEVE--ENPDLRKGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             CCCHHHHHHHHHHHH--HCTTSCHHHHHHHHTCCHHHHHHHHHTH
T ss_pred             cCCHHHHHHHHHHHH--cCCcchHHHHHHHhCCChhHHHHHHHHH
Confidence            467666665555554  3444789999999999999999998774

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=90.92  E-value=0.1  Score=39.95  Aligned_cols=28  Identities=32%  Similarity=0.460  Sum_probs=25.2

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          481 MKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      |+|.+|||..+|+|+++|.    |+|++|++.
T Consensus        30 ~~t~~eiA~~lG~sretvs----r~l~~l~~~   57 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTS----TALNSLIKE   57 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHH----HHHHHHHHT
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            6999999999999999999    788888764

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=90.88  E-value=0.34  Score=35.01  Aligned_cols=39  Identities=18%  Similarity=0.366  Sum_probs=29.1

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      |++.++.||..--.  + ...|+.|||+.+|+|+.+|..++.
T Consensus         1 lD~~D~~Il~~L~~--n-~r~s~~eiA~~l~ls~~~v~~Ri~   39 (60)
T d2cyya1           1 LDEIDKKIIKILQN--D-GKAPLREISKITGLAESTIHERIR   39 (60)
T ss_dssp             CCHHHHHHHHHHHH--C-TTCCHHHHHHHHCSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45667777776432  2 248999999999999999995543

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.48  E-value=0.11  Score=38.72  Aligned_cols=27  Identities=37%  Similarity=0.599  Sum_probs=23.9

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      |+|.+|||..+|+|+++|.    |.|++|++
T Consensus        29 ~lt~~~lA~~~G~sRetvs----r~L~~l~~   55 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVG----RILKMLED   55 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            5999999999999999999    67777765

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=90.05  E-value=0.14  Score=39.14  Aligned_cols=29  Identities=24%  Similarity=0.382  Sum_probs=25.5

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      -|+|.+|||..+|+|+++|.    |++++|++.
T Consensus        29 ~~lt~~elA~~~g~sretvs----r~l~~l~~~   57 (80)
T d3e5ua1          29 MPLSQKSIGEITGVHHVTVS----RVLASLKRE   57 (80)
T ss_dssp             SCCCHHHHHHHHTCCHHHHH----HHHHHHHHT
T ss_pred             eCCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            46899999999999999998    788888763

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=89.70  E-value=0.13  Score=38.93  Aligned_cols=27  Identities=11%  Similarity=0.310  Sum_probs=24.4

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          481 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       481 ~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      ++|.+|||..+|+|+++|.    |++++|++
T Consensus        27 ~lt~~elA~~lg~sr~tvs----r~l~~l~~   53 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNIS----KTLNELQD   53 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             ecCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4899999999999999998    78888876

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=89.22  E-value=0.15  Score=38.85  Aligned_cols=29  Identities=7%  Similarity=0.108  Sum_probs=25.3

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      -|+|.+|||..+|+|+++|.    |+|++|++.
T Consensus        28 ~~lt~~eLA~~~G~sretvs----r~L~~l~~~   56 (81)
T d2gaua1          28 IYLSREELATLSNMTVSNAI----RTLSTFVSE   56 (81)
T ss_dssp             CCCCHHHHHHHTTSCHHHHH----HHHHHHHHT
T ss_pred             ecCCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            36899999999999999998    788888763

>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=89.19  E-value=0.35  Score=35.29  Aligned_cols=39  Identities=26%  Similarity=0.435  Sum_probs=30.2

Q ss_pred             HHHHHhHHHHHHhhcCCCCchHHhHHhhcC--CHHHHHHHH
Q 009803          242 LLKLEGLREVLSERCGGSPTFAQWAAAAGV--DQRELRRRL  280 (525)
Q Consensus       242 ~~~le~~~~~l~~~~g~~pt~~ewa~a~g~--d~~~L~~~l  280 (525)
                      +-++.+...+|...+||+||.+|.|++.|+  +.+.+...+
T Consensus        11 i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l   51 (60)
T d1ku2a1          11 INKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETL   51 (60)
T ss_dssp             HHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHG
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHH
Confidence            345667788999999999999999999974  455555443

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=88.85  E-value=0.27  Score=39.52  Aligned_cols=41  Identities=12%  Similarity=0.194  Sum_probs=32.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      .|++.+..||..-+..+|  |+|..|||+.+|+++.+|+.++.
T Consensus        18 gLs~~~~~iL~~L~~~~~--~~t~~eLa~~~~i~~~tvs~~l~   58 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEIEK--PITSEELADIFKLSKTTVENSLK   58 (109)
T ss_dssp             TCCHHHHHHHHHHHHHCS--CEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHcCC--CCCHHHHHHHHCccHhHHHHHHH
Confidence            599999999876554332  59999999999999999995443

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=88.54  E-value=0.22  Score=39.20  Aligned_cols=43  Identities=26%  Similarity=0.228  Sum_probs=33.7

Q ss_pred             cCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHC--CCHHHHHHHHH
Q 009803          461 TLNPRERQVVRWR--FGLEDGRMKTLQEIGELMG--VSRERIRQIES  503 (525)
Q Consensus       461 ~L~~rER~VL~lR--ygl~~g~~~Tl~EIAe~Lg--IS~erVRqie~  503 (525)
                      +|++|+++||..-  +....|.|.+.++|++.+|  +|..+||..+.
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~   47 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMK   47 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHH
Confidence            4899999998643  2345689999999999966  58999996543

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=88.23  E-value=0.26  Score=35.88  Aligned_cols=30  Identities=20%  Similarity=0.178  Sum_probs=25.3

Q ss_pred             HHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          471 RWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       471 ~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .+|--.+    +|.+|+|+.+|||+.+|+++++-
T Consensus         6 ~~R~~~g----ltQ~elA~~lGvs~~tvs~~E~G   35 (62)
T d2ppxa1           6 IIRRALK----LTQEEFSARYHIPLGTLRDWEQG   35 (62)
T ss_dssp             HHHHHTT----CCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             HHHHHcC----CCHHHHHHHhCCCHHHHHHHHCC
Confidence            3444455    99999999999999999999973

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.99  E-value=0.48  Score=34.70  Aligned_cols=38  Identities=24%  Similarity=0.156  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          464 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       464 ~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      +|...||.+-.-  ...+.|..|+|+.||||+.||++-+.
T Consensus         7 eR~~~Il~~L~~--~~~~vs~~~La~~l~VS~~TI~rdi~   44 (65)
T d1j5ya1           7 ERLKSIVRILER--SKEPVSGAQLAEELSVSRQVIVQDIA   44 (65)
T ss_dssp             HHHHHHHHHHHH--CSSCBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH--cCCCCcHHHHHHHHCCCHHHHHHHHH
Confidence            345566655432  33458999999999999999995543

>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=87.39  E-value=0.47  Score=35.58  Aligned_cols=40  Identities=23%  Similarity=0.269  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHcCC-CHHHHHHHHh
Q 009803          371 TYRVKEARKQLYSENGRHPNNEEVAEATGL-SMKRLHAVLL  410 (525)
Q Consensus       371 ~~ki~ka~~~L~~~lgr~Pt~eEIA~~lgi-s~~~v~~~l~  410 (525)
                      -.++-..-..+..++|..||..|||+.+|+ |...|...+.
T Consensus         7 Q~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~   47 (71)
T d1jhfa1           7 QQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   47 (71)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHH
Confidence            344555666777889999999999999999 7888888764

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=87.13  E-value=0.49  Score=39.26  Aligned_cols=39  Identities=15%  Similarity=-0.037  Sum_probs=28.5

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          462 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       462 L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      ||...|+=|.-.|..+    ++..+||+.||||+.+|+.+..+
T Consensus        17 Ls~dlR~rIv~~~~~G----~s~r~iA~~~~VS~~tV~k~l~r   55 (123)
T d1pdnc_          17 LPNNIRLKIVEMAADG----IRPCVISRQLRVSHGCVSKILNR   55 (123)
T ss_dssp             CCHHHHHHHHHHHHTT----CCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhc----CCHHHHHHHHCcCHHHHHHHHHH
Confidence            5555554333345444    89999999999999999977655

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.68  E-value=0.58  Score=34.39  Aligned_cols=28  Identities=11%  Similarity=0.144  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          480 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       480 ~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .+-+..+||+.||||+.+|.    ++++||.+
T Consensus        22 ~~v~~~~iA~~L~vs~~SVt----~mvkrL~~   49 (63)
T d2isya1          22 VTPLRARIAERLDQSGPTVS----QTVSRMER   49 (63)
T ss_dssp             CCCCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCcHHHHHHHhCCCchhHH----HHHHHHHH
Confidence            34788999999999999999    56666654

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=86.60  E-value=1  Score=37.49  Aligned_cols=52  Identities=19%  Similarity=0.248  Sum_probs=39.5

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          453 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       453 ~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      +.+...+.  .|++-+-.|+.+-|..+  .|+|..|||+.+|+|+++|+    +++++|-
T Consensus        13 ~~~~~~~~~~Gl~~~~~~i~~~L~~~~--~plt~~ela~~l~vsk~~vs----~~l~~L~   66 (151)
T d1ku9a_          13 ELFSELAKIHGLNKSVGAVYAILYLSD--KPLTISDIMEELKISKGNVS----MSLKKLE   66 (151)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHCS--SCEEHHHHHHHHTCCHHHHH----HHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHhCC--CCcCHHHHHHHhCCCcchHH----HHHHHHH
Confidence            33444443  57999999998887643  56999999999999999999    4555554

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=85.21  E-value=0.52  Score=36.60  Aligned_cols=35  Identities=23%  Similarity=0.303  Sum_probs=27.0

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      ++|.+..-. +|  +|+.+||+.||||..+|+++..+.
T Consensus        13 ~aV~l~~~~-~g--~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          13 DAVALYENS-DG--ASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHTTG-GG--SCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CC--CcHHHHHHHHCCCHHHHHHHHHHH
Confidence            456555322 12  899999999999999999998765

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=85.06  E-value=0.49  Score=32.23  Aligned_cols=31  Identities=13%  Similarity=0.190  Sum_probs=25.1

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      +|..|+ ..+    ++-.+||+.|||++.+|..++.
T Consensus        10 ~V~~L~-~~G----~gat~IAk~lgI~R~SVYR~L~   40 (43)
T d1gdta1          10 AVLNMW-QQG----LGASHISKTMNIARSTVYKVIN   40 (43)
T ss_dssp             HHHHHH-HTT----CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHh
Confidence            466665 455    9999999999999999997654

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=84.85  E-value=2.1  Score=34.83  Aligned_cols=55  Identities=4%  Similarity=0.137  Sum_probs=41.0

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          451 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       451 ~~~~L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      +...+...+.  .|++.|-.||..-+.. +|.+.|..||++.+|+++.+|.    +++++|-
T Consensus        14 ~~~~~~~~l~~~glt~~q~~vL~~l~~~-~~~~it~~ela~~~~~~~~~vs----~~l~~L~   70 (135)
T d3broa1          14 MSTRFDIFAKKYDLTGTQMTIIDYLSRN-KNKEVLQRDLESEFSIKSSTAT----VLLQRME   70 (135)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHT-TTSCCBHHHHHHHHTCCHHHHH----HHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHCcCHhHHH----HHHHHHH
Confidence            3444555554  4899999998776654 4566999999999999999998    5566653

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=84.73  E-value=0.54  Score=35.05  Aligned_cols=31  Identities=19%  Similarity=0.342  Sum_probs=26.2

Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      +-.+|-..+    +|..|+|+.||||+.+|.+++.
T Consensus         6 ~k~~R~~~g----ltQ~elA~~LGvs~~ti~~yE~   36 (67)
T d2auwa1           6 FGDWMHRNN----LSLTTAAEALGISRRMVSYYRT   36 (67)
T ss_dssp             HHHHHHHTT----CCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHc
Confidence            445666666    9999999999999999999876

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=84.16  E-value=0.67  Score=37.57  Aligned_cols=41  Identities=29%  Similarity=0.237  Sum_probs=32.5

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      ..|+|-|.-.-.-++... |  +|.++||+.+|+|+.+|++++.
T Consensus        12 ~~L~p~e~A~a~~~l~~~-g--~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_          12 NELTPREIADFIGRELAK-G--KKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             TCCCHHHHHHHHHHHHHT-T--CCHHHHHHHHTCCHHHHHHHHG
T ss_pred             cCCCHHHHHHHHHHHHHh-C--CCHHHHHHHHCCcHHHHHHHHH
Confidence            358888877666665443 3  7999999999999999998865

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=83.93  E-value=0.87  Score=35.94  Aligned_cols=22  Identities=18%  Similarity=0.268  Sum_probs=20.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      +|..+||+.+|.|+.+|++++.
T Consensus        20 ~t~~~iA~~~Gks~~~V~~~Lr   41 (93)
T d1vz0a1          20 LTQEEVARRVGKARSTVANALR   41 (93)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHccchHHHHHHHH
Confidence            8999999999999999998764

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=83.88  E-value=1.3  Score=35.27  Aligned_cols=49  Identities=18%  Similarity=0.286  Sum_probs=36.8

Q ss_pred             HHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 009803          455 LEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  510 (525)
Q Consensus       455 L~~aL~--~L~~rER~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR  510 (525)
                      |.+.|.  .|++.|-.|+..-+-.+   +.|..|||+.+|+++.+|.    +++.+|-
T Consensus         9 l~~~L~~lGlt~~e~~v~~~L~~~g---~~t~~eia~~~~i~~~~v~----~~l~~L~   59 (109)
T d1sfxa_           9 LVKALEKLSFKPSDVRIYSLLLERG---GMRVSEIARELDLSARFVR----DRLKVLL   59 (109)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHHHHHC---CBCHHHHHHHHTCCHHHHH----HHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHhcC---CCCHHHHHHHhCCCcchHH----HHHHHHH
Confidence            334443  58899888887766544   3999999999999999999    4555554

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=83.45  E-value=1.6  Score=33.51  Aligned_cols=49  Identities=20%  Similarity=0.273  Sum_probs=37.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          453 EDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       453 ~~L~~aL~~L~~rER~VL~lRygl~~g---~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      ..|...+..|++.|+.|..+  .+++.   ..+|..|||+..|||..+|-..-+
T Consensus         7 ~~i~~~~~~Ls~~e~~ia~y--il~~~~~~~~~si~~lA~~~~vS~sTi~Rf~k   58 (83)
T d2o3fa1           7 AIIQSMKHKLPPSERKLADY--ILAHPHKAIESTVNEISALANSSDAAVIRLCK   58 (83)
T ss_dssp             HHHHHHGGGSCHHHHHHHHH--HHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHHHH--HHcCHHHHHHccHHHHHHHHCCCHHHHHHHHH
Confidence            45778889999999998754  34321   238999999999999999975443

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=83.40  E-value=1  Score=33.27  Aligned_cols=36  Identities=8%  Similarity=-0.009  Sum_probs=27.8

Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          467 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       467 R~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      ..||.+-+-.+   +.|-.|||+.+|+|+.+|+.+..+-
T Consensus         9 ~~Il~~l~~~g---~~sr~eLa~~~glS~~Tv~~~l~~L   44 (71)
T d1z05a1           9 GRVYKLIDQKG---PISRIDLSKESELAPASITKITREL   44 (71)
T ss_dssp             HHHHHHHHHHC---SBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            35666665433   4999999999999999999776543

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=82.89  E-value=0.64  Score=35.03  Aligned_cols=29  Identities=31%  Similarity=0.653  Sum_probs=24.9

Q ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          479 GRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       479 g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      |..+ |..|+|+.||||+.+||    +|++.|..
T Consensus        24 G~~LPs~~eLa~~~~vSr~tvr----~Al~~L~~   53 (74)
T d1hw1a1          24 GTILPAERELSELIGVTRTTLR----EVLQRLAR   53 (74)
T ss_dssp             TSBCCCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             cCCCccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4456 89999999999999999    78888864

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=82.79  E-value=0.5  Score=37.91  Aligned_cols=27  Identities=30%  Similarity=0.427  Sum_probs=23.3

Q ss_pred             CCCHHHHHHHHCCC-HHHHHHHHHHHHHHHHh
Q 009803          481 MKTLQEIGELMGVS-RERIRQIESSAFRKLKN  511 (525)
Q Consensus       481 ~~Tl~EIAe~LgIS-~erVRqie~RALkKLR~  511 (525)
                      ++|.+|||..+|+| +++|.    |.|++|++
T Consensus        31 ~lTqeeLA~~lG~s~ReTVs----R~L~~L~~   58 (100)
T d2bgca1          31 NLTMQELGYSSGIAHSSAVS----RIISKLKQ   58 (100)
T ss_dssp             CCCHHHHHHHTTCCCHHHHH----HHHHHHHH
T ss_pred             ccCHHHHHHHhCCchHHHHH----HHHHHHHH
Confidence            59999999999996 99998    67777765

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=82.78  E-value=1.3  Score=35.01  Aligned_cols=45  Identities=13%  Similarity=0.207  Sum_probs=31.3

Q ss_pred             HHHHHHhcCCHHHHH-HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          454 DLEKVLDTLNPRERQ-VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       454 ~L~~aL~~L~~rER~-VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      .+.+++..|...-|. ||.+  ..+  .++|..||++.+|+|+.+|++.+
T Consensus        12 ~la~~~kaL~~p~Rl~Il~~--L~~--~~~~v~ela~~l~is~stvS~HL   57 (98)
T d1r1ta_          12 SLAEFFAVLADPNRLRLLSL--LAR--SELCVGDLAQAIGVSESAVSHQL   57 (98)
T ss_dssp             HHHHHHHHHCCHHHHHHHHH--HTT--CCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHH--HHc--CCcCHHHHHHHHCcCHHHHHHHH
Confidence            455666666655444 4433  233  24999999999999999999664

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.82  E-value=2  Score=32.12  Aligned_cols=52  Identities=13%  Similarity=0.240  Sum_probs=43.5

Q ss_pred             cCCHHHHHHHHHHHhcCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          461 TLNPRERQVVRWRFGLEDG--RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g--~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      .+++.|..+|...|-..+.  .....++||..+|++...|+.+...-+.|+|+.
T Consensus         7 ~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~   60 (72)
T d1uhsa_           7 TMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS   60 (72)
T ss_dssp             CCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            5788999999998865332  335789999999999999999999999888864

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.73  E-value=0.87  Score=34.18  Aligned_cols=26  Identities=15%  Similarity=0.127  Sum_probs=22.0

Q ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHH
Q 009803          477 EDGRMKTLQEIGELMGVSRERIRQIE  502 (525)
Q Consensus       477 ~~g~~~Tl~EIAe~LgIS~erVRqie  502 (525)
                      ..+.|+|+.|||+.+|+++.+|..+.
T Consensus        16 ~~~~~~s~~eia~~~~~~~st~~rll   41 (75)
T d1mkma1          16 KNPGDVSVSEIAEKFNMSVSNAYKYM   41 (75)
T ss_dssp             HCSSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             hCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34567999999999999999999554

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=81.70  E-value=0.59  Score=34.62  Aligned_cols=29  Identities=31%  Similarity=0.434  Sum_probs=25.1

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          479 GRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       479 g~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      |..++..++|+.||||+.+||    +|+++|..
T Consensus        23 G~~l~~~~La~~~~vSr~tvr----~Al~~L~~   51 (69)
T d2hs5a1          23 GARLSEPDICAALDVSRNTVR----EAFQILIE   51 (69)
T ss_dssp             TCEECHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             cCccCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            455789999999999999999    78888864

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.36  E-value=0.62  Score=32.89  Aligned_cols=48  Identities=15%  Similarity=0.250  Sum_probs=38.7

Q ss_pred             cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 009803          461 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRK  508 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g-~~~Tl~EIAe~LgIS~erVRqie~RALkK  508 (525)
                      .|++.++.||.-.|-.+.. ......+||..+|++...|+.+...-..|
T Consensus         3 ~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k   51 (53)
T d1le8a_           3 SISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR   51 (53)
T ss_dssp             CCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhc
Confidence            5899999999999987632 22467899999999999999988766554

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=81.36  E-value=0.84  Score=33.57  Aligned_cols=32  Identities=19%  Similarity=0.206  Sum_probs=26.8

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          468 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       468 ~VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      .|-.+|.-.+    +|.+|+|+.+|||+.+|..+++
T Consensus        10 ~i~~~r~~~g----ltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          10 VLQEHLRNSG----LTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHHTTT----CCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHcC----CCHHHHHHHHHcCHhHHHHHHc
Confidence            3555665555    9999999999999999999986

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=81.27  E-value=0.69  Score=34.96  Aligned_cols=30  Identities=20%  Similarity=0.305  Sum_probs=25.3

Q ss_pred             CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          478 DGRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       478 ~g~~~-Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .|..+ |..++|+.||||+.+||    +|++.|..
T Consensus        18 ~G~~LPse~~La~~~~vSr~tvr----~Al~~L~~   48 (78)
T d3bwga1          18 QGDKLPVLETLMAQFEVSKSTIT----KSLELLEQ   48 (78)
T ss_dssp             TTCBCCCHHHHHHHTTCCHHHHH----HHHHHHHH
T ss_pred             CcCCCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            34456 99999999999999999    78888764

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=81.15  E-value=0.9  Score=32.83  Aligned_cols=30  Identities=30%  Similarity=0.469  Sum_probs=24.8

Q ss_pred             HHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 009803          471 RWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  504 (525)
Q Consensus       471 ~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~R  504 (525)
                      .+|-..+    +|.+|+|+.+|||+.+|+++++.
T Consensus        10 ~~R~~~g----ltq~~lA~~~gvs~~ti~~~E~g   39 (65)
T d2croa_          10 KRRIALK----MTQTELATKAGVKQQSIQLIEAG   39 (65)
T ss_dssp             HHHHHTT----CCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HHHHHcC----CCHHHHHHHHCcCHhHHHHHHCC
Confidence            3444455    99999999999999999999863

>d1nr3a_ d.236.1.1 (A:) DNA-binding protein Tfx {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding protein Tfx
superfamily: DNA-binding protein Tfx
family: DNA-binding protein Tfx
domain: DNA-binding protein Tfx
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=81.09  E-value=0.017  Score=48.58  Aligned_cols=31  Identities=16%  Similarity=0.339  Sum_probs=29.3

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 009803          482 KTLQEIGELMGVSRERIRQIESSAFRKLKNK  512 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~RALkKLR~~  512 (525)
                      +|++|||++||.|+..|..++++|++++++.
T Consensus         6 ltQ~eIA~~LgTSraNIs~IEk~A~eNIekA   36 (122)
T d1nr3a_           6 WSQKKIARELKTTRQNVSAIERKAMENIEKS   36 (122)
T ss_dssp             CSSCSTHHHHHHCCSSSCCHHHHHHTTCSSS
T ss_pred             CCHHHHHHHHCccHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999988764

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.75  E-value=2.2  Score=30.55  Aligned_cols=51  Identities=18%  Similarity=0.176  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 009803          461 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  511 (525)
Q Consensus       461 ~L~~rER~VL~lRygl~~g-~~~Tl~EIAe~LgIS~erVRqie~RALkKLR~  511 (525)
                      .+++.+..+|...|..+.. ......+||..+|+|...|+.+...-..+.|.
T Consensus         7 ~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           7 HFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            3678888999988876532 33678999999999999999999998888775

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.65  E-value=1.9  Score=31.65  Aligned_cols=32  Identities=16%  Similarity=0.103  Sum_probs=25.4

Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 009803          469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  505 (525)
Q Consensus       469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~RA  505 (525)
                      ||.+. -.+    +|..+||+.|+||..+|..+.++=
T Consensus        23 iv~~~-~~G----~s~r~aA~rf~VS~s~v~k~l~r~   54 (63)
T d1k78a1          23 IVELA-HQG----VRPCDISRQLRVSHGCVSKILGRY   54 (63)
T ss_dssp             HHHHH-HTT----CCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHH-HcC----CCHHHHHHHhCCCHHHHHHHHHHH
Confidence            55553 334    899999999999999999877653

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=80.23  E-value=0.93  Score=35.13  Aligned_cols=31  Identities=3%  Similarity=0.074  Sum_probs=26.4

Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 009803          469 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       469 VL~lRygl~~g~~~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      |-.+|--.|    +|.+++|+.+|||+.+|.++++
T Consensus        16 i~~~r~~~g----ltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1          16 LNAVIDRAR----LSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HHHHHHHTT----CCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHcC----CCHHHHHHHHHhhHhHHHHHHc
Confidence            445555555    9999999999999999999997

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.10  E-value=1.3  Score=33.03  Aligned_cols=43  Identities=16%  Similarity=0.135  Sum_probs=36.1

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-CCCHHHHHHHH
Q 009803          460 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELM-GVSRERIRQIE  502 (525)
Q Consensus       460 ~~L~~rER~VL~lRygl~~g~~~Tl~EIAe~L-gIS~erVRqie  502 (525)
                      +.|++.+++|+.+--...+.+.++.+||...| |+|...|++..
T Consensus         2 nGLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~ai   45 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAV   45 (69)
T ss_dssp             CCSCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHH
Confidence            36899999999998776655669999999999 89999998543

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=80.02  E-value=0.9  Score=32.99  Aligned_cols=22  Identities=36%  Similarity=0.511  Sum_probs=21.3

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Q 009803          482 KTLQEIGELMGVSRERIRQIES  503 (525)
Q Consensus       482 ~Tl~EIAe~LgIS~erVRqie~  503 (525)
                      +|.+|+|+.+|||+.+|.++++
T Consensus        15 ~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_          15 ISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHT
T ss_pred             CCHHHHHHhcccCHHHHHHHHc
Confidence            9999999999999999999986