Citrus Sinensis ID: 007404

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-----
Protein Sequence
MIDVAAAGLGKETQISTSSFNKNMSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
Secondary Structure (PSIPRED)
cHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccHHHHHccccHHccccHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccEEEEEcccccccccccHHHHHHcHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHccHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEEHcccccccEEEcccccccccccccccccccccEEEEEcccccccccccccccccccEEEEcEEEEEccccccHHHHHHcccHHHccccccccccccccccccccEEcccccccccccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHcHHHHHccccccccHccccccccccccccHHccccccccHHHHHHHHccHHHHHHccccccHHHHHHHHHccHccccccccccccccHHHHccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcHccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHccccHHHHcccHHHHHHHHHHHcccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHcccHHHHHHHHHccc
Coil and Loop (DISEMBL)
MIDVAAaglgketqistssfnknmscllpqfkcqpdtfsIHFRtlhnhqhhsshpskskepicfrthcvlsttspststamtTVLDveklrlpsleahSNAVAAnrqwtyfgavgpsteenlgtslatetltSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtnTSMWAQLTERERAsiigdsviveaapeeeyseqqplnksadleptHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSvksgstsrrkrpsvqevdysdplrylrattsssrlltANEEMQLSAGIQDLLKLEGLREVlsercggsptFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRgaekfdaskgfkfsTYAHWWIKQAVRKslsdqsrtirlpfhmVEATYRVKEARKQLYSengrhpnneeVAEATGLSMKRLHAVllspkaprsldqkiginqnlkpseviadpeaeTAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
Flexible Loop (DISEMBL)
midvaaaglgketqistSSFNKNMSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVlsttspststamTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtNTSMWAQLTERERASIIGDSVIVEAAPeeeyseqqplnkSADLEPTHEELKLLEeqvsqsiavrsrrqterkARRTRaaekaaanvmsvksgstsrrkrpsvqevdysdplrylRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAaaagvdqrelRRRLNYGilckdkmitsNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKfdaskgfkfstYAHWWIKQAVrkslsdqsrtirlpfhmveatYRVKEARKQLysengrhpnneEVAEATGLSMKRLHAVLLSpkaprsldqkiginqnlkpseviadpeAETAEDLLIKKFMKEDLEKvldtlnprerqvvrwrfgledgrmktlqeigelmgvsrerIRQIESsafrklknkkrtkhlmqyaits
Low Complexity Region (SEG)
MIDVAAAGLGKETQISTSSFNKNMSCLLPQFKCQPDTFSIHFRTLhnhqhhsshpsksKEPICFRTHCVLsttspststamttVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTsdeaviaaasaeavalaraavkvakdaalMVNHHNsakpkskpaisssaDTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSrrqterkarrtraaekaaaNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
Disordered region (IsUnstruct)
**********************NMSCLLPQFKCQPDTFSIHFRTLH***************ICFRTHCVLST*******AMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGP*********LATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMV************************************I******************************************************************************************************************LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK********************************************************************DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGV********************************
Disordered Region (DISOPRED)
********************NKNMSCLLPQFKCQPDTFSIHF***********************************************************************************************************************************************************************************************************************************************************LRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQ*******HPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT*
Disordered Region (DISEMBL)
********LGKETQISTSSFNKNMSCLLPQFKCQPDTFSIHFRTL**************EPICFRTHCVLSTTSPSTSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHH******************TSMWAQLTERERASIIGDSVIVEAAP***********KSADLEPTHEELKLLEEQVSQS********************************************VDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
Disordered Region (DISPRO)
MIDVAAAGLGK***IST*SFNKNMSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHH***************************************************************************************************************************YSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIDVAAAGLGKETQISTSSFNKNMSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAITS
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	605	2.2.26 [Sep-21-2011]
O22056	572	RNA polymerase sigma fact	yes	no	0.925	0.979	0.667	0.0
P26683	390	RNA polymerase sigma fact	yes	no	0.542	0.841	0.471	1e-79
P38023	399	RNA polymerase sigma fact	yes	no	0.510	0.774	0.487	3e-76
P52322	416	RNA polymerase sigma fact	yes	no	0.510	0.742	0.421	1e-70
Q9LD95	547	RNA polymerase sigma fact	no	no	0.588	0.650	0.386	3e-68
P74565	425	RNA polymerase sigma fact	N/A	no	0.388	0.552	0.512	2e-66
Q8CP24	368	RNA polymerase sigma fact	yes	no	0.408	0.671	0.463	3e-60
Q5HNY7	368	RNA polymerase sigma fact	yes	no	0.408	0.671	0.463	3e-60
Q99TT5	368	RNA polymerase sigma fact	yes	no	0.408	0.671	0.463	4e-60
P0A0I9	368	RNA polymerase sigma fact	yes	no	0.408	0.671	0.459	5e-60

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

 Score =  721 bits (1861), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/586 (66%), Positives = 459/586 (78%), Gaps = 26/586 (4%)

Query: 25  SCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTV 84
           SCLLPQFKC PD+FSIHFRT          P  +K  + F+  C +ST SP+    +T++
Sbjct: 3   SCLLPQFKCPPDSFSIHFRT------SFCAPKHNKGSVFFQPQCAVST-SPAL---LTSM 52

Query: 85  LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAASA 143
           LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL TSDEAV+ AA+A
Sbjct: 53  LDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVVAAAA 112

Query: 144 EAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIG-- 201
           EAVALARAAVKVAKDA L  N +N+        ++SS     S W Q TE+ERA I+G  
Sbjct: 113 EAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGILGHL 166

Query: 202 ---DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTERKAR 257
              D+ IV        S ++ +    DLE   +E   L E+  S S+AVRS RQTERKAR
Sbjct: 167 AVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTERKAR 223

Query: 258 RTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 317
           R +  EK A+ + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSA
Sbjct: 224 RAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSA 283

Query: 318 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 377
           GIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRL
Sbjct: 284 GIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRL 343

Query: 378 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 437
           VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKSLSDQ
Sbjct: 344 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQ 403

Query: 438 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRS 497
           SR IRLPFHMVEATYRVKEARKQLYSE G+HP NEE+AEATGLSMKRL AVLLSPK PRS
Sbjct: 404 SRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRS 463

Query: 498 LDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLE 557
           LDQKIG+NQNLKPSEVIADPEA T+ED+LIK+FM++DL+KVLD+L  RE+QV+RWRFG+E
Sbjct: 464 LDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGME 523

Query: 558 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603
           DGRMKTLQEIGE+MGVSRER+RQIESSAFRKLKNKKR  HL QY +
Sbjct: 524 DGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 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 =  298 bits (762), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 156/331 (47%), Positives = 220/331 (66%), Gaps = 3/331 (0%)

Query: 273 KSG--STSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE 330
           KSG  + SRR+  S ++    D +R         RLL A+EE++L+  I DLL+LE +RE
Sbjct: 59  KSGKAAKSRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRE 118

Query: 331 VLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGM 390
            LSE+    P  ++WA A  +     R RL+ G   KDKM+ SN+RLV+SIAK Y   G+
Sbjct: 119 RLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGL 178

Query: 391 NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA 450
           + QDL+QEG  GL+R AEKFD  KG+KFSTYA WWI+QA+ ++++DQSRTIRLP H+ E 
Sbjct: 179 SFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYET 238

Query: 451 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP 510
             R+K+  K L  E GR P  EE+A    +++++L  +  S + P SL+  IG  ++ + 
Sbjct: 239 ISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRL 298

Query: 511 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGEL 570
            + I + + ET ED + K  ++EDLEKVLD+L+PRER V+R R+GL+DGRMKTL+EIG++
Sbjct: 299 GDFI-ESDGETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQI 357

Query: 571 MGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
             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 (733), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 151/310 (48%), Positives = 207/310 (66%), Gaps = 1/310 (0%)

Query: 292 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGV 351
           D +R         RLL A+EE++L+  I DLL LE +R+ L E+    P+ A+WAAA   
Sbjct: 89  DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148

Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 411
              E RRRL  G   KDKM+ SN+RLV+SIAK Y   G++ QDL+QEG  GL+R AEKFD
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 208

Query: 412 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNN 471
             KG+KFSTYA WWI+QA+ ++++DQSRTIRLP H+ E   R+K+  K L  E GR P  
Sbjct: 209 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTE 268

Query: 472 EEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM 531
           EE+A    +++++L  +  S + P SL+  IG  ++ +  + I + + ET ED + K  +
Sbjct: 269 EEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI-EADGETPEDEVAKNLL 327

Query: 532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591
           +EDLE VL TL+PRER V+R R+GL+DGRMKTL+EIG+L  V+RERIRQIE+ A RKL++
Sbjct: 328 REDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRH 387

Query: 592 KKRTKHLMQY 601
             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 =  268 bits (684), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 147/349 (42%), Positives = 205/349 (58%), Gaps = 40/349 (11%)

Query: 292 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE--------------VLSERCG 337
           D +R         RLL A EE++L+  I DLLKLE +RE               L ER  
Sbjct: 67  DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126

Query: 338 G-------------------------SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 372
                                     +P   +W A +       +RRL +G   K+KM+ 
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186

Query: 373 SNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 432
           SN+RLV+SIAK Y   G++ QDL+QEG  GL+R AEKFD  KG+KFSTYA WWI+QA+ +
Sbjct: 187 SNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITR 246

Query: 433 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP 492
           +++DQSRTIRLP H+ E   R+K+  K L  E  R P  EE+A    +++++L  +  S 
Sbjct: 247 AIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSA 306

Query: 493 KAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRW 552
           + P SL+  IG  ++ +  + I + + ET ED + K  ++EDLE VLDTL+PRER V+R 
Sbjct: 307 QLPISLETPIGKEEDSRLGDFI-EADGETPEDEVSKNLLREDLENVLDTLSPRERDVLRL 365

Query: 553 RFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
           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: 246 VRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSR 305
           VRS+RQ ER+A+  RA +    +        TS +K+   Q  D  D L+       + +
Sbjct: 188 VRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYK-QGADNDDALQLFLWGPETKQ 246

Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
           LLTA EE +L + IQ LLKLE ++  L  + G  PT  +WA A G+    L+  ++ G  
Sbjct: 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRS 306

Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
            ++K+IT+N+RLV+ IAK YQ  G+N QDL+QEG  GL++  EKF    G +F+TYA+WW
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWW 366

Query: 426 IKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 485
           I+Q++RKS+   SRTIRLP ++     +V EARK    E    P+ EE+A   G+S ++L
Sbjct: 367 IRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKL 426

Query: 486 HAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPR 545
             +L + + P S+ Q I  +Q+    E+  D   ET    + K+ M+  +  +L+ L+P+
Sbjct: 427 DKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPK 486

Query: 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA 602
           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 =  254 bits (648), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 121/236 (51%), Positives = 168/236 (71%), Gaps = 1/236 (0%)

Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
            KDKM+ SN+RLV+SIAK Y   G++ QDL+QEG  GL+R AEKFD  KG+KFSTYA WW
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248

Query: 426 IKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 485
           I+QA+ ++++DQSRTIRLP H+ E   R+K+  K L  E  R P  EE+AE   +++++L
Sbjct: 249 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTIEKL 308

Query: 486 HAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPR 545
             +  S + P SL+  IG  ++ +  + I + + ET ED + K  ++EDLE VLDTL+PR
Sbjct: 309 RFIAKSAQLPISLETPIGKEEDSRLGDFI-EADGETPEDEVSKNLLREDLENVLDTLSPR 367

Query: 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
           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 (594), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 115/248 (46%), Positives = 165/248 (66%), Gaps = 1/248 (0%)

Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
           EL +R+  G  + K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD S
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFS 178

Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 473
           KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P  EE
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEE 238

Query: 474 VAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKE 533
           + E   L  +++  +L   + P SL+  IG   +    + I D EA++  D    + +KE
Sbjct: 239 IGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKE 298

Query: 534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593
            LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  
Sbjct: 299 QLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPS 358

Query: 594 RTKHLMQY 601
           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 (594), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 115/248 (46%), Positives = 165/248 (66%), Gaps = 1/248 (0%)

Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
           EL +R+  G  + K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD S
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFS 178

Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 473
           KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P  EE
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEE 238

Query: 474 VAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKE 533
           + E   L  +++  +L   + P SL+  IG   +    + I D EA++  D    + +KE
Sbjct: 239 IGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKE 298

Query: 534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593
            LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  
Sbjct: 299 QLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPS 358

Query: 594 RTKHLMQY 601
           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 =  233 bits (594), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 115/248 (46%), Positives = 165/248 (66%), Gaps = 1/248 (0%)

Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
           EL +R+  G  + K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178

Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 473
           KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P  EE
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEE 238

Query: 474 VAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKE 533
           + E   L  +++  VL   + P SL+  IG   +    + I D EA++  D    + +KE
Sbjct: 239 IGEEMDLPAEKVREVLKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKE 298

Query: 534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593
            LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  
Sbjct: 299 QLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPS 358

Query: 594 RTKHLMQY 601
           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 =  232 bits (592), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 114/248 (45%), Positives = 165/248 (66%), Gaps = 1/248 (0%)

Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
           EL +R+  G  + K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178

Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 473
           KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P  EE
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEE 238

Query: 474 VAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKE 533
           + E   L  +++  +L   + P SL+  IG   +    + I D EA++  D    + +KE
Sbjct: 239 IGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKE 298

Query: 534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593
            LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL++  
Sbjct: 299 QLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPS 358

Query: 594 RTKHLMQY 601
           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	605
255565968	569	RNA polymerase sigma factor rpoD1, putat	0.935	0.994	0.760	0.0
449454538	580	PREDICTED: RNA polymerase sigma factor s	0.947	0.987	0.697	0.0
296090195	575	unnamed protein product [Vitis vinifera]	0.947	0.996	0.765	0.0
225436223	578	PREDICTED: RNA polymerase sigma factor r	0.952	0.996	0.761	0.0
224126061	567	predicted protein [Populus trichocarpa]	0.932	0.994	0.730	0.0
224144900	564	predicted protein [Populus trichocarpa]	0.930	0.998	0.706	0.0
7363218	575	sigma factor 2 [Sinapis alba]	0.925	0.973	0.658	0.0
297843640	572	hypothetical protein ARALYDRAFT_470915 [	0.930	0.984	0.675	0.0
15223259	572	RNApolymerase sigma subunit 2 [Arabidops	0.925	0.979	0.667	0.0
356509511	558	PREDICTED: RNA polymerase sigma factor r	0.919	0.996	0.663	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 =  822 bits (2122), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 442/581 (76%), Positives = 500/581 (86%), Gaps = 15/581 (2%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLPQFKCQPDTFSIHFR  + H  + +  +KS+EPI +R  C+LSTTSPSTSTA   
Sbjct: 2   MSCLLPQFKCQPDTFSIHFRANYFHFSNVTQSTKSREPIYYRAQCILSTTSPSTSTA--- 58

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 142
           VLD+EKLRLPS EA S+++A N  WTY            G++LATETL TSDEAVIAAA+
Sbjct: 59  VLDLEKLRLPSFEAPSDSIAPNSPWTY---------ATFGSTLATETLITSDEAVIAAAA 109

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 202
           AEAVALARAAVKVAKDAAL+V +  SA+ +SK  ++S +  + S W Q TE ERA IIGD
Sbjct: 110 AEAVALARAAVKVAKDAALLVKNFPSAETESK--LTSPSTIDASRWPQFTETERARIIGD 167

Query: 203 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 262
           SV  E  P EE S Q  + +S  LE TH+EL+LL++Q+S+ IAVRSRRQTERKARR RA 
Sbjct: 168 SVATETGPREESSMQSSIKESDYLELTHKELELLQKQLSEGIAVRSRRQTERKARRARAV 227

Query: 263 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 322
           EKAA++V+SVK GSTS++KR S+QEVDYSDPLRYLR TTS+SRLLTA+EE++LSA IQDL
Sbjct: 228 EKAASSVVSVKPGSTSKKKRGSLQEVDYSDPLRYLRGTTSTSRLLTASEELELSAAIQDL 287

Query: 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 382
           LKLE L+E L+ER GG PTFAQWAAAAGVDQR LR+R+N+G +CKDKMI SNIRLVISIA
Sbjct: 288 LKLERLQEELAERYGGQPTFAQWAAAAGVDQRTLRKRINHGTICKDKMIKSNIRLVISIA 347

Query: 383 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 442
           KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR
Sbjct: 348 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 407

Query: 443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKI 502
           LPFHMVEATYRVKEARKQLYSENGRHP++EEVAEA GLSMKRL AVLL+PKAPRSLDQKI
Sbjct: 408 LPFHMVEATYRVKEARKQLYSENGRHPDDEEVAEAAGLSMKRLSAVLLTPKAPRSLDQKI 467

Query: 503 GINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMK 562
           G+N +LKPSEVIADPEAETAE+LL+K+FMK+DLEKVL+TLNPRE QVVRWRFGLEDGRMK
Sbjct: 468 GMNMDLKPSEVIADPEAETAEELLMKQFMKQDLEKVLNTLNPRETQVVRWRFGLEDGRMK 527

Query: 563 TLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603
           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 =  798 bits (2061), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 410/588 (69%), Positives = 480/588 (81%), Gaps = 15/588 (2%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSH-------PSKSKEPICFRTHCVLSTTSPS 76
           MSCLLPQFKC P+TFSI F+T  N+ HH S         +K ++P   RT C+LS  SP 
Sbjct: 1   MSCLLPQFKCHPETFSIQFKTAANYSHHHSFLPTAYSSYTKVRDPHSLRTQCILSAASPP 60

Query: 77  TSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEA 136
           TST   T LDV++L+LP  + ++++V+  R  +Y GAV         +SLA+  LTS+EA
Sbjct: 61  TSTGTATTLDVDRLKLPPFDTNTDSVSVERLRSYLGAVE--------SSLASTLLTSEEA 112

Query: 137 VIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERER 196
            IAAA+AEAV LA+AAVKVA+DAAL+ N+ NS++  +K   S   D     WAQ  E ER
Sbjct: 113 SIAAAAAEAVTLAKAAVKVARDAALLANNINSSRAGTKSQSSPKPDALHFKWAQFMESER 172

Query: 197 ASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKA 256
           A IIG+ V V   P E  + +    +S D+EPT EEL+LL++++S+SI V+S+RQTERKA
Sbjct: 173 ADIIGEPVGVNKRPMEGDALEPSTTESDDMEPTSEELELLQDELSESITVKSKRQTERKA 232

Query: 257 RRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLS 316
           RRTRAAEK   +V+S KSGS+SR+KR SVQEVDYSDPLRYLRATT++SRLLTA EE++LS
Sbjct: 233 RRTRAAEKTVTSVLSFKSGSSSRKKRNSVQEVDYSDPLRYLRATTNTSRLLTATEELELS 292

Query: 317 AGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIR 376
            GIQDLLKLE L+E L ER G  PTFAQWAAAAGV+QR LR+RLNYG LCKDKMI SNIR
Sbjct: 293 EGIQDLLKLERLQEELGERYGNEPTFAQWAAAAGVNQRTLRKRLNYGTLCKDKMIKSNIR 352

Query: 377 LVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 436
           LVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK LSD
Sbjct: 353 LVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKFLSD 412

Query: 437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR 496
           QSRTIRLPFHMVEATYRVKEARKQL  ENGRHP+++E+AEA GLSMKRL AVL++PKAPR
Sbjct: 413 QSRTIRLPFHMVEATYRVKEARKQLLHENGRHPDDKEIAEAAGLSMKRLAAVLMTPKAPR 472

Query: 497 SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGL 556
           SL+QKIGINQNLKPSEVI+DPEAET ED+LIK+FMK+DLEKVLD+LNPRE+QV+RWRFG+
Sbjct: 473 SLEQKIGINQNLKPSEVISDPEAETCEDMLIKQFMKQDLEKVLDSLNPREKQVIRWRFGM 532

Query: 557 EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 604
           EDGRMKTLQEIGE+MGVSRERIRQIES AFRKLKNKKRTKHL QY ++
Sbjct: 533 EDGRMKTLQEIGEIMGVSRERIRQIESCAFRKLKNKKRTKHLQQYVMS 580

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  783 bits (2023), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 446/583 (76%), Positives = 492/583 (84%), Gaps = 10/583 (1%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLPQFKC PDTFS H + LH         SK++E I FR  C LSTTSP  ST+ T 
Sbjct: 1   MSCLLPQFKCPPDTFSTHPK-LHIL-------SKNREAIYFRVQCALSTTSPPLSTSTTA 52

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 142
           VLD+EKLRLPSLE+HSN+VAA+R WTY G VGP TE N   +LA ETL TS+EAVIAAA+
Sbjct: 53  VLDIEKLRLPSLESHSNSVAAHRPWTYIGVVGPPTEANFEATLARETLLTSEEAVIAAAA 112

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPA-ISSSADTNTSMWAQLTERERASIIG 201
           AEAVALA+AAVKVAKDAA +V  +NSAK ++KPA   S  DT+     Q TE ER  I+G
Sbjct: 113 AEAVALAKAAVKVAKDAARLVGKNNSAKSETKPASFLSGDDTSQFRRIQFTETERIGILG 172

Query: 202 DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRA 261
           DSV  E    +  S Q     S DLEPT EEL+LLE + S+SI VRS RQ ERKARR RA
Sbjct: 173 DSVGAETGMVDYNSLQDVTEDSDDLEPTLEELELLEAEFSKSIVVRSNRQVERKARRARA 232

Query: 262 AEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQD 321
           AEKA+A V+SV+SGSTSRRKR S+QEVDYSDPLRYLR TTS+SRLLTA EE++LS GIQD
Sbjct: 233 AEKASAGVVSVRSGSTSRRKRVSLQEVDYSDPLRYLRGTTSTSRLLTATEELELSEGIQD 292

Query: 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381
           LLKLE L+E L ER G  PTFAQWAAAAGVDQ+ LRRR NYGI CKDKMI SNIRLVISI
Sbjct: 293 LLKLEKLQEDLEERFGVKPTFAQWAAAAGVDQKTLRRRTNYGIRCKDKMIKSNIRLVISI 352

Query: 382 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441
           AKNYQGAGMN+QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI
Sbjct: 353 AKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 412

Query: 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQK 501
           RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL+AVLL+PKAPRSLDQK
Sbjct: 413 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLNAVLLTPKAPRSLDQK 472

Query: 502 IGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRM 561
           IGINQNLKPSEVIADP+AETAE+LLIK+FM+EDLEKVL++LNPRE+QV+RWR+GLEDGR 
Sbjct: 473 IGINQNLKPSEVIADPDAETAEELLIKQFMREDLEKVLNSLNPREKQVIRWRYGLEDGRT 532

Query: 562 KTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 604
           KTLQEIGELMGVSRERIRQIES AFRKLKNK+RTKHL QY ++
Sbjct: 533 KTLQEIGELMGVSRERIRQIESCAFRKLKNKRRTKHLQQYLVS 575

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  782 bits (2020), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 444/583 (76%), Positives = 490/583 (84%), Gaps = 7/583 (1%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLPQFKC PDTFS H +      H      K++E I FR  C LSTTSP  ST+ T 
Sbjct: 1   MSCLLPQFKCPPDTFSTHPKL-----HILCKSPKNREAIYFRVQCALSTTSPPLSTSTTA 55

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 142
           VLD+EKLRLPSLE+HSN+VAA+R WTY G VGP TE N   +LA ETL TS+EAVIAAA+
Sbjct: 56  VLDIEKLRLPSLESHSNSVAAHRPWTYIGVVGPPTEANFEATLARETLLTSEEAVIAAAA 115

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPA-ISSSADTNTSMWAQLTERERASIIG 201
           AEAVALA+AAVKVAKDAA +V  +NSAK ++KPA   S  DT+     Q TE ER  I+G
Sbjct: 116 AEAVALAKAAVKVAKDAARLVGKNNSAKSETKPASFLSGDDTSQFRRIQFTETERIGILG 175

Query: 202 DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRA 261
           DSV  E    +  S Q     S DLEPT EEL+LLE + S+SI VRS RQ ERKARR RA
Sbjct: 176 DSVGAETGMVDYNSLQDVTEDSDDLEPTLEELELLEAEFSKSIVVRSNRQVERKARRARA 235

Query: 262 AEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQD 321
           AEKA+A V+SV+SGSTSRRKR S+QEVDYSDPLRYLR TTS+SRLLTA EE++LS GIQD
Sbjct: 236 AEKASAGVVSVRSGSTSRRKRVSLQEVDYSDPLRYLRGTTSTSRLLTATEELELSEGIQD 295

Query: 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381
           LLKLE L+E L ER G  PTFAQWAAAAGVDQ+ LRRR NYGI CKDKMI SNIRLVISI
Sbjct: 296 LLKLEKLQEDLEERFGVKPTFAQWAAAAGVDQKTLRRRTNYGIRCKDKMIKSNIRLVISI 355

Query: 382 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441
           AKNYQGAGMN+QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI
Sbjct: 356 AKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 415

Query: 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQK 501
           RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL+AVLL+PKAPRSLDQK
Sbjct: 416 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLNAVLLTPKAPRSLDQK 475

Query: 502 IGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRM 561
           IGINQNLKPSEVIADP+AETAE+LLIK+FM+EDLEKVL++LNPRE+QV+RWR+GLEDGR 
Sbjct: 476 IGINQNLKPSEVIADPDAETAEELLIKQFMREDLEKVLNSLNPREKQVIRWRYGLEDGRT 535

Query: 562 KTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 604
           KTLQEIGELMGVSRERIRQIES AFRKLKNK+RTKHL QY ++
Sbjct: 536 KTLQEIGELMGVSRERIRQIESCAFRKLKNKRRTKHLQQYLVS 578

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 =  766 bits (1977), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 425/582 (73%), Positives = 486/582 (83%), Gaps = 18/582 (3%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNH-QHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMT 82
           MSCLLPQFKCQPDTFS+HFR L +H  +H+  P            CVLS+ SPST+    
Sbjct: 1   MSCLLPQFKCQPDTFSVHFRNLQHHGTNHTQLP-----------QCVLSSASPSTA---- 45

Query: 83  TVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTS-DEAVIAAA 141
            VLD+EKLRLPSLE HS++++ANR WTY G +GP  +   GTSLA ETL + DEAVIAAA
Sbjct: 46  -VLDLEKLRLPSLEPHSDSISANRPWTYIGGIGPQKKPPFGTSLAAETLIANDEAVIAAA 104

Query: 142 SAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIG 201
           +AEAVALARAAVKVAKDAA M  +++S K ++K  I+S+ D+ +SMW+ LTE+ERA IIG
Sbjct: 105 AAEAVALARAAVKVAKDAAEMAKNYSSMKKETKIPIASTTDSFSSMWSLLTEKERADIIG 164

Query: 202 DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRA 261
           DSV  E    EEYS Q P  +   LEPT EEL LL++Q+S+ IAVRS+RQTERKARR RA
Sbjct: 165 DSVSAETRLREEYSVQYPTEEYDCLEPTQEELALLQKQLSEGIAVRSKRQTERKARRARA 224

Query: 262 AEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQD 321
           AEKAAANV+SVKSGSTS++KR  +QEVD SDPLR+ R  +SSSRLL+A EE++LS GIQD
Sbjct: 225 AEKAAANVVSVKSGSTSKKKRVPLQEVDQSDPLRFFRGASSSSRLLSATEEVELSEGIQD 284

Query: 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381
           LLKLE + E L ER GG P+FAQWAAAAGVDQ  LR+RLNYGILCKDKMI SN+RLVISI
Sbjct: 285 LLKLERIEEELKERFGGEPSFAQWAAAAGVDQLTLRKRLNYGILCKDKMIKSNVRLVISI 344

Query: 382 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441
           AKNYQG GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD+SRTI
Sbjct: 345 AKNYQGTGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDRSRTI 404

Query: 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQK 501
           RLPFHMV+ATYRVKEARKQLYSENGRHP+++EVAEA GLSMKRL AVLL+PKAPRSLDQK
Sbjct: 405 RLPFHMVDATYRVKEARKQLYSENGRHPDDKEVAEAAGLSMKRLSAVLLTPKAPRSLDQK 464

Query: 502 IGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRM 561
           +G N +LK SEV ADPEAETAEDLL+K+FMK+DL KVL +L+PRE QVVRWRFG+EDGRM
Sbjct: 465 MGFNMDLKLSEVTADPEAETAEDLLMKEFMKKDLAKVLGSLSPRENQVVRWRFGMEDGRM 524

Query: 562 KTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603
           KTLQEIGELMGVSRER+RQIE SAFRKLKNK RTK L QY +
Sbjct: 525 KTLQEIGELMGVSRERVRQIELSAFRKLKNKNRTKQLRQYMV 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 =  751 bits (1939), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 411/582 (70%), Positives = 474/582 (81%), Gaps = 19/582 (3%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLPQFKCQPD+FSIH                + EP CFR  C LS+    + +  T 
Sbjct: 1   MSCLLPQFKCQPDSFSIH---------------SNGEPFCFRAQCALSSA---SPSTSTA 42

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLT-SDEAVIAAAS 142
           VL++EKLRLPSLE+HS+++AANR WTY G +GP  E   GTSLATETL  +DEAVIAAA+
Sbjct: 43  VLNLEKLRLPSLESHSDSIAANRPWTYIGGIGPPKEPLFGTSLATETLIINDEAVIAAAA 102

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 202
           AEAVALARAAVKVAKDAA M  ++ S   ++K  I+S+AD+ +SMW+ LT +ERA IIG 
Sbjct: 103 AEAVALARAAVKVAKDAAEMAKNYCSVNTETKIPIASTADSFSSMWSLLTGKERADIIGV 162

Query: 203 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 262
           S   E    EE S Q P  +S    PTHEEL LLE+Q+S+SI VRS+RQT+RKA+R RAA
Sbjct: 163 SFSAETGLREECSTQYPTEESDCFGPTHEELALLEKQLSESIVVRSKRQTQRKAKRARAA 222

Query: 263 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 322
           EKAAAN + +KSGS  ++KR  VQEVD SDPLR+ R  ++SSRLL+A EE++LS GIQDL
Sbjct: 223 EKAAANFVFMKSGSACKKKRVPVQEVDQSDPLRFFRGASTSSRLLSATEEVELSEGIQDL 282

Query: 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 382
           LKLE + E L ER GG PTFAQWAAAA VDQ  LR+RLNY ILCKDKMI SNIRLVISIA
Sbjct: 283 LKLERIEEELKERFGGKPTFAQWAAAARVDQITLRKRLNYAILCKDKMIKSNIRLVISIA 342

Query: 383 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR 442
           KNYQGAGMNLQDLVQEGCRGLVRG EKFDASKGFKFSTYAHWWI+QAVR+SLSDQSRTIR
Sbjct: 343 KNYQGAGMNLQDLVQEGCRGLVRGVEKFDASKGFKFSTYAHWWIRQAVRRSLSDQSRTIR 402

Query: 443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKI 502
           LPFHMV+ATYRVKEARKQ YSENGRHP+++EVAEATGLSMKRL AVLL+PKAPRSLDQK+
Sbjct: 403 LPFHMVDATYRVKEARKQFYSENGRHPDDKEVAEATGLSMKRLSAVLLTPKAPRSLDQKM 462

Query: 503 GINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMK 562
           G N +LK SEV ADPEAETAEDLL+K+FMK+DLE+VL++L+PRE QV+RWRFG+EDGRMK
Sbjct: 463 GFNMDLKLSEVTADPEAETAEDLLMKEFMKKDLERVLESLSPRENQVIRWRFGMEDGRMK 522

Query: 563 TLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 604
           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|7363218|emb|CAB83106.1| sigma factor 2 [Sinapis alba]

 Score =  728 bits (1878), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 386/586 (65%), Positives = 459/586 (78%), Gaps = 26/586 (4%)

Query: 25  SCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTV 84
           SCLLP FKCQPD+FS+HFRT ++   HS      K    F+  C +ST+ P     +T+ 
Sbjct: 3   SCLLPNFKCQPDSFSVHFRTSYSVSKHS------KGSAFFQPQCAVSTSPP----LLTST 52

Query: 85  LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAASA 143
           LDV KLRLPS +  S++  ++R WTY   +GPSTE     +LA+ETL TSDEAV+AAA+A
Sbjct: 53  LDVAKLRLPSFDTDSDSRISDRPWTYTRTIGPSTEAKYLEALASETLLTSDEAVVAAAAA 112

Query: 144 EAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIG-- 201
           EAVALARAA+KVAKDA L  N HN+     K ++SS+AD   S W Q TE+ERA I+G  
Sbjct: 113 EAVALARAALKVAKDATLFGNSHNT-----KLSVSSAADKR-SKWDQFTEKERAGILGHL 166

Query: 202 ---DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARR 258
              D+ +V        S +     S DL P  ++     E++S S AVRS RQTERKARR
Sbjct: 167 AVSDTGVVSDRITAPGSLECNKEASDDLTPAEKQEV---EKLSVSSAVRSTRQTERKARR 223

Query: 259 TRAAEKAAANVMS-VKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 317
            +  EK A+ + S VK+GS+SR+KR + QE+D++DPLRYLR TTSSS+LLTA EE QLS 
Sbjct: 224 VKGLEKTASGMQSSVKTGSSSRKKRVASQEIDHNDPLRYLRMTTSSSKLLTAREEQQLSE 283

Query: 318 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 377
           GIQDLLKLE L+  L+ERCG  PTF+QWA+AAGVD++ LR+R+ +G  CKD+MI SNIRL
Sbjct: 284 GIQDLLKLERLQAELTERCGHQPTFSQWASAAGVDKKTLRKRITHGTQCKDRMIKSNIRL 343

Query: 378 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 437
           VISIAKNYQGAGM+ QDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKSLSDQ
Sbjct: 344 VISIAKNYQGAGMDFQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQ 403

Query: 438 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRS 497
           SR IRLPFHMVEATYRVKEARKQLYSE G+ P NEEVAEATGLSMKRL AVLLSPK PRS
Sbjct: 404 SRMIRLPFHMVEATYRVKEARKQLYSETGKQPKNEEVAEATGLSMKRLMAVLLSPKPPRS 463

Query: 498 LDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLE 557
           LDQKIGIN NLKPSEVIADPEAET+ED+L+K+FM++DL+KVLD+L+ RE+QV+RWRFG+E
Sbjct: 464 LDQKIGINLNLKPSEVIADPEAETSEDILMKQFMRQDLDKVLDSLSTREKQVIRWRFGME 523

Query: 558 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603
           DGRMKTLQEIGE MGVSRER+RQI++SAFRKLKNKKR  HL QY +
Sbjct: 524 DGRMKTLQEIGETMGVSRERVRQIDTSAFRKLKNKKRNSHLQQYLV 569

Source: Sinapis alba

Species: Sinapis alba

Genus: Sinapis

Family: Brassicaceae

Order: Brassicales

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 =  726 bits (1873), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 394/583 (67%), Positives = 460/583 (78%), Gaps = 20/583 (3%)

Query: 25  SCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTV 84
           SCLLPQFKC PD+FSIHFRT    + H+      K  + F+  C +ST SP+    +T++
Sbjct: 3   SCLLPQFKCPPDSFSIHFRTSFCARKHN------KGSVFFQPQCAVST-SPAL---LTSM 52

Query: 85  LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAASA 143
           LDV KLRLPS +  S++  ++RQWTY    GPSTE     +LA+ETL TSDEAV+ AA+A
Sbjct: 53  LDVAKLRLPSFDTDSDSRISDRQWTYTRTDGPSTEAKYLEALASETLLTSDEAVVVAAAA 112

Query: 144 EAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDS 203
           EAVALARAAVKVAKDA L  N +N+        ISS+AD   S W Q TE+ERA I+G  
Sbjct: 113 EAVALARAAVKVAKDATLFKNSNNT-----NLLISSTADKR-SKWDQFTEKERAGILGHL 166

Query: 204 VIVEAAPEEEYSEQQPLNKSA--DLEPTHEELKLLEEQV-SQSIAVRSRRQTERKARRTR 260
            + +     +       NK +  DLE   +E   L E+  S S+AVRS RQTERKARR +
Sbjct: 167 AVSDNGIVSDKITAPASNKESPGDLESEKQEEVELLEEQPSVSLAVRSTRQTERKARRAK 226

Query: 261 AAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQ 320
             EK A+ + SVK+GS  R+KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSAGIQ
Sbjct: 227 GLEKTASGIPSVKTGSNPRKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSAGIQ 286

Query: 321 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 380
           DLLKLE L+  L+ERCG  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRLVIS
Sbjct: 287 DLLKLERLQTELTERCGRQPTFAQWASAAGVDQKSLRKRIHHGTLCKDKMIKSNIRLVIS 346

Query: 381 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 440
           IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKSLSDQSR 
Sbjct: 347 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQSRM 406

Query: 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQ 500
           IRLPFHMVEATYRVKEARKQLYSE G+HP NEE+AEATGLSMKRL AVLLSPK PRSLDQ
Sbjct: 407 IRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRSLDQ 466

Query: 501 KIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGR 560
           KIG+NQNLKPSEVIADPEA T+ED+LIK+FM++DL+KVLD+L  RE+QV+RWRFG+EDGR
Sbjct: 467 KIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGMEDGR 526

Query: 561 MKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603
           MKTLQEIGE+MGVSRER+RQIESSAFRKLKNKKR+ HL QY +
Sbjct: 527 MKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRSNHLQQYLV 569

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

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 =  721 bits (1861), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 391/586 (66%), Positives = 459/586 (78%), Gaps = 26/586 (4%)

Query: 25  SCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTV 84
           SCLLPQFKC PD+FSIHFRT          P  +K  + F+  C +ST SP+    +T++
Sbjct: 3   SCLLPQFKCPPDSFSIHFRT------SFCAPKHNKGSVFFQPQCAVST-SPAL---LTSM 52

Query: 85  LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAASA 143
           LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL TSDEAV+ AA+A
Sbjct: 53  LDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVVAAAA 112

Query: 144 EAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIG-- 201
           EAVALARAAVKVAKDA L  N +N+        ++SS     S W Q TE+ERA I+G  
Sbjct: 113 EAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGILGHL 166

Query: 202 ---DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTERKAR 257
              D+ IV        S ++ +    DLE   +E   L E+  S S+AVRS RQTERKAR
Sbjct: 167 AVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTERKAR 223

Query: 258 RTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 317
           R +  EK A+ + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSA
Sbjct: 224 RAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSA 283

Query: 318 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 377
           GIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRL
Sbjct: 284 GIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRL 343

Query: 378 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 437
           VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKSLSDQ
Sbjct: 344 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQ 403

Query: 438 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRS 497
           SR IRLPFHMVEATYRVKEARKQLYSE G+HP NEE+AEATGLSMKRL AVLLSPK PRS
Sbjct: 404 SRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRS 463

Query: 498 LDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLE 557
           LDQKIG+NQNLKPSEVIADPEA T+ED+LIK+FM++DL+KVLD+L  RE+QV+RWRFG+E
Sbjct: 464 LDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGME 523

Query: 558 DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603
           DGRMKTLQEIGE+MGVSRER+RQIESSAFRKLKNKKR  HL QY +
Sbjct: 524 DGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 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 =  719 bits (1857), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/583 (66%), Positives = 459/583 (78%), Gaps = 27/583 (4%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLP F C  DTF  H   L       +H SK++  +CF+  CVLS TSPST      
Sbjct: 1   MSCLLPHFNCHLDTFRTHPYAL------PTHLSKTRPNLCFQPQCVLSATSPST------ 48

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 142
           +L +EK +L +L+A S+    N  W Y  A       N  ++L+ E+L T++EAVI AA+
Sbjct: 49  LLSLEK-KL-ALDAPSDP---NTSWPYIAAA------NFKSTLSAESLLTNEEAVIVAAA 97

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMW-AQLTERERASIIG 201
           +EA+ALA+AA KVAKDAAL+V     A+ + K  +SS +D     W  Q+ E E    + 
Sbjct: 98  SEALALAKAAAKVAKDAALLVKKKPPAEAEYKSHVSSKSDDLLLKWFKQMEEVEDG--VA 155

Query: 202 DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRA 261
           +  +   A   E  +  P  + +DLEP+HEEL+ L+EQ+S SIAVRSRRQTERKA+R RA
Sbjct: 156 EESMGAGAEIMEGVDVSPSEEESDLEPSHEELERLQEQLSDSIAVRSRRQTERKAKRVRA 215

Query: 262 AEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQD 321
            EKA  N  S K GS+SRRKR S+QEVDYSDPLRYLR TTS+SRLLT  EE++LSAGIQD
Sbjct: 216 TEKATTNFTSFKPGSSSRRKRVSMQEVDYSDPLRYLRTTTSASRLLTPTEEIKLSAGIQD 275

Query: 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381
           LLKLE ++E L+ER G  PTFAQWAA AGVDQ+ LR+RLNYGI CKDKMI SNIRLVISI
Sbjct: 276 LLKLEKIQEDLAERFGSQPTFAQWAAVAGVDQKTLRKRLNYGIFCKDKMIKSNIRLVISI 335

Query: 382 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441
           AKNYQG+GMNLQDLVQEGCRGLV+GAEKFD +KGFKFSTYAHWWIKQAVRKSLSDQSRTI
Sbjct: 336 AKNYQGSGMNLQDLVQEGCRGLVKGAEKFDGTKGFKFSTYAHWWIKQAVRKSLSDQSRTI 395

Query: 442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQK 501
           RLPFHMVEATYRVKEARKQLYSENGR P++EEVAEATGLSMKRL+AVL++PKAPRSL+QK
Sbjct: 396 RLPFHMVEATYRVKEARKQLYSENGRQPDDEEVAEATGLSMKRLNAVLMTPKAPRSLEQK 455

Query: 502 IGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRM 561
           IGINQNLKPSEVI+DP+AETAE+ L+K+FMK+DLE+ LD+LNPRERQVVRWRFG++DGR 
Sbjct: 456 IGINQNLKPSEVISDPDAETAEEQLLKQFMKKDLEEALDSLNPRERQVVRWRFGMDDGRT 515

Query: 562 KTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT 604
           KTLQEIGE++GVSRERIRQIESSAF+KLKNKKRT HL QY ++
Sbjct: 516 KTLQEIGEMLGVSRERIRQIESSAFKKLKNKKRTNHLQQYLVS 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	605
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.932	0.986	0.594	1.7e-171
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.537	0.594	0.392	3.4e-61
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.598	0.632	0.344	5.7e-59
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.413	0.675	0.434	1.4e-58
TIGR_CMR|BA_4515	373	BA_4515 "RNA polymerase sigma-	0.388	0.630	0.468	7.8e-58
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.517	0.592	0.401	1.6e-54
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.413	0.773	0.432	1.6e-54
TIGR_CMR|DET_0551	520	DET_0551 "RNA polymerase sigma	0.383	0.446	0.443	1.8e-54
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.391	0.410	0.417	9.9e-52
TIGR_CMR|ECH_0760	622	ECH_0760 "RNA polymerase sigma	0.383	0.372	0.416	2e-51

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

 Score = 1667 (591.9 bits), Expect = 1.7e-171, P = 1.7e-171
 Identities = 346/582 (59%), Positives = 404/582 (69%)

Query:    25 SCLLPQFKCQPDTFSIHFRTLXXXXXXXXXXXXXKEPICFRTHCVLXXXXXXXXXXXXXV 84
             SCLLPQFKC PD+FSIHFRT              K  + F+  C +             +
Sbjct:     3 SCLLPQFKCPPDSFSIHFRT------SFCAPKHNKGSVFFQPQCAVSTSPALLTS----M 52

Query:    85 LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTXXXXXXXXXXXX 144
             LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL             
Sbjct:    53 LDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVVAAAA 112

Query:   145 XXXXXXXXXXXXXXXXXMVNHHNXXXXXXXXXXXXXXDTNTSMWAQLTERERASIIGDSV 204
                              +  + N                  S W Q TE+ERA I+G   
Sbjct:   113 EAVALARAAVKVAKDATLFKNSNNTNLLTSSTAD-----KRSKWDQFTEKERAGILGHLA 167

Query:   205 IVEAAPEEEYSEQQPLNKSA--DLEPT-HEELKLLEEQVSQSIAVRSXXXXXXXXXXXXX 261
             + +     +       NK +  DLE    EE++LLEEQ S S+AVRS             
Sbjct:   168 VSDNGIVSDKITASASNKESIGDLESEKQEEVELLEEQPSVSLAVRSTRQTERKARRAKG 227

Query:   262 XXXXXXNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQD 321
                    + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSAGIQD
Sbjct:   228 LEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSAGIQD 287

Query:   322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381
             LLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRLVISI
Sbjct:   288 LLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRLVISI 347

Query:   382 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI 441
             AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKSLSDQSR I
Sbjct:   348 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQSRMI 407

Query:   442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQK 501
             RLPFHMVEATYRVKEARKQLYSE G+HP NEE+AEATGLSMKRL AVLLSPK PRSLDQK
Sbjct:   408 RLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRSLDQK 467

Query:   502 IGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRM 561
             IG+NQNLKPSEVIADPEA T+ED+LIK+FM++DL+KVLD+L  RE+QV+RWRFG+EDGRM
Sbjct:   468 IGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGMEDGRM 527

Query:   562 KTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI 603
             KTLQEIGE+MGVSRER+RQIESSAFRKLKNKKR  HL QY +
Sbjct:   528 KTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 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:   277 TSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERC 336
             TS +K+   Q  D  D L+       + +LLTA EE +L + IQ LLKLE ++  L  + 
Sbjct:   219 TSAKKKYK-QGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQN 277

Query:   337 GGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLV 396
             G  PT  +WA A G+    L+  ++ G   ++K+IT+N+RLV+ IAK YQ  G+N QDL+
Sbjct:   278 GCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLL 337

Query:   397 QEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKE 456
             QEG  GL++  EKF    G +F+TYA+WWI+Q++RKS+   SRTIRLP ++     +V E
Sbjct:   338 QEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSE 397

Query:   457 ARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD 516
             ARK    E    P+ EE+A   G+S ++L  +L + + P S+ Q I  +Q+    E+  D
Sbjct:   398 ARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPD 457

Query:   517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRE 576
                ET    + K+ M+  +  +L+ L+P+ER++++ RFG++ G+ ++L EIGE+ G+S+E
Sbjct:   458 SGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKE 517

Query:   577 RIRQIESSAFRKLKNKKRTKHLMQYA 602
             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:   223 SADLEPTHEELKLLEEQVSQSIAVRSXXXXXXXXXXXXXXXXXXXNVMSVKSGSTSRRKR 282
             S D   ++EEL     Q    + VRS                   +V      S  + K 
Sbjct:   194 SVDSSKSNEEL-----QSKGQVFVRSTRLLERRSKRRYAPRASIADVSCSADNSKKKEKS 248

Query:   283 PSVQEV-DYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPT 341
                  V +  +P +       ++  LTA EE  L + IQ L+K+E     L  +CG  PT
Sbjct:   249 KKYGRVLEPDEPFKLFLRDRETTEFLTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPT 308

Query:   342 FAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCR 401
              A+WA A G+  +EL+  +  G  C++KM  SN RLVI +A+ Y+G G+++QDLVQ+GC 
Sbjct:   309 LAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCS 368

Query:   402 GLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 461
             GL++  EKF+ SKG +F TYA+WWI+Q+++KS+   SR IRLP  +     +V +AR + 
Sbjct:   369 GLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLPESVYALLRKVGKARMEC 428

Query:   462 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET 521
               E G  P N  VA   G+++++L  +    + PRS+   +  ++ +   E+  DP  E 
Sbjct:   429 IME-GEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSDEGVTFQEITEDPNVEP 487

Query:   522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI 581
              +  + +  M++ +   L  L+PRE++++  RFG+ DG  KTL  IG++ G+S+ERIRQ+
Sbjct:   488 PDLSVDRMMMRQQVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQL 547

Query:   582 ESSAFRKLK 590
             ++ 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:   352 DQRELRRRLNYGIL-CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 410
             ++ EL +R   G    K K+  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKF
Sbjct:   118 EEIELAKRKEEGDEEAKRKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKF 177

Query:   411 DASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN 470
             D  KG+KFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++    + L  E GR P 
Sbjct:   178 DYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPT 237

Query:   471 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF 530
              EE+A+  G+S  ++  ++   + P SL+  IG  ++    + + DP+A+   +      
Sbjct:   238 PEEIAKEMGISEDKVREIMKIAQEPVSLETPIGEEEDSHLGDFVEDPDAKAPVEEASYTL 297

Query:   531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
             ++E L++VL TL  RE++V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL+
Sbjct:   298 LREQLDEVLKTLTEREQKVLRLRFGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLR 357

Query:   591 NKKRTKHLMQY 601
             +  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:   367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426
             K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD  KGFKFSTYA WWI
Sbjct:   137 KRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWI 196

Query:   427 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 486
             +QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  + GR P+ EE+ E   L+ +++ 
Sbjct:   197 RQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGREPSPEEIGEEMDLAPEKVR 256

Query:   487 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 546
              +L   + P SL+  IG   +    + I D EA +  D    + +KE LE VLDTL  RE
Sbjct:   257 EILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPADHAAYELLKEQLEDVLDTLTDRE 316

Query:   547 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
               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:   279 RRKRPSVQEVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCG 337
             R+ R   +    +D +R YL+     + LL A EE++L+  I+  L    L   LSER  
Sbjct:   213 RQARKDAELTASADSVRAYLKQIGKVA-LLNAEEEVELAKRIEAGLYATQLMTELSERGE 271

Query:   338 GSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 397
               P  AQ        +R++      G   K+ ++ +N+RLV+S+AK Y G GM   DL+Q
Sbjct:   272 KLPA-AQ--------RRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQ 322

Query:   398 EGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEA 457
             EG  GL+R  EKFD +KG+KFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++   
Sbjct:   323 EGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRI 382

Query:   458 RKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP 517
             +++L  + GR P  EE+A+   ++ +++  +    + P SLDQ IG   + +  + I D 
Sbjct:   383 QRELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQLGDFIEDS 442

Query:   518 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRER 577
             EA  A D +    +++ L+ VLDTL+ RE  VVR RFGL DG+ +TL EIG++ GV+RER
Sbjct:   443 EAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRER 502

Query:   578 IRQIESSAFRKLKNKKRTKHLMQY 601
             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:   353 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA 412
             +R+L   +  G   +  ++ +N+RLV+S+AK Y G GM L DL+QEG  GL+R  EKFD 
Sbjct:    73 KRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 132

Query:   413 SKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNE 472
             +KGFKFSTYA WWI+QA+ + ++DQSRTIRLP H+VE   ++   +++++   GR   +E
Sbjct:   133 TKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDE 192

Query:   473 EVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMK 532
             E+A  +G+ + +++ +L   + P SLD  +G  +     + I D EA +AE+ +I + + 
Sbjct:   193 ELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSAENAVIAELLH 252

Query:   533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
              D+  VL TL+ RE QV+R RFGL+DG+ +TL +IG+L G+SRER+RQIE     KL++ 
Sbjct:   253 TDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLRHG 312

Query:   593 KRTKHLMQYA 602
             +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:   370 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 429
             +I +N+RLV+S+AK + G GM L DL+QEG  GL+R  EKFD  +GFKFSTYA WWI+QA
Sbjct:   287 LIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWWIRQA 346

Query:   430 VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 489
             + ++++DQ+RTIR+P HMVE   ++    +QL  + GR P  +E+A    L  +++  + 
Sbjct:   347 ITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIAVEMDLPPEKVREIA 406

Query:   490 LSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQV 549
                + P SL+  IG  ++    + I D  A    D   ++ +KE ++ VL +L PRER+V
Sbjct:   407 KVSQLPVSLESPIGEEEDSHLGDFIEDQNALAPPDAASRQLLKEQIDTVLGSLTPRERRV 466

Query:   550 VRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
             ++ 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:   365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHW 424
             L K +++ +N+RLV+SIAK Y   G+   DL+QEG  GL++  +KF+  +G+KFSTYA W
Sbjct:   339 LAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATW 398

Query:   425 WIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKR 484
             WI+QA+ ++++DQ+RTIR+P HM+E   ++    +QL  E GR P+ EE+AE   L + +
Sbjct:   399 WIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPEEIAERMNLPLDK 458

Query:   485 LHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNP 544
             +  VL   K P SL+  IG  ++    + I D    +  + +IK  + E   +VL TL P
Sbjct:   459 VRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKANLSEQTARVLATLTP 518

Query:   545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
             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:   367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426
             K +MI +N+RLV+SIAK Y   G+   DLVQEG  GL++  +KFD  +G+KFSTYA WW+
Sbjct:   386 KQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWWV 445

Query:   427 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 486
             +QA+ ++++DQ+RTIR+P HM+E   ++    +Q+  E GR P  EE++    +++ ++ 
Sbjct:   446 RQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEMGREPTLEELSARLNINVDKIR 505

Query:   487 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 546
              V+   K P SL+  IG + +    + I D  A   ED  +   ++E   KVL TL P+E
Sbjct:   506 KVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPEDAAVLADLREITTKVLSTLTPKE 565

Query:   547 RQVVRWRFGL-EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 598
              +++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	0.6672	0.9256	0.9790	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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	605
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	1e-103
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	1e-102
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	3e-92
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	2e-81
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	4e-81
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	4e-78
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-77
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	4e-75
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	6e-72
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	7e-70
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	1e-62
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	1e-60
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	5e-49
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	1e-31
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	5e-31
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	9e-28
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	6e-26
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	2e-24
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	5e-24
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	1e-22
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	2e-21
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	5e-20
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	4e-19
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	5e-19
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	1e-18
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	3e-18
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	2e-17
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	3e-16
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	5e-16
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	3e-15
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	1e-14
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	5e-14
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	1e-13
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	1e-13
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	1e-13
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	8e-12
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	4e-11
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	2e-10
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	2e-10
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	4e-10
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	1e-09
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	3e-09
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	2e-08
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	3e-08
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	4e-08
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	7e-08
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	1e-05
COG1595	182	COG1595, RpoE, DNA-directed RNA polymerase special	3e-04
COG2771	65	COG2771, CsgD, DNA-binding HTH domain-containing p	0.002
smart00421	58	smart00421, HTH_LUXR, helix_turn_helix, Lux Regulo	0.002

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

 Score =  313 bits (805), Expect = e-103
 Identities = 133/300 (44%), Positives = 203/300 (67%), Gaps = 3/300 (1%)

Query: 292 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAG 350
           D +R YL+       LLT  EE++L+  +Q ++ LE LRE L E+ G  P+  +WAAAAG
Sbjct: 1   DLVRLYLQ-EIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAG 59

Query: 351 VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 410
           + + ELR+RL  G   K+KMI +N+RLV+S+AK YQ  G+ L DL+QEG  GL R  EKF
Sbjct: 60  LSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKF 119

Query: 411 DASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN 470
           D ++G+KFSTYA+WWI+Q + +++++QSRTIRLP H+ E   ++K+ +++L  + GR P+
Sbjct: 120 DPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPS 179

Query: 471 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF 530
             E+AEA  L  +++  +L   + P SLD  +G  ++ +  +++ D   E+ E+ + ++ 
Sbjct: 180 EAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDD-GESPEEQVERES 238

Query: 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           +++DLE +L  L PRERQV+R RFGL+ G   TL EIG  + +SRER+RQIE+ A RKL+
Sbjct: 239 LRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 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 =  315 bits (809), Expect = e-102
 Identities = 153/383 (39%), Positives = 220/383 (57%), Gaps = 12/383 (3%)

Query: 219 PLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTS 278
                 +L    E+ +        S                + A+  A            
Sbjct: 1   TPELEDELLLLEEDRQPAATDDLDSDEDEESSSENADELSEKEAKAKA-----------L 49

Query: 279 RRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGG 338
            R +   ++V   D +R         RLL  +EE++L+  I DLL+LE LRE      G 
Sbjct: 50  ARIKIGPKKVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGR 109

Query: 339 SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQE 398
            P+  +WA    +   + RRRL  G   K+KM+ SN+RLV+SIAK Y   G++ QDL+QE
Sbjct: 110 EPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQE 169

Query: 399 GCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEAR 458
           G  GL+R AEKFD  KG+KFSTYA WWI+QA+ ++++DQSRTIRLP H+ E   R+K+  
Sbjct: 170 GSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTT 229

Query: 459 KQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE 518
           K L  E GR P  EE+AE+  +++++L  +  S + P SL+  IG  ++ +  + I + +
Sbjct: 230 KVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI-EAD 288

Query: 519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERI 578
            ET ED + K  ++EDLE VL TL+PRER V+R R+GL+DGRMKTL+EIG++  V+RERI
Sbjct: 289 GETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERI 348

Query: 579 RQIESSAFRKLKNKKRTKHLMQY 601
           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 =  283 bits (726), Expect = 3e-92
 Identities = 105/235 (44%), Positives = 160/235 (68%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426
           K +++ SN+RLV+SIAK Y   G++  DL+QEG  GL++  EKFD  KG+KFSTYA WWI
Sbjct: 2   KKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWI 61

Query: 427 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 486
           +QA+ ++++DQ+RTIR+P HMVE   ++ +A +QL  E GR P +EE+AE  G+  +++ 
Sbjct: 62  RQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVR 121

Query: 487 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 546
            +    + P SL+  IG  ++    + I D   E+ +D   K+ ++E L++VL+TL  RE
Sbjct: 122 EIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTERE 181

Query: 547 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
            +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 =  258 bits (662), Expect = 2e-81
 Identities = 127/304 (41%), Positives = 198/304 (65%), Gaps = 3/304 (0%)

Query: 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAA 349
           +D +R YLR       LLT  EE+     +Q L+ L+ +RE L+E  G  PT A+WA AA
Sbjct: 7   TDLVRTYLREIGRVP-LLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAA 65

Query: 350 GVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 409
            + + ELR  +  G   K KM+ +N+RLV+S+AK Y    ++L DL+QEG  G+ RG EK
Sbjct: 66  KLSEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEK 125

Query: 410 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 469
           FD +KG++FSTYA+WWI+QA+ ++++++SRTIRLP H+ E   ++K+A++QL  + GR  
Sbjct: 126 FDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAA 185

Query: 470 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 529
              E+AE   L+ K++   L   + P SLD ++G NQ+ +  E++ D    + ED   + 
Sbjct: 186 TIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT-GASPEDFATQS 244

Query: 530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 589
            ++ DLE++++ L P++++V+  RFGLEDG+  TL +IGE + +SRER+RQIE  A  KL
Sbjct: 245 SLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKL 304

Query: 590 KNKK 593
           + +K
Sbjct: 305 RKRK 308

Length = 317

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

 Score =  258 bits (662), Expect = 4e-81
 Identities = 127/319 (39%), Positives = 188/319 (58%), Gaps = 22/319 (6%)

Query: 305 RLLTANEEMQLSAGIQDLLKLEGLREVL-SERCGGSPTFAQWAAAAGVDQ---------- 353
            LL    E++L+  ++D   L  L E L   + G  P+      A  +            
Sbjct: 22  PLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPL 81

Query: 354 ------RELRRRLNYGIL---CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLV 404
                 + L RRL  G      K K++ SN+RLV+SIAK Y G G+   DL+QEG  GL+
Sbjct: 82  LTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLM 141

Query: 405 RGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSE 464
           +  EKFD  KGFKFSTYA WWI+QA+ ++++DQ+RTIR+P H VE   +++  +++L  E
Sbjct: 142 KAVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQE 201

Query: 465 NGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED 524
            GR P  EE+AE  G+S  ++  +L     P SLD  IG +++ +  + + D ++ + ED
Sbjct: 202 LGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDEDSELGDFLEDDKSVSPED 261

Query: 525 LLIKKFMKEDLEKVLDT-LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583
            + ++ +KEDL +VL   L  RER+V+R RFGL+DG  KTL+E+GE  G+SRER+RQIE+
Sbjct: 262 AVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEA 321

Query: 584 SAFRKLKNK-KRTKHLMQY 601
            A RKL+   +R+  L  Y
Sbjct: 322 KALRKLRRHPERSALLRSY 340

Length = 342

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

 Score =  250 bits (639), Expect = 4e-78
 Identities = 122/301 (40%), Positives = 185/301 (61%), Gaps = 21/301 (6%)

Query: 306 LLTANEEMQLS----AGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 361
           LLTA +E++L+    AG+     LE  + +   R                 +R+L   + 
Sbjct: 40  LLTAADEVELAKRIEAGLYAEHLLETRKRLSEAR-----------------KRDLAAVVR 82

Query: 362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTY 421
            G   +  ++ +N+RLV+S+AK Y G GM L DL+QEG  GL+R  EKFD +KGFKFSTY
Sbjct: 83  DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTY 142

Query: 422 AHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLS 481
           A WWI+QA+ + ++DQSRTIRLP H+VE   ++   +++L+ + GR   +EE+AE +G+ 
Sbjct: 143 ATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIP 202

Query: 482 MKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT 541
            +++  +L   + P SLD  +G ++     + I D EA +AE+ +I   +  D+  VL T
Sbjct: 203 EEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLAT 262

Query: 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
           L+ RE+QV+R RFGL+DG+ +TL +IG+L G+SRER+RQIE     KL+N +R   L  Y
Sbjct: 263 LDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322

Query: 602 A 602
           A
Sbjct: 323 A 323

Length = 324

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

 Score =  254 bits (652), Expect = 1e-77
 Identities = 144/491 (29%), Positives = 237/491 (48%), Gaps = 56/491 (11%)

Query: 124 TSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADT 183
           + +  +T  + E+ I     +  A A AA   AK         +S K + K A+    D 
Sbjct: 60  SGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLK-DELDSSKKAEKKNALDKDDDL 118

Query: 184 NTSMWAQLTE--RERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVS 241
           N      +     +      D  + +   +++  ++       D +   E+ +  E +  
Sbjct: 119 NYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKEL 178

Query: 242 QSIAVRSRRQTE-------RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPL 294
           + ++       +       R+AR+       A                         DP+
Sbjct: 179 EKLSDDDDFVWDEDDSEALRQARKDAKLTATA-------------------------DPV 213

Query: 295 R-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 353
           + YL+      +LL A EE++L+  I+      GL        G               +
Sbjct: 214 KAYLK-QIGKVKLLNAEEEVELAKRIE-----AGLYAEELLAEGEKLDPEL--------R 259

Query: 354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
           R+L+     G   K+ ++ +N+RLV+S+AK Y   G++  DL+QEG  GL++  EKFD +
Sbjct: 260 RDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYT 319

Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEE 473
           KG+KFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++    ++L  E GR P  EE
Sbjct: 320 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEE 379

Query: 474 VAEATGLSMKRLHAVLLSPK---APRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF 530
           +A+  G + ++   V    K    P SLD+ IG   + +  + I D EA +  D +    
Sbjct: 380 LAKEMGFTPEK---VREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTL 436

Query: 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           +++ L++VL+TL+ RE  V+R RFGL DG+ KTL EIG++ GV+RERIRQIES   RKL+
Sbjct: 437 LQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496

Query: 591 NKKRTKHLMQY 601
           +  R++ L  +
Sbjct: 497 HPSRSQVLRDF 507

Length = 509

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

 Score =  243 bits (623), Expect = 4e-75
 Identities = 110/235 (46%), Positives = 157/235 (66%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426
           K ++  +N+RLV+SIAK Y G GM   DL+QEG  GL++  EKFD  KGFKFSTYA WWI
Sbjct: 131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWI 190

Query: 427 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 486
           +QA+ ++++DQ+RTIR+P HMVE   ++   ++QL  E GR P  EE+AE   +  +++ 
Sbjct: 191 RQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVR 250

Query: 487 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 546
            +L   + P SL+  IG   +    + I D +A +  D    + +KE LE VLDTL  RE
Sbjct: 251 EILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDRE 310

Query: 547 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
             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 =  233 bits (597), Expect = 6e-72
 Identities = 110/288 (38%), Positives = 184/288 (63%), Gaps = 1/288 (0%)

Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
           LLT  +E+     +Q ++ L   +E L+++ G  P+  +WA A  + + EL++ L  G  
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
            K KMI +N+RLV++IAK YQ   M   DL+QEG  GL RG EKFD ++G+KFSTYA+WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 426 IKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL 485
           I+QA+ ++++ Q+RTIRLP H+ E   ++K+ +++L  + GR     E+A+   L   ++
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQI 211

Query: 486 HAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPR 545
              L   + P SLD ++G NQ+ + SE++ D E  + +  + ++ +++DL  +L  L P+
Sbjct: 212 REYLSMARQPISLDVRVGDNQDTELSELLED-EGPSPDQYITQELLRQDLNNLLAELTPQ 270

Query: 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK 593
           +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 =  231 bits (591), Expect = 7e-70
 Identities = 119/331 (35%), Positives = 195/331 (58%), Gaps = 33/331 (9%)

Query: 295 RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQR 354
           RY++       ++ AN   +    I+  L+L  +RE L+   G  P+  +WA  A +   
Sbjct: 89  RYMKL------IVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADISLA 142

Query: 355 ELRRRLNY----------------------GILCKDKMITSNIRLVISIAKNYQGAGMNL 392
           +L+  L                        G+  K+ MI +N+RLV+S+AK YQ  G+ L
Sbjct: 143 DLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLEL 202

Query: 393 QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY 452
            DLVQEG  GL R  EKFD +KG++FSTYA+WWI+Q + ++++ QSRTIRLP H+ E   
Sbjct: 203 LDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLN 262

Query: 453 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR--SLDQKIGINQNLKP 510
           ++K+A++++  E GR P  E++A+   ++  ++  VLL  + PR  SL+ K+G +++ + 
Sbjct: 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL--RVPRSVSLETKVGKDKDTEL 320

Query: 511 SEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGEL 570
            +++ + +  + E++L+++ ++ DL+ +L  L  RER V+R RFGL DG   +L EIG  
Sbjct: 321 GDLL-ETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRA 379

Query: 571 MGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
           + +SRER+RQIES A +KL+  KR   +  Y
Sbjct: 380 LDLSRERVRQIESKALQKLRQPKRRNRIRDY 410

Length = 415

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

 Score =  217 bits (556), Expect = 1e-62
 Identities = 103/235 (43%), Positives = 153/235 (65%), Gaps = 6/235 (2%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQ--DLVQEGCRGLVRGAEKFDASKGFKFSTYAHW 424
           K +M+ +N+RLVISIAK Y   G  LQ  DL+QEG  GL++  +KF+  +G+KFSTYA W
Sbjct: 382 KKEMVEANLRLVISIAKKYTNRG--LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 439

Query: 425 WIKQAVRKSLSDQSRTIRLPFHMVEATYR-VKEARKQLYSENGRHPNNEEVAEATGLSMK 483
           WI+QA+ +S++DQ+RTIR+P HM+E   +  + +R Q+  E GR P  EE+AE  G+   
Sbjct: 440 WIRQAITRSIADQARTIRIPVHMIETINKLNRISR-QMLQEIGREPTPEELAERLGMPED 498

Query: 484 RLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLN 543
           ++  VL   K P SL+  IG +++    + I D  AE   D  I++ ++E    VL +L 
Sbjct: 499 KVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

Query: 544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 598
           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 =  203 bits (517), Expect = 1e-60
 Identities = 88/225 (39%), Positives = 138/225 (61%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426
           +  MI SN+RLV+SIAK+Y   G+ L DL++EG  GL+   EKFD  +GF+FSTYA WWI
Sbjct: 48  RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWI 107

Query: 427 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 486
           +Q + +++ +Q+RTIRLP H+++       A +QL  + GR P+ EE+AE     ++ + 
Sbjct: 108 RQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVS 167

Query: 487 AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRE 546
            VL   +   SLD  +  + +    + IAD ++   E L+    +K+ +E  L  LN R+
Sbjct: 168 RVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQ 227

Query: 547 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591
           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 =  172 bits (439), Expect = 5e-49
 Identities = 84/222 (37%), Positives = 133/222 (59%)

Query: 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ 428
           +MI SN+RLV+ IAK Y   G+ L DL++EG  GL+R  EKFD  +GF+FSTYA WWI+Q
Sbjct: 90  RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 149

Query: 429 AVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAV 488
            + +++ +Q+RTIRLP H+V+       A ++L  +    P+ EE+AE     +  +  +
Sbjct: 150 TIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRM 209

Query: 489 LLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQ 548
           L   +   SLD  +G +      +++AD +    ED      MK+ + K L  LN ++R+
Sbjct: 210 LALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQRE 269

Query: 549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           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 =  123 bits (310), Expect = 1e-31
 Identities = 75/253 (29%), Positives = 129/253 (50%), Gaps = 16/253 (6%)

Query: 346 AAAAGVDQRELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAG-MNLQDLVQEGCR 401
            A   + + E  + L Y   G     ++I   + LV SIA+ ++  G     DL+Q G  
Sbjct: 1   NAPQPLSKEEEEKLLEYYAEGDEEARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMI 60

Query: 402 GLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL 461
           GL++  E++D SKG KFSTYA   I+  +   L     ++++P  + E   R++EA  +L
Sbjct: 61  GLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDEL 119

Query: 462 YSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIADPEA 519
             E GR P +EE+AE  G+  +     LL+       SLD+ +     LK  +   D + 
Sbjct: 120 EQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDV-----LKDDDDDVDDQI 174

Query: 520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIR 579
           E  +D + K+ + E L++ ++ L  RE+ V+  R+  E     T +EI E++G+S  R+ 
Sbjct: 175 ENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE----LTQKEIAEVLGISESRVS 230

Query: 580 QIESSAFRKLKNK 592
           ++   A +KL+ +
Sbjct: 231 RLHKKAIKKLRKE 243

Length = 247

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

 Score =  120 bits (303), Expect = 5e-31
 Identities = 72/232 (31%), Positives = 120/232 (51%), Gaps = 19/232 (8%)

Query: 368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 427
           +K++  N+ LV SIA+ ++  G   +DLVQ G  GLV+  ++FD S G KFST+A   I 
Sbjct: 6   EKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIM 65

Query: 428 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHA 487
             +++   D +  +R+P  + E   ++ +A ++L    GR P   E+AE  G+S + +  
Sbjct: 66  GEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEVVE 125

Query: 488 VLLSPKA--PRSLDQKIGINQNLKPSEVI-----ADPEAETAEDLLIKKFMKEDLEKVLD 540
            L +  A    SLD  I  + +  P  ++      D   ET ED       +  L+ +L 
Sbjct: 126 ALEAGNAYQALSLDASIE-DDDGDPIALLDTLGDEDDALETVED-------RLALKPLLA 177

Query: 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
            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 =  112 bits (283), Expect = 9e-28
 Identities = 75/242 (30%), Positives = 126/242 (52%), Gaps = 31/242 (12%)

Query: 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQ 428
           ++I++++RLVIS+A  ++  G+ + DL+QEG  GL+  A +F+  +  +FSTYA WWI+ 
Sbjct: 44  RIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRA 103

Query: 429 A-----------VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA 477
           +           VR   S   +   L F++     R+ +A ++L     +   + E+A A
Sbjct: 104 SIQDYILRNWSIVRGGTSSAQKA--LFFNLRRLRARLAQADEEL----TKQEIHREIATA 157

Query: 478 TGLSMK-------RLHAVLLSPKAPRSLDQKIGINQ--NLKPSEVIADPEAETAEDLLIK 528
            G+S+        RL     S  AP+S + +    +   L     + D   E  E  +  
Sbjct: 158 LGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPD---EQVESSIDG 214

Query: 529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 588
           +  +  L + L TLN RE +++R R   EDG   TL+ +GE +G+S+ER+RQIE+ A  K
Sbjct: 215 ERRRRWLTQALQTLNERELRIIRERRLREDGA--TLEALGEELGISKERVRQIEARALEK 272

Query: 589 LK 590
           L+
Sbjct: 273 LR 274

Length = 289

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

 Score =  105 bits (265), Expect = 6e-26
 Identities = 65/214 (30%), Positives = 111/214 (51%), Gaps = 22/214 (10%)

Query: 388 AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV----RKSLSDQSRTIRL 443
           + + L DL+Q G  GL+   E++D S+G KF TYA   I+ A+    R+ L    R++R 
Sbjct: 22  SSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRR-LDWVPRSLRQ 80

Query: 444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR--SLDQK 501
               +E       A ++L +  GR P  EE+AE  G+ +K     L    A    SLD+ 
Sbjct: 81  KARKLE------RAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDEL 134

Query: 502 IGINQNL-KPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVV--RWRFGLED 558
           +    +     + I D ++E  E+ L ++ ++E L + +++L+ RE+ V+   +   L  
Sbjct: 135 LESGDDGGSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQLVLSLYYYEEL-- 192

Query: 559 GRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
                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 =  102 bits (255), Expect = 2e-24
 Identities = 73/243 (30%), Positives = 127/243 (52%), Gaps = 15/243 (6%)

Query: 352 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 410
           + REL  R+  G    ++K+I  N+RLV+S+ + +   G  + DL Q GC GL++  + F
Sbjct: 20  EMRELFIRMQSGDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNF 79

Query: 411 DASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN 470
           D S+  KFSTYA   I   +R+ L D +  IR+   + +  Y+  + R +L SEN + P 
Sbjct: 80  DLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDKLISENSKEPT 138

Query: 471 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV---IADPEAETAEDLLI 527
             E+A+   +  + +   L + + P SL + I  N    P  V   I+D E       L 
Sbjct: 139 VSEIAKELKVPQEEVVFALDAIQDPVSLFEPI-YNDGGDPIYVMDQISD-EKNKDSQWLE 196

Query: 528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 587
              +KE +++    LN RE+ ++  RF   +G  KT  E+ E +G+S+ ++ ++E +A +
Sbjct: 197 GIALKEAMKR----LNEREKMILNMRF--FEG--KTQMEVAEEIGISQAQVSRLEKAALK 248

Query: 588 KLK 590
            ++
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 =  100 bits (251), Expect = 5e-24
 Identities = 71/227 (31%), Positives = 123/227 (54%), Gaps = 12/227 (5%)

Query: 368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 427
           DK+I  N+RLV SI K +   G   +DL Q GC GLV+  +KFD S   KFSTYA   I 
Sbjct: 14  DKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIM 73

Query: 428 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHA 487
             +++ L D    I++   + E   +++  +++L  E GR P   E+AEA G+S + +  
Sbjct: 74  GEIKRFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVM 132

Query: 488 VLLSPKAPRSLDQKIGINQN--LKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPR 545
            L S ++P+SL   +  +    +   + IAD  +E  +   ++K     L++ +  L+ R
Sbjct: 133 ALESARSPQSLYDTVHQDDGDPIYLLDQIADKGSE--DSDWLEKIA---LKEAISKLDER 187

Query: 546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
           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 = 97.0 bits (242), Expect = 1e-22
 Identities = 63/201 (31%), Positives = 100/201 (49%), Gaps = 10/201 (4%)

Query: 393 QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY 452
            DL   G  GL    EKFD S+  KF TYA + I+ A+   L  +     LP  M E T 
Sbjct: 53  DDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW---LPRSMREKTK 109

Query: 453 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR--SLDQKIGINQNLK- 509
           +V+ A ++L     R+   +EVA   G++ + + A +         S+D+K     + + 
Sbjct: 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGEN 169

Query: 510 PSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGE 569
            S  I D +  T E+ L+K+ + E+L + +  L+ +E+ V+   +  E     TL EIG+
Sbjct: 170 VSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEE----LTLTEIGQ 225

Query: 570 LMGVSRERIRQIESSAFRKLK 590
           ++ +S  RI QI S A  KLK
Sbjct: 226 VLNLSTSRISQIHSKALFKLK 246

Length = 251

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

 Score = 93.9 bits (234), Expect = 2e-21
 Identities = 75/243 (30%), Positives = 131/243 (53%), Gaps = 15/243 (6%)

Query: 353 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 411
            REL  R+  G    ++K+I  N+RLV+S+ + +   G N+ DL Q GC GL++  + FD
Sbjct: 24  MRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFD 83

Query: 412 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNN 471
            S+  KFSTYA   I   +R+ L D +  IR+   + +  Y+  + R++L +EN + P  
Sbjct: 84  LSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTV 142

Query: 472 EEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV---IADPEAETAEDLLIK 528
           EE+A+   +  + +   L + + P SL + I  +    P  V   I+D E    E+ L +
Sbjct: 143 EEIAKELEVPREEVVFALDAIQDPVSLFEPI-YHDGGDPIYVMDQISD-EKNKDENWLEE 200

Query: 529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 588
             +KE ++K    LN RE+ ++  RF    G  KT  E+ E +G+S+ ++ ++E +A + 
Sbjct: 201 IALKEAMKK----LNDREKLILNLRF--FQG--KTQMEVAEEIGISQAQVSRLEKAALKH 252

Query: 589 LKN 591
           ++ 
Sbjct: 253 MRK 255

Length = 258

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

 Score = 89.3 bits (222), Expect = 5e-20
 Identities = 62/225 (27%), Positives = 121/225 (53%), Gaps = 10/225 (4%)

Query: 368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 427
           D ++  N+RLV S+ + +   G    DL Q GC GL++  +KFD S   KFSTYA   I 
Sbjct: 35  DTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMII 94

Query: 428 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHA 487
             +++ L D   T+++   + E   ++++ + +L  E GR P  EE+AE  G++ + +  
Sbjct: 95  GEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVL 153

Query: 488 VLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRER 547
              + ++P+S+ +   +++N      + D  A+ +E+     F K  L++ +  L+ RER
Sbjct: 154 AQEASRSPQSIHET--VHENDGDPITLLDQIADQSEE---DWFDKIALKEAIRELDERER 208

Query: 548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
            +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 = 81.5 bits (202), Expect = 4e-19
 Identities = 29/71 (40%), Positives = 44/71 (61%)

Query: 370 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA 429
           ++   + LV S+A+ Y G G + +DLVQEG  GL+R  E+FD  +G  FST+ +  I+ A
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 430 VRKSLSDQSRT 440
           +  +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 = 87.0 bits (216), Expect = 5e-19
 Identities = 62/208 (29%), Positives = 111/208 (53%), Gaps = 18/208 (8%)

Query: 393 QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAV---RKSLSDQSRTIRLPFHMVE 449
            DLV  G  GL+   EKFD  +  KF TYA   I+ A+    +S+    R++R     +E
Sbjct: 62  DDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRSVRQKARQIE 121

Query: 450 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL--LSPKAPRSLDQ-KIGINQ 506
               + EAR       GR P++EE+A+  G+S++  +++L  LS  +  SL+    G ++
Sbjct: 122 RAIAMLEARL------GRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDE 175

Query: 507 NLKPS--EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTL 564
             + S  + +  P A   +++  ++ +K  + + + TL  RE++V+   +  ED    TL
Sbjct: 176 GDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYY-YED---LTL 231

Query: 565 QEIGELMGVSRERIRQIESSAFRKLKNK 592
           +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 = 85.4 bits (212), Expect = 1e-18
 Identities = 60/191 (31%), Positives = 103/191 (53%), Gaps = 17/191 (8%)

Query: 391 NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA 450
             +DLVQ G  GL+R  E+FD SKG  FS++A  +I+  ++  L D+S T+R+P    E 
Sbjct: 52  PYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQEL 111

Query: 451 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNL 508
             + K+ R++L  E GR P ++E+A+A  +S++    + L+   + P SLD  +  +++ 
Sbjct: 112 QRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDG 171

Query: 509 KPS--EVIADPEAETAEDLLIKKFMKED---LEKVLDTLNPRERQVVRWRFGLEDGRMKT 563
             S  +++ DP           +  +ED   L++ L  L  R R+V+ + F L D    T
Sbjct: 172 STSLGDLLPDPRYR------SFQLAQEDRIRLQQALAQLEERTREVLEFVF-LHD---LT 221

Query: 564 LQEIGELMGVS 574
            +E  E +G+S
Sbjct: 222 QKEAAERLGIS 232

Length = 256

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

 Score = 83.7 bits (208), Expect = 3e-18
 Identities = 64/217 (29%), Positives = 108/217 (49%), Gaps = 29/217 (13%)

Query: 387 GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ-------SR 439
            A ++L DL+Q G  GL+  A ++D  +G  F TYA     Q +R ++ D+        R
Sbjct: 33  PASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYA----GQRIRGAMLDELRSLDWVPR 88

Query: 440 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPR--S 497
           ++R     V       +A +QL  E GR P + EVAE  GLS++    +LL     +  S
Sbjct: 89  SVRRNAREVA------QAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFS 142

Query: 498 LDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVR--WRFG 555
           +D+  G + +     V  D + E     L  + ++E L + +++L  RE+ V+   ++  
Sbjct: 143 IDELRGEHGD--SILVTEDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEE 200

Query: 556 LEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
           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 = 76.5 bits (189), Expect = 2e-17
 Identities = 26/78 (33%), Positives = 48/78 (61%)

Query: 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL 508
           E   ++K A+++L  E GR P  EE+AE  G+S +++  VL + + P SLD  +G  ++ 
Sbjct: 1   ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDG 60

Query: 509 KPSEVIADPEAETAEDLL 526
           +  +++ 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|218139 pfam04545, Sigma70_r4, Sigma-70, region 4

 Score = 72.5 bits (179), Expect = 3e-16
 Identities = 29/54 (53%), Positives = 37/54 (68%), Gaps = 4/54 (7%)

Query: 538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591
            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|235644 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed

 Score = 78.1 bits (192), Expect = 5e-16
 Identities = 69/236 (29%), Positives = 108/236 (45%), Gaps = 22/236 (9%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGM----NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 422
           +D +I   + LV ++A     +GM      +DL   G  GLVR  E+FD  K  +F  YA
Sbjct: 25  RDVLIEFYLPLVKNVAHRL-ISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYA 83

Query: 423 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM 482
            + IK A+   L  Q     +P  + +   ++ +A   L    G+ P + E+ E   +S 
Sbjct: 84  LFLIKAAIIDDLRKQD---WVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQ 140

Query: 483 KRLH--------AVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKED 534
           + L         A++LS                L+  E IAD  AET  D++ KK     
Sbjct: 141 QELSGWFSSARPALILSLNEEFPCQSDDEAGLALE--ERIADERAETGYDVVDKKEFSSI 198

Query: 535 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           L + +  L  +ER+V+   +  E      L+EIG+++GVS  R+ QI S A  KL+
Sbjct: 199 LAEAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKLR 250

Length = 257

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

 Score = 75.7 bits (186), Expect = 3e-15
 Identities = 62/230 (26%), Positives = 111/230 (48%), Gaps = 16/230 (6%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426
           ++K++     LV SIA  Y   G   +DLVQ G  GL+    ++D S G  F  +A   I
Sbjct: 31  QEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTI 90

Query: 427 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 486
              +++ L D++ ++ +P  + E   ++K+A  +L     R P   E+A+  GLS + + 
Sbjct: 91  IGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVL 150

Query: 487 AVLLSPKAPR--SLDQKIGINQNLKPSEVIAD----PEAETAEDLLIKKFMKEDLEKVLD 540
            ++   ++ R  S+D  I   +       +A      E E   D   ++ +   LEK+L 
Sbjct: 151 EIMEMGQSYRALSVDDVI---EADSDGSTVARLDSVGEVEDGYDQTERRMV---LEKILP 204

Query: 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
            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 = 74.2 bits (183), Expect = 1e-14
 Identities = 26/77 (33%), Positives = 47/77 (61%), Gaps = 2/77 (2%)

Query: 353 QRELRRRLNYG--ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 410
           + +L +RL     +    K++ S++R V+ IA+ Y+G G+   DL+QEG  GL++  ++F
Sbjct: 21  EYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

Query: 411 DASKGFKFSTYAHWWIK 427
           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 = 72.5 bits (179), Expect = 5e-14
 Identities = 22/59 (37%), Positives = 39/59 (66%)

Query: 369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 427
           +++ S++R V+ IA+ Y+G G+   DL+QEG  GL++  ++FD   G +  ++A  WIK
Sbjct: 52  QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIK 110

Length = 284

>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 = 65.2 bits (160), Expect = 1e-13
 Identities = 24/59 (40%), Positives = 36/59 (61%), Gaps = 4/59 (6%)

Query: 532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           +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|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed

 Score = 70.4 bits (173), Expect = 1e-13
 Identities = 26/74 (35%), Positives = 44/74 (59%)

Query: 518 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRER 577
           E +   + +  K   E L K +D L+ RE++V+  R+GL +G+ KT +EI + +G+SR  
Sbjct: 152 EEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSY 211

Query: 578 IRQIESSAFRKLKN 591
           + +IE  A +KL  
Sbjct: 212 VSRIEKRALKKLFK 225

Length = 233

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

 Score = 70.6 bits (173), Expect = 1e-13
 Identities = 59/232 (25%), Positives = 103/232 (44%), Gaps = 17/232 (7%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426
           +D+++T  + L   IA+ + G G    DLVQ    GLV    +FD   G  F ++A   I
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTI 101

Query: 427 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLH 486
              VR+   D S ++++P  + E   R+  A  +L    GR P   E+A   G+  + + 
Sbjct: 102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVV 161

Query: 487 AVLLSPKA--PRSLDQKIGINQNLKPSEVIA----DPEAETAEDLLIKKFMKEDLEKVLD 540
             L++  A    S+D   G   +   +        D   +  E+       +E L  +L 
Sbjct: 162 EGLVAGSAYNTLSIDSGGGSGDDDARAIADTLGDVDAGLDQIEN-------REALRPLLA 214

Query: 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
            L  RER V+  RF      M T  +I E +G+S+  + ++ +    +L+++
Sbjct: 215 ALPERERTVLVLRFF---ESM-TQTQIAERVGISQMHVSRLLAKTLARLRDQ 262

Length = 264

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

 Score = 65.5 bits (160), Expect = 8e-12
 Identities = 58/226 (25%), Positives = 111/226 (49%), Gaps = 28/226 (12%)

Query: 377 LVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD 436
           LV S+A  Y     + +DLVQ G  GL+    ++D S G  F  +A   I   +++ L D
Sbjct: 41  LVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRD 100

Query: 437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLS---------MKRLHA 487
           ++ ++ +P  + E   ++K+A  +L +E  R P   E+A+  G+S         M + + 
Sbjct: 101 KTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQ 160

Query: 488 VLLSPKAPRSLDQKIGINQNLKPSEV-IAD--PEAETAEDLLIKKFMKEDLEKVLDTLNP 544
            L       S+D  I  + +   S V + D   + E   +L  ++ +   LEK+L  L+ 
Sbjct: 161 AL-------SVDHSIEADSD--GSTVTLLDIVGQQEDGYELTEQRMI---LEKILPVLSD 208

Query: 545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           RE+ +++  F   +    + +E GE +G+S+  + +++  A +KL+
Sbjct: 209 REKSIIQCTF--IEN--LSQKETGERLGISQMHVSRLQRQAIKKLR 250

Length = 257

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

 Score = 63.7 bits (156), Expect = 4e-11
 Identities = 24/56 (42%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 535 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           L   L+ L+ R R ++  R+  +D    TLQE+    GVS ER+RQIE +A +KLK
Sbjct: 224 LADALEGLDERSRDIIEARWLDDDK--STLQELAAEYGVSAERVRQIEKNAMKKLK 277

Length = 284

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

 Score = 61.1 bits (149), Expect = 2e-10
 Identities = 29/76 (38%), Positives = 43/76 (56%), Gaps = 3/76 (3%)

Query: 516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSR 575
           DPE    E+   +   ++ L   L +L+ R R+++  R+  +D    TLQE+    GVS 
Sbjct: 194 DPEDTLEEEQWEEL-QRQALANALGSLDARSRRIIEARWLDDDK--LTLQELAAEYGVSA 250

Query: 576 ERIRQIESSAFRKLKN 591
           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|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor

 Score = 60.9 bits (148), Expect = 2e-10
 Identities = 27/76 (35%), Positives = 44/76 (57%)

Query: 514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGV 573
           I   + ++  + +      + L K L  L+ RER+V+  R+GL DGR KT +EI +++G+
Sbjct: 147 ILGSDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGI 206

Query: 574 SRERIRQIESSAFRKL 589
           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|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family

 Score = 58.5 bits (142), Expect = 4e-10
 Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 4/75 (5%)

Query: 518 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRER 577
              + E+ L ++  +E L + L+ L  RER+V+  R+        + +EI E++G+S   
Sbjct: 87  SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGT 142

Query: 578 IRQIESSAFRKLKNK 592
           +++    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 = 58.7 bits (142), Expect = 1e-09
 Identities = 22/59 (37%), Positives = 38/59 (64%)

Query: 532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           +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 = 57.3 bits (139), Expect = 3e-09
 Identities = 23/56 (41%), Positives = 35/56 (62%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 422
           ++ +I  N+RLV  I K ++  G ++ DL+  G  GL++  E FDA KG K +TYA
Sbjct: 51  RNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA 106

Length = 233

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

 Score = 53.1 bits (128), Expect = 2e-08
 Identities = 28/144 (19%), Positives = 52/144 (36%), Gaps = 10/144 (6%)

Query: 368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIK 427
           +++    + LV   A+ Y G   + +DLVQE    L+   ++FD      F  +     +
Sbjct: 4   EELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIAR 61

Query: 428 QAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA-TGLSMKRLH 486
             +   L  + R  R    + E         ++L  E       E + EA   L  +   
Sbjct: 62  NLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEE----EREALREALEKLPERERE 117

Query: 487 AVLLSPKAPRSLDQ---KIGINQN 507
            ++L      S  +    +GI+  
Sbjct: 118 VLVLRYLEGLSYKEIAEILGISVG 141

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

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

 Score = 54.5 bits (132), Expect = 3e-08
 Identities = 21/59 (35%), Positives = 39/59 (66%)

Query: 532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           ++ L+K L  L+ RE+Q++  RFGL  G  KT +E+ +++G+S+  I ++E    ++LK
Sbjct: 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227

Length = 234

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

 Score = 54.1 bits (130), Expect = 4e-08
 Identities = 28/86 (32%), Positives = 47/86 (54%), Gaps = 1/86 (1%)

Query: 356 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASK 414
           L ++L  G    K  +I  N+RLV+ IA+ ++  G+ ++DLV  G  GL++    F+ SK
Sbjct: 42  LLQKLTQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSK 101

Query: 415 GFKFSTYAHWWIKQAVRKSLSDQSRT 440
             K +TYA   I+  +   L   ++T
Sbjct: 102 KIKLATYASRCIENEILMYLRRNNKT 127

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

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

 Score = 53.2 bits (128), Expect = 7e-08
 Identities = 20/58 (34%), Positives = 33/58 (56%)

Query: 365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 422
             ++ +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|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed

 Score = 46.8 bits (112), Expect = 1e-05
 Identities = 20/56 (35%), Positives = 35/56 (62%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 422
           +  +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 = 42.0 bits (99), Expect = 3e-04
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVS 574
               A    +LL+ +   E L + L  L PR+R+    R+        + +EI E++G+S
Sbjct: 101 EADPAPDLAELLLAEEELERLRRALARLPPRQREAFLLRYLEG----LSYEEIAEILGIS 156

Query: 575 RERIRQIESSAFRKLKNK 592
              ++     A +KL+ +
Sbjct: 157 VGTVKSRLHRARKKLREQ 174

Length = 182

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 6/62 (9%)

Query: 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
           L PRER+++R    +  G  K+ +EI  ++G+S E ++    + +RKL  K R   L+  
Sbjct: 5   LTPREREILRL---VAQG--KSNKEIARILGISEETVKTHLRNIYRKLGVKNRV-ELVAL 58

Query: 602 AI 603
           A+
Sbjct: 59  AL 60

Length = 65

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL 598
           L +L PRER+V+R    L +G   T +EI E +G+S + ++   S+  RKL  + RT   
Sbjct: 1   LASLTPREREVLRL---LAEG--LTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRT-QA 54

Query: 599 MQYA 602
           ++ 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	605
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
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	100.0
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	100.0
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	100.0
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	100.0
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	100.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	100.0
PRK08583	257	RNA polymerase sigma factor SigB; Validated	100.0
PRK05572	252	sporulation sigma factor SigF; Validated	100.0
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	100.0
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	100.0
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	100.0
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.96
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.94
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.93
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.92
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.91
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.9
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.89
PRK12513	194	RNA polymerase sigma factor; Provisional	99.89
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.89
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.89
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.89
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.89
PRK11922	231	RNA polymerase sigma factor; Provisional	99.88
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.88
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.88
PRK12519	194	RNA polymerase sigma factor; Provisional	99.88
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.88
PRK12514	179	RNA polymerase sigma factor; Provisional	99.88
PRK12524	196	RNA polymerase sigma factor; Provisional	99.87
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	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
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.87
PRK12538	233	RNA polymerase sigma factor; Provisional	99.87
PRK12542	185	RNA polymerase sigma factor; Provisional	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
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.86
PRK12543	179	RNA polymerase sigma factor; Provisional	99.86
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.85
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.85
PRK12531	194	RNA polymerase sigma factor; Provisional	99.85
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.84
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.84
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.84
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.84
PRK12520	191	RNA polymerase sigma factor; Provisional	99.84
PRK12522	173	RNA polymerase sigma factor; Provisional	99.84
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.84
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.84
PRK12536	181	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
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.83
PRK12529	178	RNA polymerase sigma factor; Provisional	99.83
PRK12533	216	RNA polymerase sigma factor; Provisional	99.83
PRK12512	184	RNA polymerase sigma factor; Provisional	99.82
PRK12518	175	RNA polymerase sigma factor; Provisional	99.82
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.82
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.82
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.82
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.82
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.82
PRK12516	187	RNA polymerase sigma factor; Provisional	99.82
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.81
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.81
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.81
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.81
PRK12528	161	RNA polymerase sigma factor; Provisional	99.81
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.81
PRK12532	195	RNA polymerase sigma factor; Provisional	99.8
PRK12541	161	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
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.8
PRK12535	196	RNA polymerase sigma factor; Provisional	99.79
PRK12544	206	RNA polymerase sigma factor; Provisional	99.79
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.79
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.78
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.78
PRK12517	188	RNA polymerase sigma factor; Provisional	99.78
PRK12540	182	RNA polymerase sigma factor; Provisional	99.78
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.77
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.77
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	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	99.74
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.72
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.7
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.69
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.68
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.55
PRK09191	261	two-component response regulator; Provisional	99.52
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.41
PF07638	185	Sigma70_ECF: ECF sigma factor	99.39
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.24
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.21
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	99.06
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	98.91
PRK06930	170	positive control sigma-like factor; Validated	98.64
PRK00118	104	putative DNA-binding protein; Validated	98.43
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.27
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.07
PRK04217	110	hypothetical protein; Provisional	98.06
PRK03975	141	tfx putative transcriptional regulator; Provisiona	97.99
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	97.98
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	97.95
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	97.86
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.75
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.65
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.59
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	97.59
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.54
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.53
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.44
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.09
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.09
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.06
PRK10840	216	transcriptional regulator RcsB; Provisional	97.06
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.04
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.03
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.03
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.03
COG2197	211	CitB Response regulator containing a CheY-like rec	96.96
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	96.95
PRK13870	234	transcriptional regulator TraR; Provisional	96.93
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	96.9
COG4566	202	TtrR Response regulator [Signal transduction mecha	96.86
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	96.86
PRK15369	211	two component system sensor kinase SsrB; Provision	96.69
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.68
COG3413	215	Predicted DNA binding protein [General function pr	96.67
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	96.65
PRK09483	217	response regulator; Provisional	96.65
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.59
COG4941	415	Predicted RNA polymerase sigma factor containing a	96.56
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.51
PRK09390	202	fixJ response regulator FixJ; Provisional	96.31
PRK10651	216	transcriptional regulator NarL; Provisional	96.22
PRK01381	99	Trp operon repressor; Provisional	96.1
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	96.04
COG1342	99	Predicted DNA-binding proteins [General function p	95.92
PRK13558	665	bacterio-opsin activator; Provisional	95.31
PRK10403	215	transcriptional regulator NarP; Provisional	95.09
PRK09935	210	transcriptional regulator FimZ; Provisional	95.03
PRK15320	251	transcriptional activator SprB; Provisional	95.0
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	94.98
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	94.9
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	94.85
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	94.79
COG1356	143	tfx Transcriptional regulator [DNA replication, re	94.65
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.57
PRK04841	903	transcriptional regulator MalT; Provisional	94.5
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	94.49
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	94.15
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	93.85
PF13730	55	HTH_36: Helix-turn-helix domain	93.73
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	93.29
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	93.27
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	93.02
PRK15418	318	transcriptional regulator LsrR; Provisional	92.85
PF10668	60	Phage_terminase: Phage terminase small subunit; In	92.81
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	92.74
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	92.56
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	92.32
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	92.26
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	92.16
PHA00675	78	hypothetical protein	91.38
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	91.33
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	91.04
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	90.8
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	90.79
PRK07598	415	RNA polymerase sigma factor SigC; Validated	90.69
PF13518	52	HTH_28: Helix-turn-helix domain	89.87
PRK05901	509	RNA polymerase sigma factor; Provisional	89.85
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	89.66
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	89.53
smart00351	125	PAX Paired Box domain.	89.42
COG3355	126	Predicted transcriptional regulator [Transcription	89.4
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	89.35
PRK11083	228	DNA-binding response regulator CreB; Provisional	89.1
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	88.86
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	88.62
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	88.48
PRK12423	202	LexA repressor; Provisional	88.44
PRK15479	221	transcriptional regulatory protein TctD; Provision	88.28
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	88.19
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	88.02
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	88.0
PHA02591	83	hypothetical protein; Provisional	87.86
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	87.79
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	87.77
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	87.75
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	87.65
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	87.64
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	87.64
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	87.55
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	87.55
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	87.07
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	87.05
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	86.74
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	86.71
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	86.4
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	85.56
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	85.17
cd00131	128	PAX Paired Box domain	84.99
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	84.43
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	84.41
PRK10046	225	dpiA two-component response regulator DpiA; Provis	84.31
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	84.02
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	84.0
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	83.69
COG1522	154	Lrp Transcriptional regulators [Transcription]	83.36
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	83.26
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	83.13
PRK00215	205	LexA repressor; Validated	83.11
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	83.06
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	83.04
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	82.93
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	82.84
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	82.8
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	82.77
PF12728	51	HTH_17: Helix-turn-helix domain	82.49
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	82.44
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	82.17
PHA02547	179	55 RNA polymerase sigma factor; Provisional	82.05
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	81.98
PRK05949	327	RNA polymerase sigma factor; Validated	81.88
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	81.82
PRK11169	164	leucine-responsive transcriptional regulator; Prov	81.65
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	81.49
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	81.46
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	81.39
CHL00148	240	orf27 Ycf27; Reviewed	80.98
COG1654	79	BirA Biotin operon repressor [Transcription]	80.94
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	80.93
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	80.82
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	80.53
TIGR01764	49	excise DNA binding domain, excisionase family. An	80.46
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	80.29
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	80.26
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	80.18
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	80.16
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	80.01

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=5e-64  Score=539.50  Aligned_cols=313  Identities=39%  Similarity=0.696  Sum_probs=295.4

Q ss_pred             CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH--------------------HHhHHHHHHhhcCCCCchHHHHH
Q 007404          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAA  347 (605)
Q Consensus       289 ~~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~--------------------le~~~~~L~~~~G~~pt~~ewA~  347 (605)
                      ...|+++ ||++| ++.||||++||++|+++||.+++                    |++++..|.+++|++||..+||.
T Consensus        57 ~~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~  135 (415)
T PRK07598         57 RSTDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAK  135 (415)
T ss_pred             CCCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            3479999 99999 99999999999999999999999                    89999999999999999999996


Q ss_pred             hhcC----------------------CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH
Q 007404          348 AAGV----------------------DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR  405 (605)
Q Consensus       348 a~g~----------------------d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLir  405 (605)
                      ++|+                      +.+.|.+.++.|..|+++||.+|+++|++||++|.++|++++||||||++|||+
T Consensus       136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~r  215 (415)
T PRK07598        136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER  215 (415)
T ss_pred             HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence            6555                      455555556778899999999999999999999999999999999999999999


Q ss_pred             hhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHH
Q 007404          406 GAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRL  485 (605)
Q Consensus       406 A~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V  485 (605)
                      |+++|||++|++|+||++||||++|.+++.+++++||+|.|+.+.+++++++.+.+.+++||.|+.+|||+.+|+++++|
T Consensus       216 avekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~v  295 (415)
T PRK07598        216 AVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQV  295 (415)
T ss_pred             HHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHH
Q 007404          486 HAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQ  565 (605)
Q Consensus       486 ~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~  565 (605)
                      +.++.....++|||.+++++++..+.+.+.++ ..+|++.+....+...|..+|..||++||.||.||||++||.++|++
T Consensus       296 r~~l~~~~~~~SLd~~vg~~~d~~l~d~l~~~-~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~~~Tl~  374 (415)
T PRK07598        296 REVLLRVPRSVSLETKVGKDKDTELGDLLETD-DISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLA  374 (415)
T ss_pred             HHHHHHccCCcccccccCCCccccHHHhccCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCCCHH
Confidence            99999889999999999988888888877654 45899999999999999999999999999999999999999999999


Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          566 EIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       566 EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      |||+.||||+++|||++++|++|||+.-....|++|+.
T Consensus       375 EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~  412 (415)
T PRK07598        375 EIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE  412 (415)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence            99999999999999999999999999999999999985

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=6.1e-62  Score=519.48  Aligned_cols=311  Identities=48%  Similarity=0.794  Sum_probs=299.6

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHH
Q 007404          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  368 (605)
Q Consensus       290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e  368 (605)
                      ..|++. ||++| +++|+||++||++|+++|++++.+++++.+|++..|+.|+..+||.++|++...|.+++..|..|++
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             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404          369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  448 (605)
Q Consensus       369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~  448 (605)
                      .||..|+++|+++|++|.++|.+++||+|||++|||+++++|||.+|++|+|||+||||++|.++|++++++||+|.|+.
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 007404          449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  528 (605)
Q Consensus       449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~  528 (605)
                      ..+++++++...|.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++++. .+|++.+..
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 478988999


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhh
Q 007404          529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA  602 (605)
Q Consensus       529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl  602 (605)
                      ..+...|..+|..||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+......|+.|+
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=6.8e-61  Score=504.90  Aligned_cols=310  Identities=37%  Similarity=0.688  Sum_probs=296.9

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHH
Q 007404          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  368 (605)
Q Consensus       290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e  368 (605)
                      ..|++. ||++| +++|+||++||++|+++|+.++.++..+..|....|+.|+..+|+.+++++...|...++.|..|++
T Consensus        16 ~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~   94 (327)
T PRK05949         16 SADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ   94 (327)
T ss_pred             CCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence            478999 99999 9999999999999999999999999999999999999999999999999999999999999989999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404          369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  448 (605)
Q Consensus       369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~  448 (605)
                      .||..|+++|+++|++|.+++.+++|||||||+|||+++++|||++|++|+|||+||||++|.+++.+++++||+|.|+.
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 007404          449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  528 (605)
Q Consensus       449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~  528 (605)
                      ..+++++++.+.+.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++|+. .+|++.+..
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            9999999999999999999999999999999999999999998899999999998777777888888765 589999999


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      ..+...|..+|+.||++||.||.+|||++|++++|++|||+.||||+++|||++.+|++|||+.  ...|+.|+.
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  467888874

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

Probab=100.00  E-value=4e-60  Score=493.10  Aligned_cols=297  Identities=45%  Similarity=0.778  Sum_probs=284.2

Q ss_pred             CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHH
Q 007404          292 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM  370 (605)
Q Consensus       292 d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~L  370 (605)
                      |++. ||++| +++|+||++||.+|+++++.++.++.++.+|+++.|++|+..+||+++|++...|...++.|..|++.|
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 999999999999999999999999999999999999999999999999999999999999899999999


Q ss_pred             HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHH
Q 007404          371 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA  450 (605)
Q Consensus       371 I~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~  450 (605)
                      |.+|+++|++||++|.++|.+++|||||||+|||+|+++|||.+|++|+||++||||++|.+++.+++++||+|.++...
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 007404          451 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF  530 (605)
Q Consensus       451 i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~e  530 (605)
                      +++++++.+.+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++++ ..+|++.+...+
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            9999999999999999999999999999999999999999888999999999776666677777764 458999999999


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      +...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++++|++|||
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=7.9e-60  Score=495.12  Aligned_cols=309  Identities=41%  Similarity=0.705  Sum_probs=295.4

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHH
Q 007404          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  369 (605)
Q Consensus       291 ~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~  369 (605)
                      +|++. ||++| +++|+||++||++|+++|++++.+++++..|++++|++|+..+||+++++++..|...+..|..|+++
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            67899 99999 99999999999999999999999999999999999999999999999999999999999989999999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHH
Q 007404          370 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE  449 (605)
Q Consensus       370 LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~  449 (605)
                      ||..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+..
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 007404          450 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK  529 (605)
Q Consensus       450 ~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~  529 (605)
                      .+++++++.+.+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.+.++|+. .+|++.+...
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 5899999999


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      .+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++||||++.+|++|||+.  ...|..|+.
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            999999999999999999999999999988999999999999999999999999999999995  467888874

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

Probab=100.00  E-value=3.3e-59  Score=488.37  Aligned_cols=312  Identities=42%  Similarity=0.708  Sum_probs=286.6

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHh-hcCCCCchH---------------HHHHhhcCCH
Q 007404          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVDQ  353 (605)
Q Consensus       291 ~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~-~~G~~pt~~---------------ewA~a~g~d~  353 (605)
                      .|.+. |+.++ +..++++.++|..+...++....+..+...|.. ..|..|+..               +|+.....++
T Consensus         8 ~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E   86 (342)
T COG0568           8 ADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE   86 (342)
T ss_pred             hhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence            56788 99999 999999999999999999887766666777766 567778876               5555555444


Q ss_pred             -HHHHHHHhcc---HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHH
Q 007404          354 -RELRRRLNYG---ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  429 (605)
Q Consensus       354 -~~L~~~l~~g---~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqa  429 (605)
                       ..|..++..|   ..|+.+||.+|+|||++||++|.|+|+++.||||||+||||+|+++|||++||+|||||+|||||+
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             5666666655   559999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCC
Q 007404          430 VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLK  509 (605)
Q Consensus       430 I~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~  509 (605)
                      |.++|.+++|+||+|+|+.+.++++++..+++.+++|++|+.+|||+.+|+++++|.+++.....++|||.|++++++..
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            99999999999999999999999999999999999999999999999999999999999999989999999999998889


Q ss_pred             CCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc-CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 007404          510 PSEVIADPEAETAEDLLIKKFMKEDLEKVLDT-LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK  588 (605)
Q Consensus       510 l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~-L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkK  588 (605)
                      +.|+++|+...+|++.+....+.+.+...|.. |+++|+.||++|||++|++|.|++|||+.+|||++|||||+.+||+|
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            99999999888999999999999999999999 99999999999999999999999999999999999999999999999


Q ss_pred             HH-hHHhhhhHhhhhc
Q 007404          589 LK-NKKRTKHLMQYAI  603 (605)
Q Consensus       589 LR-~~l~~~~L~~yl~  603 (605)
                      || .......+++|++
T Consensus       327 Lr~~~~~~~~~~~~l~  342 (342)
T COG0568         327 LRRHPERSALLRSYLD  342 (342)
T ss_pred             HHHhhhhhhHHHHhhC
Confidence            99 5555666788874

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=1.2e-58  Score=508.81  Aligned_cols=301  Identities=40%  Similarity=0.674  Sum_probs=276.0

Q ss_pred             CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHH
Q 007404          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK  367 (605)
Q Consensus       289 ~~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~  367 (605)
                      ...|+++ ||++| +++|+||++||++|+++|+.+..++.   .+.       ...+|+..   ....|+.+++.|..|+
T Consensus       208 ~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~---~~~-------~~~~~~~~---~~~~l~~~~~~g~~Ar  273 (509)
T PRK05901        208 ATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEE---LLA-------EGEKLDPE---LRRDLQWIGRDGKRAK  273 (509)
T ss_pred             ccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhh---hhh-------hcccchhh---hhhhhhhhccchHHHH
Confidence            3578999 99999 99999999999999999987532221   111       11234422   4567888888999999


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccH
Q 007404          368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM  447 (605)
Q Consensus       368 e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~  447 (605)
                      ++||.+|+|||++||++|.++|++++||||||+||||+|+++|||++|++|+|||+||||++|.++|++++|+||+|.|+
T Consensus       274 ~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~  353 (509)
T PRK05901        274 NHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHM  353 (509)
T ss_pred             HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHH
Q 007404          448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI  527 (605)
Q Consensus       448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~  527 (605)
                      .+.+++++++.+.|.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.+++.|+....|++.+.
T Consensus       354 ~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~~p~~~~~  433 (509)
T PRK05901        354 VETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVS  433 (509)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCCCHHHHHH
Confidence            99999999999999999999999999999999999999999998889999999998777778889999887778999999


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       528 ~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      ...++..|..+|..|+++||.||.+|||+++++++|++|||+.||||++|||||+.+||+|||+......|+.|++
T Consensus       434 ~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~  509 (509)
T PRK05901        434 FTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD  509 (509)
T ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999999999999999998899999999999999999999999999999999999999999974

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=7.4e-58  Score=481.11  Aligned_cols=300  Identities=42%  Similarity=0.710  Sum_probs=275.1

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHH
Q 007404          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  368 (605)
Q Consensus       290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e  368 (605)
                      .+|++. ||++| +++|+||++||++|+++|+....++..           |+..+|....  ....+...++.|..|++
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            468899 99999 999999999999999999976544432           2223332111  44578888899999999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404          369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  448 (605)
Q Consensus       369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~  448 (605)
                      +||..|+++|+++|++|.+++.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+.
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 007404          449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  528 (605)
Q Consensus       449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~  528 (605)
                      +.+++++++.+.|.+++|+.||.+|||+.+|+++++|..++.....++|||.+++++++.++.++++|+...+|++.+..
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            99999999999999999999999999999999999999999888889999999987777778899988777789999999


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      .+++..|..+|..|+++|+.||.+|||++|++++|++|||+.||||++|||||+.+||+|||.......|+.|+.
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            999999999999999999999999999998899999999999999999999999999999999999999999863

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=4.1e-54  Score=460.08  Aligned_cols=274  Identities=45%  Similarity=0.765  Sum_probs=261.5

Q ss_pred             CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHH
Q 007404          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK  367 (605)
Q Consensus       289 ~~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~  367 (605)
                      ...|+++ ||++| +++|+||++||.+|+++++.                                        |+..|+
T Consensus        93 ~~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~----------------------------------------Gd~~A~  131 (367)
T PRK09210         93 KINDPVRMYLKEI-GRVPLLTAEEEIELAKRIEE----------------------------------------GDEEAK  131 (367)
T ss_pred             ccCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHh----------------------------------------hHHHHH
Confidence            3478999 99999 99999999999999988764                                        346799


Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccH
Q 007404          368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM  447 (605)
Q Consensus       368 e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~  447 (605)
                      +.||..|+++|+++|++|.+++.+++||+||||+|||+|+++|||.+|++|+|||+||||++|.++|++++|++|+|.|+
T Consensus       132 ~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~  211 (367)
T PRK09210        132 QRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM  211 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHH
Q 007404          448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI  527 (605)
Q Consensus       448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~  527 (605)
                      .+.++++.++.+.|.+++||.||.+|||+.+|+++++|..++.....++|||.+++++++..+.++++|+...+|++.+.
T Consensus       212 ~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~~~~  291 (367)
T PRK09210        212 VETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAA  291 (367)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHHHHH
Confidence            99999999999999999999999999999999999999999998888999999998777778889999887778999999


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       528 ~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      ...++..|..+|..||++||.||.+|||++||+++|++|||+.||||++|||||+.+||+|||+......|+.|++
T Consensus       292 ~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~  367 (367)
T PRK09210        292 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE  367 (367)
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999974

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=2.7e-51  Score=464.56  Aligned_cols=270  Identities=40%  Similarity=0.667  Sum_probs=252.3

Q ss_pred             HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHH
Q 007404          296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI  375 (605)
Q Consensus       296 yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nl  375 (605)
                      ||+++ ...+.||++|+..++++|+.               |..                      .+..|+++||.+|+
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 77777777777777777664               320                      12468999999999


Q ss_pred             HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHH
Q 007404          376 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK  455 (605)
Q Consensus       376 rLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~  455 (605)
                      |||++||++|.++|++++||||||+||||+|+++|||.+|++|+|||+||||++|.++|++++|+||+|.|+.+.+++++
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 007404          456 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDL  535 (605)
Q Consensus       456 ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L  535 (605)
                      ++.+.+.+++||.||.+|||+.+|+++++|..++.....++|||.|++++++.++.++++|....+|++.+....++..|
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            99999999999999999999999999999999999989999999999888888899999988878899999999999999


Q ss_pred             HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          536 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       536 ~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      ..+|..||++|+.||++|||++++.++|++|||+.||||++|||||+.+||+|||+......|+.|++
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=3.7e-47  Score=383.33  Aligned_cols=238  Identities=45%  Similarity=0.777  Sum_probs=226.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404          366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  445 (605)
Q Consensus       366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~  445 (605)
                      |+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+|+|.
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 007404          446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  525 (605)
Q Consensus       446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~  525 (605)
                      ++...++++.++.+.+.+++|+.||.+|||+.+|+++++|..++......+|||.+++++++.++.+.++|+...+|++.
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            99999999999999999999999999999999999999999999887789999999977766677788888877789988


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      +...++...|..+|+.||++||.||.++||+++++++|++|||+.||||+++|+|++.+|++|||+.+....|+.|++
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            888899999999999999999999999999887788999999999999999999999999999999999999999975

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=2.4e-44  Score=373.51  Aligned_cols=262  Identities=26%  Similarity=0.418  Sum_probs=225.9

Q ss_pred             CHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHH
Q 007404          292 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM  370 (605)
Q Consensus       292 d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~L  370 (605)
                      +..+ ||++| +++|+||+++|.+|+.+++.                                       .||..|+++|
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            4556 99999 99999999999999987652                                       1457899999


Q ss_pred             HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHH-
Q 007404          371 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE-  449 (605)
Q Consensus       371 I~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~-  449 (605)
                      |..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++++|+|.+... 
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            9999999999999999999999999999999999999999999999999999999999999999999999999998765 


Q ss_pred             -HHHHHHHHHHHHHH---HcCCCCCHHHHHHhcCCCHHHHHHHH-hCCCCCCCccccccccCCC--CCCcccCCCCCCCH
Q 007404          450 -ATYRVKEARKQLYS---ENGRHPNNEEVAEATGLSMKRLHAVL-LSPKAPRSLDQKIGINQNL--KPSEVIADPEAETA  522 (605)
Q Consensus       450 -~i~ki~ka~~~L~~---elgr~PT~eEIAe~lgis~e~V~~~l-~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~sp  522 (605)
                       ...++++.+..+.+   .+|+.||.+|||+.||+++++|..+. .....++|||.+++++++.  ++.+.++|+.. +|
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  56778877643 56


Q ss_pred             HHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          523 EDLLIK----KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       523 Ee~l~~----~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      ++.+..    ......|..+|+.||++||.||.+||+..  +++|++|||+.||||++||+|++++|++|||..+...
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  2399999999999999999999999999999988753

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=4.1e-44  Score=370.92  Aligned_cols=261  Identities=28%  Similarity=0.440  Sum_probs=223.3

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHH
Q 007404          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  368 (605)
Q Consensus       290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e  368 (605)
                      +.+++. |++++ +++|+||.++|.+|+.+++.                                       .|+..|++
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 99999999999999886542                                       14578999


Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404          369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  448 (605)
Q Consensus       369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~  448 (605)
                      .||..|+++|+++|++|.+.+.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++++++++||+|.+..
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 007404          449 --EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQN--LKPSEVIADPEAETAE  523 (605)
Q Consensus       449 --~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~-~~~~~~SLD~~i~~d~~--~~l~d~l~D~~~~spE  523 (605)
                        ....++++....+.  .+++||.+|||+.||+++++|..++. .....+|||.+++++++  .++.+.++|+. .+|+
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              23444555555443  35999999999999999999999875 34578999999865532  34667777763 4677


Q ss_pred             HHHHHH----HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          524 DLLIKK----FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       524 e~l~~~----el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      +.++..    .+...|..+|+.||++||.||.+||+.+  +++|++|||+.||||++||||++.+|++|||..+..
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    3578899999999999999999999753  459999999999999999999999999999998754

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=100.00  E-value=7.1e-44  Score=375.60  Aligned_cols=269  Identities=36%  Similarity=0.568  Sum_probs=250.4

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHH
Q 007404          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  369 (605)
Q Consensus       291 ~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~  369 (605)
                      .|.++ ||++| +..|+||+++|.+|..+++.                                        |+..|++.
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            57788 99999 99999999999999887764                                        45789999


Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHH
Q 007404          370 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVE  449 (605)
Q Consensus       370 LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~  449 (605)
                      ||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||.+|.++++++.+.+|+|.++.+
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 007404          450 ATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK  529 (605)
Q Consensus       450 ~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~  529 (605)
                      .++.+.++.+.+.+.+|+.|+.+|||+.+|+++++|..++.......|||.+++.+...++.+.+.++...+|++.+...
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            99989999999999999999999999999999999999998888899999998877666777888877667899999888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhh
Q 007404          530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ  600 (605)
Q Consensus       530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~  600 (605)
                      +....|..+|..||+++|.||.+|||+.+.+.+|++|||+.||||++||+++++||+++||+.+...++..
T Consensus       251 e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~~  321 (325)
T PRK05657        251 DMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLSI  321 (325)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccch
Confidence            89999999999999999999999998776667999999999999999999999999999999998877653

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=1.3e-43  Score=364.36  Aligned_cols=257  Identities=29%  Similarity=0.489  Sum_probs=216.7

Q ss_pred             HHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHH
Q 007404          293 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI  371 (605)
Q Consensus       293 ~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI  371 (605)
                      ++. ||+++ +++|+|++++|.+|+.++..                                       .|+..|++.||
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 99999999999999886432                                       14578999999


Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH--H
Q 007404          372 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV--E  449 (605)
Q Consensus       372 ~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~--~  449 (605)
                      ..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++++++++++|+|.+..  +
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 007404          450 ATYRVKEARKQLYSENGRHP-NNEEVAEATGLSMKRLHAVLL-SPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDL  525 (605)
Q Consensus       450 ~i~ki~ka~~~L~~elgr~P-T~eEIAe~lgis~e~V~~~l~-~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~spEe~  525 (605)
                      ...++++....+.  .++.| +.+|||+.||+++++|..++. .....+|||.+++++++.  .+.+.+.|+. .+|++.
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            4555555555443  22555 699999999999999999865 334589999998765432  4556677654 367776


Q ss_pred             HHHH----HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          526 LIKK----FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       526 l~~~----el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      +...    .+...|..+|..||++||.||.+||+.+  +++|++|||+.||||+++|+|++.+||+|||+.+.
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    3568899999999999999999999752  34999999999999999999999999999998764

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=6.6e-43  Score=358.40  Aligned_cols=221  Identities=25%  Similarity=0.372  Sum_probs=201.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  443 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl  443 (605)
                      ..++++||..|++||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++++.++||+
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 007404          444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNL--KPSEVIADPEA  519 (605)
Q Consensus       444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~--~~~~~SLD~~i~~d~~~--~l~d~l~D~~~  519 (605)
                      |.++.+.+++++++...+.+++|+.||.+|||+.||+++++|.+++..  ...++|||.+++++++.  .+.+.++    
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  45689999998653332  3333333    


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       520 ~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                       +++..++..+....|..+|+.||++||.||.++|+.+    +|++|||+.||||.++|++++++|+++||+.+
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             3455566677788899999999999999999999876    99999999999999999999999999999875

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=2.5e-41  Score=345.09  Aligned_cols=227  Identities=27%  Similarity=0.453  Sum_probs=201.9

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  440 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~-g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~  440 (605)
                      ++..|+++||..|+++|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||+||||++|.++++++.++
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             ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh--CCCCCCCccccccccCC--CCCCcccCC
Q 007404          441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQN--LKPSEVIAD  516 (605)
Q Consensus       441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~--~~~~~~SLD~~i~~d~~--~~l~d~l~D  516 (605)
                      ||+|.++.+.+++++++...|.+++|++||.+|||+.+|+++++|..++.  .....+|||.+++++++  ..+.+.+++
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  34568899999865433  245666666


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      +... +..  ...+....|..+|..||+++|.||.++|+.+    +|++|||+.||+|.++|++++++|++|||+.+..
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 211  2334567799999999999999999999877    9999999999999999999999999999998764

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=3.6e-40  Score=341.12  Aligned_cols=271  Identities=37%  Similarity=0.561  Sum_probs=246.2

Q ss_pred             CCCCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHH
Q 007404          287 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL  365 (605)
Q Consensus       287 ~~~~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~  365 (605)
                      +...+|.++ ||.+| +.+|.||.++|.+|+.+++.                                        |+..
T Consensus         8 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~   46 (285)
T TIGR02394         8 ETRVADVTQLYLREI-GFKPLLTAEEEIAYARRALA----------------------------------------GDFE   46 (285)
T ss_pred             ccCcchHHHHHHHHH-hccCCCCHHHHHHHHHHHHc----------------------------------------CCHH
Confidence            345688999 99999 99999999999999887664                                        3478


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404          366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  445 (605)
Q Consensus       366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~  445 (605)
                      |++.||..|.++|+++|++|.+++.+++||+||||+|||+++++||+.+|++|+||++|||+.++.+++.++.+.+++|.
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 007404          446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  525 (605)
Q Consensus       446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~  525 (605)
                      ++...++.+.+..+.+.+.+|+.|+.+++|..+|++++++..++......+|+|.++..++...+.+.+.++...+|++.
T Consensus       127 ~~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~  206 (285)
T TIGR02394       127 HVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESL  206 (285)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHH
Confidence            99999999999888888999999999999999999999999999888889999988765555555566666655689999


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404          526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  598 (605)
Q Consensus       526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  598 (605)
                      +...+....|..+|..||+++|.||.|+||+.+.+.+|++|||+.||||.++|++++++|+++||+.+...+.
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            9999999999999999999999999999976544559999999999999999999999999999999876543

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=2.9e-40  Score=336.48  Aligned_cols=242  Identities=28%  Similarity=0.425  Sum_probs=215.5

Q ss_pred             hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 007404          301 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS  380 (605)
Q Consensus       301 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvs  380 (605)
                      |+++|+||++||.+|+.+++.                                        ++..|++.||..|+++|++
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                                        3477999999999999999


Q ss_pred             HHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHH
Q 007404          381 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQ  460 (605)
Q Consensus       381 IAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~  460 (605)
                      +|++|.+++.+++||+||||+|||+++++|||.+|.+|+||++|||++.|.++++++. .+|+|.++.+.++++.++...
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 007404          461 LYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKV  538 (605)
Q Consensus       461 L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~spEe~l~~~el~~~L~~a  538 (605)
                      +.+++|+.||.+|||+.+|+++++|..++.....+.|||.++.++++.  ++.+.+.|+.. .++    .......|..+
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            999999999999999999999999999998888889999988544332  35666666432 122    22345578999


Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      |..|++++|.||.++|+.+    +|++|||+.||+|+++|++++.+|++|||+.
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            9999999999999999766    9999999999999999999999999999985

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

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=100.00  E-value=1.3e-39  Score=332.81  Aligned_cols=227  Identities=30%  Similarity=0.422  Sum_probs=205.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  438 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~---~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s  438 (605)
                      ++..|+++||..|+++|+++|++|.+   .+.+++||+|||+||||+|+++|||++|++|+||++||||++|.++++++.
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   356899999999999999999999999999999999999999999999987


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCC--CCCCccccccc--cC--CCCCCc
Q 007404          439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPK--APRSLDQKIGI--NQ--NLKPSE  512 (605)
Q Consensus       439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~--~~~SLD~~i~~--d~--~~~l~d  512 (605)
                      |   +|.++.+.++++.++...+.+++|+.|+.+|||+.+|+++++|..++....  .++|||.++..  ++  +.++.+
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            6   899999999999999999999999999999999999999999999986543  46899987643  11  235677


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          513 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       513 ~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .++|+....|++.+...+....|..+|..||++||.||.++|+.+    +|++|||+.||||+++|++++++|+++||+.
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            888876667888888888999999999999999999999999877    9999999999999999999999999999998


Q ss_pred             Hhh
Q 007404          593 KRT  595 (605)
Q Consensus       593 l~~  595 (605)
                      +..
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=1.4e-38  Score=324.51  Aligned_cols=243  Identities=28%  Similarity=0.442  Sum_probs=215.0

Q ss_pred             hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 007404          301 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS  380 (605)
Q Consensus       301 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvs  380 (605)
                      +.++|+|+++|+..|+.+++.                                        ++..|++.||..|+++|++
T Consensus        13 ~~~~~~l~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~~~~~v~~   52 (258)
T PRK08215         13 TSKLPVLKNEEMRELFERMQN----------------------------------------GDKEAREKLINGNLRLVLS   52 (258)
T ss_pred             CCCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence            367899999999999877653                                        3478999999999999999


Q ss_pred             HHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHH
Q 007404          381 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQ  460 (605)
Q Consensus       381 IAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~  460 (605)
                      +|++|.+++.+++||+|||++|||+++++||+.+|.+|+||+++||+++|.++++++. .+|+|.++.....++.++...
T Consensus        53 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~  131 (258)
T PRK08215         53 VIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREK  131 (258)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999985 789999999999999999999


Q ss_pred             HHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCC--CCCcccCCCCCCCHHHHHHHHHHHHHHHHH
Q 007404          461 LYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKV  538 (605)
Q Consensus       461 L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~spEe~l~~~el~~~L~~a  538 (605)
                      +.+++|+.|+.+|||+.+|+++++|..++.....+.|||.++.++++.  ++.+.++++.. .++.    ......|..+
T Consensus       132 l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-~~~~----~~~~~~l~~~  206 (258)
T PRK08215        132 LINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-KDEN----WLEEIALKEA  206 (258)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-cHHH----HHhHHHHHHH
Confidence            999999999999999999999999999988777888999988654432  34555655432 2222    2334578899


Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      |+.||++|+.||.++|+.+    +|++|||+.||||.++|++++++|++|||+.+
T Consensus       207 l~~L~~~er~vi~~~~~~~----~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l  257 (258)
T PRK08215        207 MKKLNDREKLILNLRFFQG----KTQMEVAEEIGISQAQVSRLEKAALKHMRKYI  257 (258)
T ss_pred             HHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999766    99999999999999999999999999999875

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=100.00  E-value=2.1e-37  Score=317.72  Aligned_cols=249  Identities=24%  Similarity=0.353  Sum_probs=222.0

Q ss_pred             hcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHH
Q 007404          301 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS  380 (605)
Q Consensus       301 ~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvs  380 (605)
                      +|++|+||.++|.+|+.+++.               +                        ++..+++.|+..|.++|+.
T Consensus         6 ~~~~~~~~~~~e~~l~~~~~~---------------~------------------------~d~~a~~~l~~~y~~lv~~   46 (268)
T PRK06288          6 SGKIPKYAQQDETELWREYKK---------------T------------------------GDPKIREYLILKYSPLVKY   46 (268)
T ss_pred             cCCCccccchHHHHHHHHHHH---------------c------------------------CCHHHHHHHHHHHHHHHHH
Confidence            588999999999999987663               1                        3478999999999999999


Q ss_pred             HHHHhh-C--CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHH
Q 007404          381 IAKNYQ-G--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEA  457 (605)
Q Consensus       381 IAkrY~-~--~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka  457 (605)
                      +|++|. +  .+.+++||+||||+|||+++++||+.+|++|+||++||||+.|.+++++..   ++|.++....++++++
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  567899999999999999999999999999999999999999999999754   5899999999999999


Q ss_pred             HHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCC--CCCCCccccccccC---CCCCCcccCCCCCCCHHHHHHHHHHH
Q 007404          458 RKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQ---NLKPSEVIADPEAETAEDLLIKKFMK  532 (605)
Q Consensus       458 ~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~--~~~~SLD~~i~~d~---~~~l~d~l~D~~~~spEe~l~~~el~  532 (605)
                      ...|.+++|+.||.+|||+.+|++.+++..++...  ...+|||.++..++   ...+.+.++++..++|++.+...+..
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            99999999999999999999999999999987533  45789998764222   23456777777777899988888999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      ..|..+|+.||+++|.||.++|+.+    +|++|||+.||+|.++|+++++||+++||+.+..
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

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

Probab=100.00  E-value=1.9e-37  Score=313.75  Aligned_cols=222  Identities=31%  Similarity=0.477  Sum_probs=202.1

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCC-CHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGM-NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  440 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~-d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~  440 (605)
                      ++..++ .||+.|+|||.++|++|.+++. +.+||+|-|+|||++|+++|||++|.+|+|||...|+++|.+++|++. .
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            457788 9999999999999999998887 999999999999999999999999999999999999999999999999 8


Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCC--CCCCCccccccccCCCCCCcccCCCC
Q 007404          441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPE  518 (605)
Q Consensus       441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~D~~  518 (605)
                      +++|..+.+..+++..+...+.+++||+||.+|||+.+|++.++|..++...  ...+|+|..+..+++..     .++.
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            9999999999999999999999999999999999999999999999998755  36788887765443333     2223


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ..+|.+.+...+....|.+++..|++|||.||.+||+.+    +|++|||+.||||..+|+|++.+|++|||+.+.
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            346777888888888999999999999999999999988    999999999999999999999999999999775

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=100.00  E-value=1.1e-36  Score=309.70  Aligned_cols=245  Identities=26%  Similarity=0.342  Sum_probs=216.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHH
Q 007404          304 SRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAK  383 (605)
Q Consensus       304 ~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAk  383 (605)
                      .|.||+++|.+|..+++.               |                        ++..|+++||..|.++|+.+|+
T Consensus         7 ~~~l~~~~~~~li~~~~~---------------~------------------------gd~~a~~~l~~~y~~~v~~~a~   47 (255)
T TIGR02941         7 PTNLTKEDVIQWIAEFQQ---------------N------------------------QNGEAQEKLVDHYQNLVYSIAY   47 (255)
T ss_pred             CCCCCHHHHHHHHHHHHH---------------C------------------------CCHHHHHHHHHHhHHHHHHHHH
Confidence            367899999988877663               1                        3478999999999999999999


Q ss_pred             HhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHH
Q 007404          384 NYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYS  463 (605)
Q Consensus       384 rY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~  463 (605)
                      +|.+++.+++||+||||+|||+++++||++.|.+|.||+++||++.|.++++++.+.+++|.++....++++++...+.+
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 007404          464 ENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT  541 (605)
Q Consensus       464 elgr~PT~eEIAe~lgis~e~V~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~  541 (605)
                      .+|+.|+.+|||+.+|++.+++..++..  .....|||.+++.+++......+ +. ..+|++.+...+....|..+|+.
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  34678999988765443322222 11 12466667777778889999999


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ||+++|.||.++|+.+    +|++|||+.||+|.++|++++++|+++||+.+
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=1.4e-36  Score=304.32  Aligned_cols=223  Identities=32%  Similarity=0.483  Sum_probs=199.3

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404          361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  440 (605)
Q Consensus       361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~  440 (605)
                      .++..|++.||..|.++|+++|++|.+++.+++||+|||++|||+++++|||.+|.+|+||++|||++.|.++++++. .
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             ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCC--CCCcccCCCC
Q 007404          441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPE  518 (605)
Q Consensus       441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~  518 (605)
                      +++|.++...+++++++...+..++|+.||.+|||+.+|+++++|..++.....+.|||.++.++++.  ++.+.+.++.
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  3456665543


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      .  +++.   ......|..+++.||++|++||.++|+.+    +|++|||+.||||+++|++++++|++|||..+
T Consensus       166 ~--~~~~---~~~~~~l~~~l~~L~~~e~~i~~~~~~~~----~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l  231 (231)
T TIGR02885       166 S--EDSD---WLEKIALKEAISKLDERERQIIMLRYFKD----KTQTEVANMLGISQVQVSRLEKKVLKKMKEKL  231 (231)
T ss_pred             c--cHHh---HHHHHHHHHHHHcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence            2  2222   22356788999999999999999999876    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=5.8e-36  Score=298.87  Aligned_cols=221  Identities=29%  Similarity=0.445  Sum_probs=198.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  443 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl  443 (605)
                      ..|++.||..|.++|+++|++|.+++.+.+||+|||++|||+++++||+.+|.+|+||++|||++.|.++++++.+.+++
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            56899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCC--CCCccccccccCC--CCCCcccCCCCC
Q 007404          444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKA--PRSLDQKIGINQN--LKPSEVIADPEA  519 (605)
Q Consensus       444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~--~~SLD~~i~~d~~--~~l~d~l~D~~~  519 (605)
                      |.++...+++++++...+.+++|+.|+.+|+|+.+|++.+++..++.....  ..|||.++.++++  .++.+.+.    
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~d~~~----  157 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGDPIALLDTLG----  157 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCCCcccccccC----
Confidence            999999999999999999999999999999999999999999998875544  8999998863222  12333333    


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       520 ~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                       ++++.+...+....|..+|..||++|++||.++|+.+    +|++|||+.||+|+++|++++++|+++||+.+
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             3344455566778899999999999999999999877    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=1.6e-35  Score=300.97  Aligned_cols=226  Identities=30%  Similarity=0.358  Sum_probs=203.1

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  438 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~---~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s  438 (605)
                      ++..|++.||..|.++|+++|++|.+   ++.+.+||+||||+|||+++++||+.+|.+|+||+++||+|.|.++++++.
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            35889999999999999999999975   678999999999999999999999999999999999999999999999876


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh--CCCCCCCccccccccCCC-CCCcccC
Q 007404          439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGINQNL-KPSEVIA  515 (605)
Q Consensus       439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~--~~~~~~SLD~~i~~d~~~-~l~d~l~  515 (605)
                         ++|.++.+.+++++++.+.+.+.+|+.|+.+|||+.+|+++++|..++.  ......|||.++.++++. .+.+.+.
T Consensus        99 ---~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~  175 (251)
T PRK07670         99 ---WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIR  175 (251)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhc
Confidence               5899999999999999999999999999999999999999999999975  456789999988654432 2334445


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ++...++++.+...+....|..+|..||+++|.||.++|+.+    +|++|||+.||+|.++|+++++||+++||..+.
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            555567888888888889999999999999999999999877    999999999999999999999999999998764

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=8.9e-35  Score=296.13  Aligned_cols=248  Identities=25%  Similarity=0.329  Sum_probs=215.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHH
Q 007404          303 SSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA  382 (605)
Q Consensus       303 ~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIA  382 (605)
                      ..|+|+++||.+|..+++.                                       .++..|++.||..|.++|+++|
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                                       1347899999999999999999


Q ss_pred             HHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHH
Q 007404          383 KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLY  462 (605)
Q Consensus       383 krY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~  462 (605)
                      ++|.+++.+++||+||||++||+++++||+.+|.+|+||+++||+|.|.++++++.+.+++|.+.....++++++...+.
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 007404          463 SENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD  540 (605)
Q Consensus       463 ~elgr~PT~eEIAe~lgis~e~V~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~  540 (605)
                      ..+++.|+.+|+++.+|++.+++..+....  ....|+|.+++.+++....... + ...+|++.+...+....|..+|.
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            999999999999999999999998876543  4678999887654332111111 1 11245566666777788999999


Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      .||+++|+||.++|+.+    +|++|||+.||||.++|++++++|+++||+.+..
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=2e-34  Score=293.19  Aligned_cols=241  Identities=29%  Similarity=0.452  Sum_probs=211.2

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 007404          302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  381 (605)
Q Consensus       302 ~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsI  381 (605)
                      ...|.||.+++.+|..+++.                                        ++..|++.||..|.++|+++
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                                        34779999999999999999


Q ss_pred             HHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHH
Q 007404          382 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL  461 (605)
Q Consensus       382 AkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L  461 (605)
                      |++|.+++.+++||+||||+++|+++++|++.+|.+|.||+++||++.|.+++++.. .+|+|.++....++++++...+
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 007404          462 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL--KPSEVIADPEAETAEDLLIKKFMKEDLEKVL  539 (605)
Q Consensus       462 ~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~--~l~d~l~D~~~~spEe~l~~~el~~~L~~aL  539 (605)
                      ..++|+.|+.+|+|+.+|++++++..++.....+.||+.++.+++..  ++.+.+.++..   +.    ......|..+|
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            99999999999999999999999999888777889999887654332  23344443321   11    23456789999


Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ..||+++++||.++|+.+    +|++|||+.+|+|.++|++++++|+++||+.+.
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            999999999999999876    999999999999999999999999999998764

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

Probab=100.00  E-value=8.3e-35  Score=290.48  Aligned_cols=217  Identities=30%  Similarity=0.467  Sum_probs=196.1

Q ss_pred             HHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404          370 MITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  446 (605)
Q Consensus       370 LI~~nlrLVvsIAkrY~~---~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~  446 (605)
                      |+..|.++|+++|++|.+   ++.+++||+|||++|||+++++|||++|++|+||+++||++.+.+++++..   ++|.+
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            688999999999999986   789999999999999999999999999999999999999999999999875   48999


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh--CCCCCCCcccccccc-CCCCCCcccCCCCCCCHH
Q 007404          447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL--SPKAPRSLDQKIGIN-QNLKPSEVIADPEAETAE  523 (605)
Q Consensus       447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~--~~~~~~SLD~~i~~d-~~~~l~d~l~D~~~~spE  523 (605)
                      +...++++.++..++.+.+|+.|+.+|||+.+|+++++|..++.  ......|+|.++.++ +...+.+.++++...+|+
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPE  157 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHH
Confidence            99999999999999999999999999999999999999999985  344567888876543 234555666655666888


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      +.+...+....|..+|+.||+++|+||.++|+.+    +|++|||+.||+|.++|++++++|+++||+.+
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            8888888899999999999999999999999887    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=7.2e-34  Score=286.30  Aligned_cols=210  Identities=20%  Similarity=0.360  Sum_probs=181.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404          366 CKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  442 (605)
Q Consensus       366 A~e~LI~~nlrLVvsIAkrY~~---~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR  442 (605)
                      -...|+..|+++|.++|++|..   .+.+.+||+|||++|||+|+++|||.+| +|+||++||||++|.+++++..+   
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            3557899999999999999875   4679999999999999999999998666 89999999999999999998765   


Q ss_pred             ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhC--CCCCCCccccccccCCCCCCcccCCCCCC
Q 007404          443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIADPEAE  520 (605)
Q Consensus       443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~D~~~~  520 (605)
                      +|.++...+++++++.+.+.+++|+.||.+|||+.+|++.++|.+++..  .....|||.+++++++..   .+++   .
T Consensus        92 ~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~---~~~~---~  165 (231)
T PRK12427         92 RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHND---ILQS---R  165 (231)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCccc---ccCC---C
Confidence            5778888999999999999999999999999999999999999998753  456899999986554322   2222   1


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          521 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       521 spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .+++..   .....|..++..||+++|.||.++|+.+    +|++|||+.||||.++|+|++.++++|||..
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            344322   2456789999999999999999999877    9999999999999999999999999999964

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=100.00  E-value=1.8e-33  Score=283.07  Aligned_cols=224  Identities=30%  Similarity=0.437  Sum_probs=198.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  438 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~---~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s  438 (605)
                      .|.-+++.||..|.++|+++|++|.   +++.+++||+||||+|||+++++|||++|.+|+||+++||+|.|.++++++.
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            4577899999999999999999997   6789999999999999999999999999999999999999999999999986


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhC--CCCCCCccccccccCCCCCCcccCC
Q 007404          439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIAD  516 (605)
Q Consensus       439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~D  516 (605)
                      +   +|.++....+++.++...+.+.+|++|+.+|||+.+|++.++|..++..  .....|++..++++++. +.. ..+
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   6877777888899999999999999999999999999999999998863  34567888887654443 222 223


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      +..++|++.+...+....|..+|+.||+++|.||.++|+.+    +|++|||+.||||.++|+++++||+++||+.+.
T Consensus       160 ~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~  233 (236)
T PRK06986        160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEE----LNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG  233 (236)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHhccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence            33457888888888889999999999999999999999887    999999999999999999999999999999775

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.96  E-value=4.8e-28  Score=243.50  Aligned_cols=209  Identities=29%  Similarity=0.488  Sum_probs=168.4

Q ss_pred             HH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHH
Q 007404          294 LR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT  372 (605)
Q Consensus       294 l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~  372 (605)
                      +. |+.++ ++.|+||+++|..|...++.                                        ++..|++.|+.
T Consensus        18 ~~~~~~~~-~~~~~~~~~~e~~l~~~~~~----------------------------------------gd~~a~~~l~~   56 (233)
T PRK05803         18 LVSYVKNN-SFPQPLSEEEERKYLELMKE----------------------------------------GDEEARNILIE   56 (233)
T ss_pred             HHHHHHHh-cccCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHH
Confidence            45 99999 99999999999988766543                                        34789999999


Q ss_pred             HHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHH
Q 007404          373 SNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY  452 (605)
Q Consensus       373 ~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~  452 (605)
                      .|.++|++++.+|.+++.+++||+|||++++|+++++||+++|.+|.||+++|+|+.+.+++++..+..+          
T Consensus        57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~~----------  126 (233)
T PRK05803         57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTKK----------  126 (233)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhcccc----------
Confidence            9999999999999999999999999999999999999999988899999999999999999987643100          


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCcccccccc---CCCCCCcccCCCCCCCHHHHHHHH
Q 007404          453 RVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGIN---QNLKPSEVIADPEAETAEDLLIKK  529 (605)
Q Consensus       453 ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d---~~~~l~d~l~D~~~~spEe~l~~~  529 (605)
                                                                ..+++.+.+.+   ...++.+.+++. .+++++.+..+
T Consensus       127 ------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  163 (233)
T PRK05803        127 ------------------------------------------EVSLQDPIGVDKEGNEISLIDILGSE-EDDVIEQVELK  163 (233)
T ss_pred             ------------------------------------------CCCccccccCCCCcCcccHHHHccCC-CCCHHHHHHHH
Confidence                                                      01111111101   011222233332 23577777777


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      ...+.|..+|..||+++|+||.++|++++.+.+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus       164 ~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~~  230 (233)
T PRK05803        164 MEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRA  230 (233)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            7888899999999999999999999754444599999999999999999999999999999987653

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.94  E-value=8.7e-25  Score=219.23  Aligned_cols=205  Identities=28%  Similarity=0.487  Sum_probs=157.9

Q ss_pred             HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHH
Q 007404          296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI  375 (605)
Q Consensus       296 yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nl  375 (605)
                      |.-.--++.+.|++.+|.+|..+++.                                        ++..|++.|+..|.
T Consensus        19 ~~~~~~~~~~~~~~~~~~~li~~~~~----------------------------------------gd~~af~~l~~~y~   58 (227)
T TIGR02846        19 YVTNNGSFPQPLSEEEEKKYLDRLKE----------------------------------------GDEEARNVLIERNL   58 (227)
T ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhH
Confidence            54222266788999999888776653                                        44789999999999


Q ss_pred             HHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHH
Q 007404          376 RLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK  455 (605)
Q Consensus       376 rLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~  455 (605)
                      ++|+++|.+|.++..+++||+||+|+++|+++++|+++++.+|.||+++|++|.+.+++++..+..+             
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            9999999999999999999999999999999999999988899999999999999999988653110             


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCcccccccc---CCCCCCcccCCCCCCCHHHHHHHHHHH
Q 007404          456 EARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGIN---QNLKPSEVIADPEAETAEDLLIKKFMK  532 (605)
Q Consensus       456 ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d---~~~~l~d~l~D~~~~spEe~l~~~el~  532 (605)
                                                             ..+++...+.+   ....+.+...+ ...++++.....+..
T Consensus       126 ---------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  165 (227)
T TIGR02846       126 ---------------------------------------EVSLQDPIGVDKEGNEISLIDILGS-DGDSVIEQVELNLEI  165 (227)
T ss_pred             ---------------------------------------ceeccccccCCcccCcccHHHHhcC-CCCChHHHHHHHHHH
Confidence                                                   00111111000   00011112221 123566666666677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      +.|..+|+.||+++|+||.++|+++..+.+|++|||++||+|.++|++++++|+++||+.+
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            8899999999999999999999743222399999999999999999999999999999864

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

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.93  E-value=1.1e-24  Score=218.69  Aligned_cols=180  Identities=28%  Similarity=0.498  Sum_probs=137.8

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      ++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||+++++||.+.++++++.+..
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            45789999999999999999999999999999999999999999999999988889999999999999999998765410


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccc--cCC-CCCCcccCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI--NQN-LKPSEVIADPE  518 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~--d~~-~~l~d~l~D~~  518 (605)
                      .                                                    ..+++.+...  ++. ..+.+...+. 
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 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ...++...........|..+|+.||+++|+||.|+|++...+.+|++|||+.||||.+||+++++||+++||+.+.
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            1233344445556677999999999999999999995211112999999999999999999999999999999764

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.92  E-value=9.6e-24  Score=212.63  Aligned_cols=180  Identities=30%  Similarity=0.513  Sum_probs=139.4

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      ++..|++.|+..|.+.|+.+|++|.+++.+++||+||+|+++|+++++|++..+++|.||++.+++|.+.++++++.+..
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            45789999999999999999999999999999999999999999999999988888999999999999999999865411


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccc--cCC-CCCCcccCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI--NQN-LKPSEVIADPE  518 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~--d~~-~~l~d~l~D~~  518 (605)
                      ..                                                    .+++..+..  +++ ....+. .++.
T Consensus       129 ~~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~-~~~~  155 (234)
T TIGR02835       129 SE----------------------------------------------------VSFDEPLNVDWDGNELLLSDV-LGTD  155 (234)
T ss_pred             Cc----------------------------------------------------ccccccccCCCCCCcchHHHh-cCCC
Confidence            00                                                    111111100  000 000111 1112


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ...+++.+........|..+|+.||+++|.||.++|++.+++.+|++|||+.||||.++|+++.+||+++||+.+.
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            2234444555566678999999999999999999996432233999999999999999999999999999999775

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=5.9e-23  Score=201.34  Aligned_cols=192  Identities=23%  Similarity=0.303  Sum_probs=147.1

Q ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404          354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  433 (605)
Q Consensus       354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~  433 (605)
                      ..+.....++..|++.|+..|.++|+.+|++|.++..+++|++||+|++||+++.+||+.++.+|.||++.++++.+.++
T Consensus        13 ~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~   92 (208)
T PRK08295         13 ELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITA   92 (208)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHH
Confidence            33444456778999999999999999999999999999999999999999999999999887899999999999999999


Q ss_pred             HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccc-cCCCCCCc
Q 007404          434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI-NQNLKPSE  512 (605)
Q Consensus       434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~-d~~~~l~d  512 (605)
                      +++..+..+.+.                                               ....|++.++.+ +.+..+.+
T Consensus        93 ~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~~~~~  125 (208)
T PRK08295         93 IKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDRTLLD  125 (208)
T ss_pred             HHHhhhhccccc-----------------------------------------------cceeecCCcccCCccchhHHH
Confidence            886543211110                                               001222322211 11112233


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHH-HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          513 VIADPEAETAEDLLIKKFMKEDL-EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       513 ~l~D~~~~spEe~l~~~el~~~L-~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .+.++...+|++.+...+....+ ..++..||+++|.||.+ |..+    +|++|||+.||+|.++|+..++||+++||+
T Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~~e~----~s~~EIA~~lgis~~tV~~~l~rar~~Lr~  200 (208)
T PRK08295        126 VISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-YLDG----KSYQEIAEELNRHVKSIDNALQRVKRKLEK  200 (208)
T ss_pred             HhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-HHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            33333334677766655555555 45679999999999999 8777    999999999999999999999999999999


Q ss_pred             HHhhhh
Q 007404          592 KKRTKH  597 (605)
Q Consensus       592 ~l~~~~  597 (605)
                      .+....
T Consensus       201 ~l~~~~  206 (208)
T PRK08295        201 YLENRE  206 (208)
T ss_pred             HHHhhc
Confidence            886543

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.90  E-value=3e-22  Score=193.76  Aligned_cols=172  Identities=16%  Similarity=0.235  Sum_probs=141.9

Q ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404          354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  433 (605)
Q Consensus       354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~  433 (605)
                      ..+.....++..|++.|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.++
T Consensus         9 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~d~   87 (186)
T PRK05602          9 ELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCYDR   87 (186)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHHHH
Confidence            344455567799999999999999999999999999999999999999999999999986 4579999999999999999


Q ss_pred             HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404          434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV  513 (605)
Q Consensus       434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~  513 (605)
                      ++++...   +                                                     .+.         ..+ 
T Consensus        88 ~R~~~~~---~-----------------------------------------------------~~~---------~~~-  101 (186)
T PRK05602         88 LRRRREV---P-----------------------------------------------------VED---------APD-  101 (186)
T ss_pred             HHhcCCC---C-----------------------------------------------------ccc---------ccc-
Confidence            9875421   0                                                     000         000 


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       514 l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ..+. ...+++.+...+....+..+|..||+++|+||.|+|..+    +|++|||+.||+|..+|+++++||+++||+.+
T Consensus       102 ~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  176 (186)
T PRK05602        102 VPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQG----LSNIEAAAVMDISVDALESLLARGRRALRAQL  176 (186)
T ss_pred             cCCC-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHHhcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence            0011 124566666666777899999999999999999999887    99999999999999999999999999999988


Q ss_pred             hhhh
Q 007404          594 RTKH  597 (605)
Q Consensus       594 ~~~~  597 (605)
                      ...+
T Consensus       177 ~~~~  180 (186)
T PRK05602        177 ADLP  180 (186)
T ss_pred             Hhcc
Confidence            7654

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.89  E-value=3.6e-22  Score=192.16  Aligned_cols=181  Identities=15%  Similarity=0.229  Sum_probs=144.0

Q ss_pred             CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404          352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  431 (605)
Q Consensus       352 d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~  431 (605)
                      |...+.....++..|+..|+..|.++|+.+|++|.+++.+++|++||+|+++|+++.+|++..  +|.+|++..++|.+.
T Consensus         5 ~~~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~   82 (187)
T TIGR02948         5 IKKRIKEVRKGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTI   82 (187)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHH
Confidence            344556666778999999999999999999999999999999999999999999999999865  599999999999999


Q ss_pred             HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404          432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS  511 (605)
Q Consensus       432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~  511 (605)
                      +++++..+...+                                                       +.....++.....
T Consensus        83 ~~~rk~~~~~~~-------------------------------------------------------~~~~~~~~~~~~~  107 (187)
T TIGR02948        83 DRLRKRKPDFYL-------------------------------------------------------DDEVQGTDGLTME  107 (187)
T ss_pred             HHHHhhcccccc-------------------------------------------------------cccccCccccccc
Confidence            998864421000                                                       0000000011111


Q ss_pred             cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +...+ ..+.|++.+...+....+..+|..||+++|.||.++|..+    +|++|||+.||+|.++|++.++||+++||.
T Consensus       108 ~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~  182 (187)
T TIGR02948       108 SQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKYMED----LSLKEISEILDLPVGTVKTRIHRGREALRK  182 (187)
T ss_pred             ccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            11111 1235677777777778899999999999999999999887    999999999999999999999999999999


Q ss_pred             HHh
Q 007404          592 KKR  594 (605)
Q Consensus       592 ~l~  594 (605)
                      .+.
T Consensus       183 ~l~  185 (187)
T TIGR02948       183 QLR  185 (187)
T ss_pred             Hhh
Confidence            775

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

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=2.3e-22  Score=195.78  Aligned_cols=180  Identities=17%  Similarity=0.182  Sum_probs=146.4

Q ss_pred             CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404          352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  431 (605)
Q Consensus       352 d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~  431 (605)
                      +...+.....++..|++.|+..|.+.|+++|++|.++..+++|++||+|+++|++.++|++.  ..|.+|++.++++.++
T Consensus        13 ~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~--~~f~~wl~~i~~n~~~   90 (194)
T PRK12513         13 DEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARNLLI   90 (194)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CchHHHHHHHHHHHHH
Confidence            44555566667799999999999999999999999999999999999999999999999975  3699999999999999


Q ss_pred             HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404          432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS  511 (605)
Q Consensus       432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~  511 (605)
                      +++++..+....+.                                                   ..+.      .  . 
T Consensus        91 ~~~R~~~~~~~~~~---------------------------------------------------~~~~------~--~-  110 (194)
T PRK12513         91 DHWRRHGARQAPSL---------------------------------------------------DADE------Q--L-  110 (194)
T ss_pred             HHHHHhcccccccc---------------------------------------------------ccch------h--h-
Confidence            99988765221100                                                   0000      0  0 


Q ss_pred             cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ....+ ...+|++.+...+....|..+|+.||+++|.||.|+|+.|    +|++|||+.||+|.++|+++++||+++||+
T Consensus       111 ~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~  185 (194)
T PRK12513        111 HALAD-DGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGD----LELEEIAELTGVPEETVKSRLRYALQKLRE  185 (194)
T ss_pred             hhcCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeehccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            00111 1235777777777888999999999999999999999887    999999999999999999999999999999


Q ss_pred             HHhhhhH
Q 007404          592 KKRTKHL  598 (605)
Q Consensus       592 ~l~~~~L  598 (605)
                      .+...++
T Consensus       186 ~l~~~~~  192 (194)
T PRK12513        186 LLAEEVA  192 (194)
T ss_pred             HHHHhhc
Confidence            8876543

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.89  E-value=3.6e-22  Score=194.96  Aligned_cols=172  Identities=15%  Similarity=0.172  Sum_probs=138.7

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404          356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  435 (605)
Q Consensus       356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir  435 (605)
                      +.....++..+++.|+..|.++|+++|.+|.++..+++|++||+|+++|+++++||+.+| .|.+|++..++|.++++++
T Consensus        21 i~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~r   99 (194)
T PRK09646         21 LRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVDRVR   99 (194)
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHHHHH
Confidence            334445668999999999999999999999999999999999999999999999998766 6999999999999999998


Q ss_pred             hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404          436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  515 (605)
Q Consensus       436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  515 (605)
                      ++.+..+.-                                                   .+    .. .  .   +.  
T Consensus       100 ~~~~~~~~~---------------------------------------------------~~----~~-~--~---~~--  116 (194)
T PRK09646        100 SEQAASQRE---------------------------------------------------VR----YG-A--R---NV--  116 (194)
T ss_pred             hhccccccc---------------------------------------------------cc----cc-c--c---cc--
Confidence            765311100                                                   00    00 0  0   00  


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      +.....+++.+...+....|..+|..||+++|.||.|+|..+    +|++|||+.||+|..+|+++++||+++||+.+..
T Consensus       117 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~~  192 (194)
T PRK09646        117 DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGG----LTYREVAERLAVPLGTVKTRMRDGLIRLRDCLGV  192 (194)
T ss_pred             cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhcc
Confidence            001113444444456667899999999999999999999888    9999999999999999999999999999998753

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.89  E-value=1.1e-21  Score=190.11  Aligned_cols=167  Identities=16%  Similarity=0.274  Sum_probs=137.0

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCC----CCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404          359 RLNYGILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  434 (605)
Q Consensus       359 ~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~----g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i  434 (605)
                      ...++..|++.|+..|.+.|+.+|.++.++    +.+++|++||+|+++|+++.+|++. +..|.+|++..++|.+.+++
T Consensus        18 ~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~d~~   96 (189)
T PRK09648         18 AVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVADAH   96 (189)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHHHHH
Confidence            334568999999999999999999998765    3689999999999999999999864 45799999999999999999


Q ss_pred             hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404          435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  514 (605)
Q Consensus       435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  514 (605)
                      +++.+....+                                                     .+         ...+..
T Consensus        97 r~~~r~~~~~-----------------------------------------------------~~---------~~~~~~  114 (189)
T PRK09648         97 RAAGRDKAVP-----------------------------------------------------TE---------EVPERP  114 (189)
T ss_pred             HHhCCCcccc-----------------------------------------------------cc---------cccccc
Confidence            8865421100                                                     00         000011


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      .  ...+|++.+...+..+.|..+|..||+++|+||.++|+.|    +|++|||+.||+|..+|+++++||+++||+.+.
T Consensus       115 ~--~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~  188 (189)
T PRK09648        115 S--DDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVG----LSAEETAEAVGSTPGAVRVAQHRALARLRAEIE  188 (189)
T ss_pred             c--cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence            1  1135777777777788899999999999999999999988    999999999999999999999999999998763

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.89  E-value=9.2e-22  Score=189.35  Aligned_cols=177  Identities=14%  Similarity=0.192  Sum_probs=141.3

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404          356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  435 (605)
Q Consensus       356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir  435 (605)
                      +.....++..+++.|+..|.++|+++|++|.++..+++|++||++++||+++.+|++..  +|.+|++..+|+.+.++++
T Consensus         9 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R   86 (187)
T PRK09641          9 IKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLR   86 (187)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHH
Confidence            33444566899999999999999999999999999999999999999999999999853  6999999999999999998


Q ss_pred             hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404          436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  515 (605)
Q Consensus       436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  515 (605)
                      ++.+...                                                       ++.....++.....+.+.
T Consensus        87 ~~~~~~~-------------------------------------------------------~~~~~~~~~~~~~~~~~~  111 (187)
T PRK09641         87 KRKPDYY-------------------------------------------------------LDAEVAGTEGLTMYSQLA  111 (187)
T ss_pred             hcCcccc-------------------------------------------------------ccccccCCcchhhhcccc
Confidence            7643110                                                       000000011111111122


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      +. ..+|++.+...+....|..+|..||+++++||.++|..+    ++++|||+.||||.++|++.++||+++||+.+.
T Consensus       112 ~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~~~~----~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~  185 (187)
T PRK09641        112 AD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIED----LSLKEISEILDLPVGTVKTRIHRGREALRKQLR  185 (187)
T ss_pred             cC-cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence            21 235777777777778899999999999999999999877    999999999999999999999999999999774

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.89  E-value=6.6e-22  Score=192.27  Aligned_cols=186  Identities=20%  Similarity=0.259  Sum_probs=139.5

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404          356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  435 (605)
Q Consensus       356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir  435 (605)
                      +.....++..|++.||..|.+.|+.+|+++.++..+++||+||+|+.+|+++.+|++..+..|.||++.+|++.+.++++
T Consensus        10 ~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~~~~r   89 (198)
T TIGR02859        10 VELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIK   89 (198)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHHHHHH
Confidence            33344556899999999999999999999999999999999999999999999999988779999999999999988887


Q ss_pred             hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccc-cCCCCCCccc
Q 007404          436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGI-NQNLKPSEVI  514 (605)
Q Consensus       436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~-d~~~~l~d~l  514 (605)
                      ...+..+.+.                                               ....|++.+... +++.++.+.+
T Consensus        90 ~~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~  122 (198)
T TIGR02859        90 TATRQKHIPL-----------------------------------------------NSYVSLNKPIYDEESDRTLLDVI  122 (198)
T ss_pred             HHHHhcccch-----------------------------------------------hhhcCcccccccccccchHHHHh
Confidence            5432111100                                               011233322211 1111222222


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          515 ADPEAETAEDLLIKKFMKEDLEKVLDTL-NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       515 ~D~~~~spEe~l~~~el~~~L~~aL~~L-~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      .+....+|++.+...+....|.++|+.| ++.++.|+ ++|..+    +|++|||+.||+|.++|++.++||+++||+.+
T Consensus       123 ~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~-~~~~~~----~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l  197 (198)
T TIGR02859       123 SGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVL-QSYLDG----KSYQEIACDLNRHVKSIDNALQRVKRKLEKYL  197 (198)
T ss_pred             hccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHH-HHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence            2222346787777778788899999995 55666665 557666    99999999999999999999999999999865

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.

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=1.5e-21  Score=196.28  Aligned_cols=193  Identities=19%  Similarity=0.192  Sum_probs=153.9

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHH
Q 007404          302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  381 (605)
Q Consensus       302 ~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsI  381 (605)
                      .+.|+|++..+.+|...++.                                        ++..|++.|+..|.+.|+++
T Consensus         7 ~~~~~~~~~~~~~l~~~~~~----------------------------------------gd~~a~~~l~~~y~~~l~~~   46 (231)
T PRK11922          7 SRPPPLSAASDRELVARVLA----------------------------------------GDEAAFEALMRRHNRRLYRT   46 (231)
T ss_pred             CCCCCcCcccHHHHHHHHHc----------------------------------------CCHHHHHHHHHHHHHHHHHH
Confidence            56788888888877665543                                        45789999999999999999


Q ss_pred             HHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHH
Q 007404          382 AKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQL  461 (605)
Q Consensus       382 AkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L  461 (605)
                      ++++.++..+++||+||+|+++|+++++|++.  ..|.+|++..+++.+.+++++..+..+++..               
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            99999999999999999999999999999986  3799999999999999999886642211000               


Q ss_pred             HHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q 007404          462 YSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT  541 (605)
Q Consensus       462 ~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~  541 (605)
                                                         ..+. .. .++  ...... ....+|++.+...+..+.|..+|+.
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 1223677777788888899999999


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      ||+++|+||.++|..+    +|++|||+.||+|.++|+++++||+++||+.+..
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

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.88  E-value=2e-21  Score=184.87  Aligned_cols=174  Identities=17%  Similarity=0.169  Sum_probs=139.8

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404          359 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  438 (605)
Q Consensus       359 ~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s  438 (605)
                      ...++..|++.|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+  .+.+|.+|++.++++.+.+++++..
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            34567889999999999999999999999999999999999999999999999  3458999999999999999998765


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC
Q 007404          439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE  518 (605)
Q Consensus       439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~  518 (605)
                      +....+                                                  ..+.+    +.++....+...+  
T Consensus        82 ~~~~~~--------------------------------------------------~~~~~----~~~~~~~~~~~~~--  105 (182)
T PRK09652         82 RRPPAS--------------------------------------------------DVDAE----EAEDFDLADALRD--  105 (182)
T ss_pred             CCCCcc--------------------------------------------------ccccc----ccccccccccccc--
Confidence            421110                                                  00000    0011111111111  


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ..+|++.+...+....+..+|..||+++++||.++|+.+    +|++|||+.||+|..+|++.++||+++||+.+.
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

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

Probab=99.88  E-value=2.8e-21  Score=183.01  Aligned_cols=166  Identities=19%  Similarity=0.306  Sum_probs=137.6

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404          359 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  438 (605)
Q Consensus       359 ~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s  438 (605)
                      ...++..|++.|+..|.+.+++++.++.++..+++|++||+|+.+|+.+++|+...+ .|.+|++.++++.+.++++++.
T Consensus         5 ~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~   83 (170)
T TIGR02952         5 AQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSK   83 (170)
T ss_pred             HHccCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcC
Confidence            344678999999999999999999999998899999999999999999999997555 7999999999999999999865


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC
Q 007404          439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE  518 (605)
Q Consensus       439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~  518 (605)
                      +....                                                     +++..         .+...  .
T Consensus        84 ~~~~~-----------------------------------------------------~~~~~---------~~~~~--~   99 (170)
T TIGR02952        84 RHPLF-----------------------------------------------------SLDVF---------KELLS--N   99 (170)
T ss_pred             CCCCC-----------------------------------------------------cHHHH---------hhcCC--C
Confidence            42110                                                     00000         00000  1


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ..+|++.+...+....+..+|..|||++|+||.++|..|    +|++|||+.||||..+|+++++||+++||+.+
T Consensus       100 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l  170 (170)
T TIGR02952       100 EPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQN----LPIAEVARILGKTEGAVKILQFRAIKKLARQM  170 (170)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            125677777777778899999999999999999999887    99999999999999999999999999999853

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

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=2.3e-21  Score=188.52  Aligned_cols=171  Identities=16%  Similarity=0.199  Sum_probs=136.8

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404          356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  435 (605)
Q Consensus       356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir  435 (605)
                      +.+...++..+++.|+..|.+.|+.+++++.++..+++|++||+|+++|+. ..|++..+ .|.||++.++++.++++++
T Consensus        20 ~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~R   97 (194)
T PRK12519         20 FSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLR   97 (194)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHH
Confidence            344455678999999999999999999999999999999999999999976 67887655 7999999999999999998


Q ss_pred             hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404          436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  515 (605)
Q Consensus       436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  515 (605)
                      ++.+..+..                  .         +                        .+        ..   ...
T Consensus        98 k~~~~~~~~------------------~---------~------------------------~~--------~~---~~~  115 (194)
T PRK12519         98 SRRSRQRLL------------------E---------R------------------------WQ--------QE---LLG  115 (194)
T ss_pred             hcccccchh------------------h---------h------------------------hh--------hh---hcc
Confidence            765411100                  0         0                        00        00   000


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      +.....+++.+...+....|..+|..||+++++||.|+|..|    +|++|||+.||+|.++|+++++||+++||+.+.
T Consensus       116 ~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~  190 (194)
T PRK12519        116 EASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEG----LSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ  190 (194)
T ss_pred             cccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhhhcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence            011124556666666677899999999999999999999887    999999999999999999999999999999764

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.88  E-value=1.3e-21  Score=182.80  Aligned_cols=151  Identities=20%  Similarity=0.246  Sum_probs=124.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  443 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl  443 (605)
                      ..|++.|++.|.++|+.+++++ +...+++|++||+++++|+++++|++..| .|.+|++..+++.++++++++.+... 
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            5689999999999999999986 55679999999999999999999998776 79999999999999999987632000 


Q ss_pred             cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404          444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  523 (605)
Q Consensus       444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE  523 (605)
                                          .                              ...       +         +     .|+
T Consensus        80 --------------------~------------------------------~~~-------~---------~-----~~~   88 (154)
T PRK06759         80 --------------------K------------------------------CVC-------V---------G-----EYE   88 (154)
T ss_pred             --------------------c------------------------------ccc-------c---------C-----CCc
Confidence                                0                              000       0         0     111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      +.....+....|..+|..||+++|+||.++|+.|    +|++|||+.||+|..+|+++++||+++||+.
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            1222233456799999999999999999999988    9999999999999999999999999999974

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=4e-21  Score=184.58  Aligned_cols=168  Identities=14%  Similarity=0.116  Sum_probs=136.6

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404          357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  436 (605)
Q Consensus       357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~  436 (605)
                      .....++..++..|+..|.+.|+.+|.+|.++..+++|++||+|+++|+++++|++..+ .|.||++..++|.+.+++++
T Consensus        11 ~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R~   89 (179)
T PRK12514         11 VRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLRA   89 (179)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHh
Confidence            33445668899999999999999999999999999999999999999999999987544 69999999999999999987


Q ss_pred             ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404          437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  516 (605)
Q Consensus       437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D  516 (605)
                      +.+. ..+                                                     ++.      .   .+ ..+
T Consensus        90 ~~~~-~~~-----------------------------------------------------~~~------~---~~-~~~  105 (179)
T PRK12514         90 RKAV-AVD-----------------------------------------------------IDE------A---HD-LAD  105 (179)
T ss_pred             cCCc-ccc-----------------------------------------------------ccc------c---hh-ccc
Confidence            5431 000                                                     000      0   00 001


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      . ..+|++.+...+....|..+|..||+++|+||.++|+.|    +|++|||+.||+|..+|++.++||+++||+++.
T Consensus       106 ~-~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  178 (179)
T PRK12514        106 P-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEG----LSYKELAERHDVPLNTMRTWLRRSLLKLRECLS  178 (179)
T ss_pred             c-CCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCChHHHHHHHHHHHHHHHHHhc
Confidence            1 124666655555556799999999999999999999877    999999999999999999999999999999764

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=5.4e-21  Score=187.00  Aligned_cols=174  Identities=22%  Similarity=0.194  Sum_probs=141.5

Q ss_pred             HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHH
Q 007404          353 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  432 (605)
Q Consensus       353 ~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r  432 (605)
                      ...+.+...++..|++.|+..|.+.|+.+|.++.++..+++|++||+++.+|+.+.+|++.. ..|.+|++..+++.+.+
T Consensus        14 ~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d   92 (196)
T PRK12524         14 EALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLCTD   92 (196)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHHHH
Confidence            34444455567999999999999999999999999999999999999999999999998643 36999999999999999


Q ss_pred             HHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCc
Q 007404          433 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE  512 (605)
Q Consensus       433 ~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d  512 (605)
                      +++++.+..                                                      ..++..   .      +
T Consensus        93 ~~Rk~~~~~------------------------------------------------------~~~~~~---~------~  109 (196)
T PRK12524         93 RLRRRRRAS------------------------------------------------------VDLDDA---P------E  109 (196)
T ss_pred             HHHhhcCCC------------------------------------------------------CCcccc---c------c
Confidence            988754300                                                      000000   0      0


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          513 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       513 ~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      . .+. ...+++.+...+....|..+|+.||+++|.||.|+|..+    ++++|||+.||||..+|+++++||+++||+.
T Consensus       110 ~-~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~~~g----~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~  183 (196)
T PRK12524        110 P-ADA-APGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEG----LSNPEIAEVMEIGVEAVESLTARGKRALAAL  183 (196)
T ss_pred             c-ccc-CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            0 111 124566667677778899999999999999999999987    9999999999999999999999999999998


Q ss_pred             Hhhh
Q 007404          593 KRTK  596 (605)
Q Consensus       593 l~~~  596 (605)
                      +...
T Consensus       184 l~~~  187 (196)
T PRK12524        184 LAGQ  187 (196)
T ss_pred             HHhc
Confidence            8753

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.87  E-value=5.9e-21  Score=184.17  Aligned_cols=178  Identities=15%  Similarity=0.150  Sum_probs=140.0

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404          355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  434 (605)
Q Consensus       355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i  434 (605)
                      .+.....++..+++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+++++|++.  .+|.+|++..+++.+.+++
T Consensus        10 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~~~~   87 (190)
T TIGR02939        10 LVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAKNHL   87 (190)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHHHHH
Confidence            34444456789999999999999999999999999999999999999999999999975  3699999999999999998


Q ss_pred             hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404          435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  514 (605)
Q Consensus       435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  514 (605)
                      +++.+.....                                                  ..+.+..      ....+..
T Consensus        88 r~~~r~~~~~--------------------------------------------------~~~~~~~------~~~~~~~  111 (190)
T TIGR02939        88 VAQGRRPPTS--------------------------------------------------DVEIEDA------EHFEGAD  111 (190)
T ss_pred             HHhccCCCcc--------------------------------------------------cccccch------hhhcccc
Confidence            7654311100                                                  0000000      0000000


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ......+|++.+...+....|..+|..||+++|+||.++|..+    +|++|||+.||+|..+|++.++||+++||+.+.
T Consensus       112 ~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~  187 (190)
T TIGR02939       112 RLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRELEG----LSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR  187 (190)
T ss_pred             cccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhhhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            0001235677677777788899999999999999999999887    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.

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.87  E-value=4e-21  Score=185.48  Aligned_cols=172  Identities=17%  Similarity=0.202  Sum_probs=133.0

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404          355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  434 (605)
Q Consensus       355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i  434 (605)
                      .+.....++..|++.|+..|.+.|+.++++|.+++.+++|++||+|+.+|+++++|++..+ .|.+|++..++|.+.+++
T Consensus        13 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~   91 (186)
T PRK13919         13 LLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAVDHV   91 (186)
T ss_pred             HHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHHHHH
Confidence            3444446678999999999999999999999999999999999999999999999987644 699999999999999999


Q ss_pred             hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404          435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  514 (605)
Q Consensus       435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  514 (605)
                      ++..+..+.                                                    .+.+     .......+ .
T Consensus        92 rk~~~~~~~----------------------------------------------------~~~~-----~~~~~~~~-~  113 (186)
T PRK13919         92 RRRAARPQP----------------------------------------------------LEPD-----EREPEAFD-L  113 (186)
T ss_pred             Hhhhccccc----------------------------------------------------cccc-----cccccccc-C
Confidence            876431000                                                    0000     00000000 0


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      +++.  ..   .........|..+|+.||+++|+||.++|..+    +|++|||+.||+|..+|+.+++||+++||+.+.
T Consensus       114 ~~~~--~~---~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~  184 (186)
T PRK13919        114 PGPG--LD---EEGHLDRTRLGRALKALSPEERRVIEVLYYQG----YTHREAAQLLGLPLGTLKTRARRALSRLKEVLR  184 (186)
T ss_pred             CCcc--cc---HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            0111  11   11223346689999999999999999999887    999999999999999999999999999999764

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.87  E-value=8.6e-21  Score=184.37  Aligned_cols=177  Identities=13%  Similarity=0.128  Sum_probs=139.6

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404          356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  435 (605)
Q Consensus       356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir  435 (605)
                      +.....++..+++.|+..|.+.|+.++++|.++..+++|++||+++++|+++.+|++..  .|.+|++..+++.+.++++
T Consensus        11 l~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~r   88 (193)
T PRK11923         11 VERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLV   88 (193)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHH
Confidence            33444466889999999999999999999999999999999999999999999999874  5999999999999999998


Q ss_pred             hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404          436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  515 (605)
Q Consensus       436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  515 (605)
                      ++.+.....                                                  ...++......+.    +.+.
T Consensus        89 k~~~~~~~~--------------------------------------------------~~~~~~~~~~~~~----~~~~  114 (193)
T PRK11923         89 SRGRRPPDS--------------------------------------------------DVSSEDAEFYDGD----HALK  114 (193)
T ss_pred             HhcCCCccc--------------------------------------------------cccccchhhhccc----cccc
Confidence            755411100                                                  0000000000000    0011


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                        ...+|++.+...+....|..+|..||+++|.||.++|..|    +|++|||+.||+|..+|+++.+||+++||+++.
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              1235677777777788899999999999999999999877    999999999999999999999999999999875

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=6.6e-21  Score=184.11  Aligned_cols=170  Identities=14%  Similarity=0.165  Sum_probs=136.9

Q ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404          354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  433 (605)
Q Consensus       354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~  433 (605)
                      ..+.....++..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..+++.+.++
T Consensus        12 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~d~   90 (182)
T PRK12537         12 ACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLALNV   90 (182)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHH
Confidence            34455556679999999999999999999999999999999999999999999999986544 69999999999999999


Q ss_pred             HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404          434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV  513 (605)
Q Consensus       434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~  513 (605)
                      ++++.+...+                                                       +.    . .   .+.
T Consensus        91 ~r~~~~~~~~-------------------------------------------------------~~----~-~---~~~  107 (182)
T PRK12537         91 LRDTRREVVL-------------------------------------------------------DD----D-A---EET  107 (182)
T ss_pred             HHhccccCcc-------------------------------------------------------cc----c-h---hhh
Confidence            9886531100                                                       00    0 0   000


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       514 l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ..+  ...+++..........|..+|+.||+++|+||.++|..|    +|++|||+.||||.++|+++++||+++||+.+
T Consensus       108 ~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~~----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l  181 (182)
T PRK12537        108 AQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDG----CSHAEIAQRLGAPLGTVKAWIKRSLKALRECM  181 (182)
T ss_pred             ccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCChhhHHHHHHHHHHHHHHHh
Confidence            000  112333444445567799999999999999999999888    99999999999999999999999999999875

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=5.8e-21  Score=184.71  Aligned_cols=172  Identities=13%  Similarity=0.120  Sum_probs=138.2

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404          355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  434 (605)
Q Consensus       355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i  434 (605)
                      .+.....++..+++.|+..|.++|+.+|++|.++..+++|++||+|+++|+++++|++.++ .|.+|++..++|.+++++
T Consensus        15 l~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~   93 (187)
T PRK12534         15 LLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHL   93 (187)
T ss_pred             HHHHHHcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHH
Confidence            4445556778999999999999999999999999999999999999999999999998655 589999999999999999


Q ss_pred             hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404          435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  514 (605)
Q Consensus       435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  514 (605)
                      +++.+..+.                                                    .+++..         .+..
T Consensus        94 R~~~~~~~~----------------------------------------------------~~~~~~---------~~~~  112 (187)
T PRK12534         94 RANAPQRRN----------------------------------------------------VALDDA---------GELR  112 (187)
T ss_pred             Hhccccccc----------------------------------------------------ccccch---------hhhc
Confidence            876431000                                                    000000         0000


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                       ++ ..++++.....+....|..+|..||++++.||.++|..|    +|++|||+.||+|.++|+++++||+++||+.+.
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 113444445556678899999999999999999999877    999999999999999999999999999999764

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.87  E-value=7e-21  Score=185.17  Aligned_cols=171  Identities=20%  Similarity=0.265  Sum_probs=138.8

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCC---CCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404          355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG---MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  431 (605)
Q Consensus       355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g---~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~  431 (605)
                      .+.+...++..|++.|+..|.+.|++++.++.+++   .+++|++||+++++|+++++|++..+ .|.+|++..++|.+.
T Consensus         8 li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~~   86 (189)
T PRK06811          8 FIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKAI   86 (189)
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHHH
Confidence            34444556689999999999999999999998853   47999999999999999999997655 799999999999999


Q ss_pred             HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404          432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS  511 (605)
Q Consensus       432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~  511 (605)
                      ++++++.+....                                                    .+.+.           
T Consensus        87 d~~rk~~~~~~~----------------------------------------------------~~~~~-----------  103 (189)
T PRK06811         87 DYKRKLTKNNEI----------------------------------------------------DSIDE-----------  103 (189)
T ss_pred             HHHHHhcccccc----------------------------------------------------ccchh-----------
Confidence            999886541110                                                    00000           


Q ss_pred             cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                       ...+ ..++|++.+...+....|..+|..||+++|.||.|+|..|    +|++|||+.||+|..+|+++++||+++||+
T Consensus       104 -~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~  177 (189)
T PRK06811        104 -FILI-SEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLG----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQK  177 (189)
T ss_pred             -hhhc-ccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence             0000 1125666677777778899999999999999999999877    999999999999999999999999999998


Q ss_pred             HHhh
Q 007404          592 KKRT  595 (605)
Q Consensus       592 ~l~~  595 (605)
                      ..-+
T Consensus       178 ~~~~  181 (189)
T PRK06811        178 NKLN  181 (189)
T ss_pred             cccC
Confidence            6543

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=6.7e-21  Score=192.45  Aligned_cols=164  Identities=16%  Similarity=0.208  Sum_probs=135.6

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404          361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  440 (605)
Q Consensus       361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~  440 (605)
                      .|+..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..++|.++++++++.+.
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            4568899999999999999999999999999999999999999999999987554 799999999999999998764210


Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCC
Q 007404          441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE  520 (605)
Q Consensus       441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~  520 (605)
                       .+                                                       +. .  .      +.. + ...
T Consensus       138 -~~-------------------------------------------------------~~-~--~------~~~-~-~~~  150 (233)
T PRK12538        138 -NV-------------------------------------------------------DA-V--P------EVA-D-GKP  150 (233)
T ss_pred             -cc-------------------------------------------------------cc-c--c------ccc-c-CCC
Confidence             00                                                       00 0  0      000 0 012


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          521 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       521 spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      .+++.+...+....|..+|..||+++|+||.|+|..|    +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus       151 ~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~~eg----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~  222 (233)
T PRK12538        151 DAVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHEN----MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRH  222 (233)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            3455555666677899999999999999999999988    99999999999999999999999999999988754

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=3.2e-21  Score=186.56  Aligned_cols=175  Identities=19%  Similarity=0.216  Sum_probs=139.8

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404          361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  440 (605)
Q Consensus       361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~  440 (605)
                      .++..|++.|+..|.+.++.+|+++.++..+++|++||+|+.+|+++++|++..+..|.||++..++|.++++++++.+.
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            35688999999999999999999999999999999999999999999999875445799999999999999999886531


Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCC
Q 007404          441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE  520 (605)
Q Consensus       441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~  520 (605)
                      ...                  .                                    +     +...   +.... ..+
T Consensus        85 ~~~------------------~------------------------------------~-----~~~~---~~~~~-~~~  101 (185)
T PRK12542         85 ETF------------------L------------------------------------E-----EYER---ESIEA-VDE  101 (185)
T ss_pred             hhh------------------h------------------------------------h-----hccc---cchhh-hhc
Confidence            000                  0                                    0     0000   00000 011


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhh
Q 007404          521 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ  600 (605)
Q Consensus       521 spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~  600 (605)
                      .+++.....+....|..+|..||+++|+||.|+|..+    +|++|||+.||+|.++|+++++||+++||+.+.......
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            3344344444556799999999999999999999988    999999999999999999999999999999998776666


Q ss_pred             hh
Q 007404          601 YA  602 (605)
Q Consensus       601 yl  602 (605)
                      |+
T Consensus       178 ~~  179 (185)
T PRK12542        178 FK  179 (185)
T ss_pred             HH
Confidence            54

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=2.6e-20  Score=176.78  Aligned_cols=171  Identities=19%  Similarity=0.162  Sum_probs=141.9

Q ss_pred             HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhc
Q 007404          358 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  437 (605)
Q Consensus       358 ~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~  437 (605)
                      ....++..|++.|++.|.+.|+.+++++.++..+++|++||+++.||++.++|+  .+.+|.+|++..+++.+.+++++.
T Consensus         6 ~~~~~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~   83 (179)
T PRK11924          6 VDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRR   83 (179)
T ss_pred             HHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhc
Confidence            344567899999999999999999999999999999999999999999999998  345899999999999999999876


Q ss_pred             cccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCC
Q 007404          438 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP  517 (605)
Q Consensus       438 sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~  517 (605)
                      .+....                                                     ..+     +.    .+...+.
T Consensus        84 ~~~~~~-----------------------------------------------------~~~-----~~----~~~~~~~  101 (179)
T PRK11924         84 RREKAV-----------------------------------------------------LSD-----DA----LEPEFAE  101 (179)
T ss_pred             cccccc-----------------------------------------------------Ccc-----cc----cccccCC
Confidence            541110                                                     000     00    0000000


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          518 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       518 ~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      ...+|++.+...+....|..+|..||++++.||.++|..+    +|++|||+.||+|+.+|+++++||+++||+.+...
T Consensus       102 ~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~~~~----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~  176 (179)
T PRK11924        102 TAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEG----LSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ  176 (179)
T ss_pred             ccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            2346888888888889999999999999999999999877    99999999999999999999999999999988754

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

Probab=99.86  E-value=1.7e-20  Score=180.57  Aligned_cols=180  Identities=14%  Similarity=0.152  Sum_probs=138.7

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404          361 NYGILCKDKMITSNIRLVISIAKNYQG----AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  436 (605)
Q Consensus       361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~----~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~  436 (605)
                      .++..|++.|+..|.+.|+.+|++|.+    +..+++|++||+++.+|+++..|++..+.+|.+|++..+++.+.+++++
T Consensus         3 ~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~   82 (189)
T TIGR02984         3 GGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR   82 (189)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence            356889999999999999999999853    5678999999999999999999998666689999999999999999886


Q ss_pred             ccc-cccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccC-CCCCCccc
Q 007404          437 QSR-TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ-NLKPSEVI  514 (605)
Q Consensus       437 ~sr-~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~-~~~l~d~l  514 (605)
                      +.+ ..+.                         +                       ....+++.....++ ...+.+.+
T Consensus        83 ~~~~~~r~-------------------------~-----------------------~~~~~~~~~~~~~~~~~~~~~~~  114 (189)
T TIGR02984        83 HLGAQKRD-------------------------I-----------------------RREQSLDAGGRLDESSVRLAAQL  114 (189)
T ss_pred             HHHHHhhh-------------------------c-----------------------ccccCCCcccccCCcchhHHHHc
Confidence            521 0000                         0                       00012221110011 11122222


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      .+ ..++|++.+...+....|..+|..||+++|.||.++|+.+    +|++|||+.||||.++|++.++||+++||+.+
T Consensus       115 ~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~~~g----~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l  188 (189)
T TIGR02984       115 AA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRHLEG----LSFAEVAERMDRSEGAVSMLWVRGLARLRQIL  188 (189)
T ss_pred             cC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            22 2336777777777778899999999999999999999877    99999999999999999999999999999875

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=2.1e-20  Score=181.54  Aligned_cols=176  Identities=20%  Similarity=0.240  Sum_probs=143.1

Q ss_pred             CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404          352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  431 (605)
Q Consensus       352 d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~  431 (605)
                      |...+.....++..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|++.++|++.  ..|.+|++..+++.+.
T Consensus         9 ~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~   86 (189)
T PRK12515          9 DEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKAL   86 (189)
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHH
Confidence            33444555567799999999999999999999999999999999999999999999999974  3799999999999999


Q ss_pred             HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404          432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS  511 (605)
Q Consensus       432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~  511 (605)
                      +++++..+. .+                                                       ..    + .  . 
T Consensus        87 d~~r~~~~~-~~-------------------------------------------------------~~----~-~--~-  102 (189)
T PRK12515         87 SALRRRKHE-EI-------------------------------------------------------DD----E-A--A-  102 (189)
T ss_pred             HHHHccCCC-CC-------------------------------------------------------cc----c-c--c-
Confidence            999865421 00                                                       00    0 0  0 


Q ss_pred             cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ....+ ..++|++.....+....+..+|+.||+++|+||.++|..+    +|++|||+.||+|..+|+++++||+++||+
T Consensus       103 ~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~~----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~  177 (189)
T PRK12515        103 AAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHE----KSVEEVGEIVGIPESTVKTRMFYARKKLAE  177 (189)
T ss_pred             cccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            00111 1235666666667778899999999999999999999988    999999999999999999999999999999


Q ss_pred             HHhhhhH
Q 007404          592 KKRTKHL  598 (605)
Q Consensus       592 ~l~~~~L  598 (605)
                      .+...+.
T Consensus       178 ~l~~~~~  184 (189)
T PRK12515        178 LLKAAGV  184 (189)
T ss_pred             HHHHhcc
Confidence            8876543

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.8e-20  Score=185.23  Aligned_cols=173  Identities=14%  Similarity=0.170  Sum_probs=135.1

Q ss_pred             HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404          359 RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  438 (605)
Q Consensus       359 ~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s  438 (605)
                      ...++..+++.|+..|.+.|+.++.++.++..+++|++||+|+.+|++++.|++.++ .|.||++.++||.+.++++++.
T Consensus        32 ~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~  110 (206)
T PRK12526         32 AISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIK  110 (206)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhc
Confidence            344678999999999999999999999999899999999999999999999998766 5999999999999999998865


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC
Q 007404          439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE  518 (605)
Q Consensus       439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~  518 (605)
                      +.....                                                     ++     ++.....+.+.+..
T Consensus       111 ~~~~~~-----------------------------------------------------~~-----~~~~~~~~~~~~~~  132 (206)
T PRK12526        111 AKKEQN-----------------------------------------------------LG-----DDIWPIEQALAESQ  132 (206)
T ss_pred             cccccc-----------------------------------------------------cc-----cccchhhhhccccc
Confidence            411000                                                     00     00000000111111


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                       ..+. ..........|..+|..||+++|+||.++|+.+    +|++|||+.||+|..+|+.+++||+++||+.+...
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 222333446789999999999999999999988    99999999999999999999999999999988643

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.86  E-value=6.3e-21  Score=185.17  Aligned_cols=172  Identities=20%  Similarity=0.286  Sum_probs=134.0

Q ss_pred             CCHHHHHHHHh----ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHH
Q 007404          351 VDQRELRRRLN----YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI  426 (605)
Q Consensus       351 ~d~~~L~~~l~----~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wI  426 (605)
                      ++.+.|...++    ++..|++.|+..|.+.|+.+|.+|.++..+++|++||+|+.+|+++++|++.  ..|.+|++.++
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            44444555544    4799999999999999999999999999999999999999999999999863  47999999999


Q ss_pred             HHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccC
Q 007404          427 KQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQ  506 (605)
Q Consensus       427 RqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~  506 (605)
                      +|.+.+++++..+....                                                     ..+...    
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 007404          507 NLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  586 (605)
Q Consensus       507 ~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL  586 (605)
                           +...++.    ++.....+....|..+|+.||+++|+||.|+|..+    +|++|||+.||||..+|+.++.||+
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    00011123446689999999999999999999988    9999999999999999999999999


Q ss_pred             HHHHhHHh
Q 007404          587 RKLKNKKR  594 (605)
Q Consensus       587 kKLR~~l~  594 (605)
                      ++||+.+.
T Consensus       176 ~~Lr~~l~  183 (188)
T PRK09640        176 DKLREKFA  183 (188)
T ss_pred             HHHHHHHH
Confidence            99999764

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=2.9e-20  Score=179.19  Aligned_cols=166  Identities=16%  Similarity=0.242  Sum_probs=134.9

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404          361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  440 (605)
Q Consensus       361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~  440 (605)
                      .++..|++.|+..|.+.|+.+++.|.++..+++|++||+|+.+|+++.+|++..  .|.+|++..+++.+.+++++..+.
T Consensus         3 ~~d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~   80 (179)
T PRK12543          3 SGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRR   80 (179)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhccc
Confidence            356789999999999999999999999999999999999999999999999864  699999999999999988765421


Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCC
Q 007404          441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAE  520 (605)
Q Consensus       441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~  520 (605)
                      .+.                                                      ++..   . +  ..+.   ....
T Consensus        81 ~~~------------------------------------------------------~~~~---~-~--~~~~---~~~~   97 (179)
T PRK12543         81 FRI------------------------------------------------------FEKA---E-E--QRKP---VSID   97 (179)
T ss_pred             ccc------------------------------------------------------cccc---c-c--cccc---cccc
Confidence            000                                                      0000   0 0  0000   0111


Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          521 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       521 spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      .|+. +...+....|..+|..||+++|+||.|+|..|    +|++|||+.||||..+|+..++||+++||+.+...
T Consensus        98 ~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~~e~----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~  168 (179)
T PRK12543         98 FSED-VLSKESNQELIELIHKLPYKLRQVIILRYLHD----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE  168 (179)
T ss_pred             ChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcc----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444 55666778899999999999999999999988    99999999999999999999999999999998754

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.85  E-value=5.4e-20  Score=179.71  Aligned_cols=169  Identities=14%  Similarity=0.134  Sum_probs=137.1

Q ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404          354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  433 (605)
Q Consensus       354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~  433 (605)
                      ..+.....++..+++.|++.|.+.|++++.++.++..+++|++||+|+.+|+.+++|++..  .|.+|++..+++.+.++
T Consensus        16 ~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~~d~   93 (192)
T PRK09643         16 ELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDR   93 (192)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHHHHH
Confidence            3445555677999999999999999999999999999999999999999999999999753  69999999999999999


Q ss_pred             HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404          434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV  513 (605)
Q Consensus       434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~  513 (605)
                      +++..+..+.                                                     +++.    . .    + 
T Consensus        94 ~Rk~~~~~~~-----------------------------------------------------~~~~----~-~----~-  110 (192)
T PRK09643         94 LRRAKARPTV-----------------------------------------------------PLDD----V-Y----P-  110 (192)
T ss_pred             HHccccCCCC-----------------------------------------------------Cccc----c-c----c-
Confidence            9876531100                                                     0000    0 0    0 


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       514 l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ...    .+++.+...+....|..+|+.||+++|+||.|+|..+    +|++|||+.||+|..+|+.++.||+++||+.+
T Consensus       111 ~~~----~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~~~g----~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l  182 (192)
T PRK09643        111 VAQ----LERDPTARVETALAVQRALMRLPVEQRAALVAVDMQG----YSVADAARMLGVAEGTVKSRCARGRARLAELL  182 (192)
T ss_pred             ccC----CcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            000    1222334445567799999999999999999999987    99999999999999999999999999999988


Q ss_pred             hh
Q 007404          594 RT  595 (605)
Q Consensus       594 ~~  595 (605)
                      ..
T Consensus       183 ~~  184 (192)
T PRK09643        183 GY  184 (192)
T ss_pred             HH
Confidence            64

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.85  E-value=4.1e-20  Score=176.44  Aligned_cols=164  Identities=13%  Similarity=0.094  Sum_probs=131.3

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      ++..+++.|+..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++.. ..|.+|++..++|.+.++++++.+..
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            45889999999999999999999999989999999999999999999997533 36999999999999999998764310


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  521 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s  521 (605)
                      ..                                                     ..      ++..   + .++.   .
T Consensus        85 ~~-----------------------------------------------------~~------~~~~---~-~~~~---~   98 (173)
T PRK09645         85 VE-----------------------------------------------------GG------DDVL---G-VPEQ---S   98 (173)
T ss_pred             cc-----------------------------------------------------cc------cccc---c-CCCC---C
Confidence            00                                                     00      0000   0 0011   1


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      +++..........|..+|+.||+++|+||.|+|+.|    +|++|||+.||+|..+|+.+++||+++||+.+...
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            122233334456789999999999999999999988    99999999999999999999999999999988653

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=4.1e-20  Score=180.51  Aligned_cols=176  Identities=18%  Similarity=0.147  Sum_probs=134.9

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404          356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  435 (605)
Q Consensus       356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir  435 (605)
                      +.+...++..+++.|+..|.+.|+.+|.++.++..+++|++||+|+.+|+..++|++.++ .|.+|++..++|.++++++
T Consensus        18 i~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~R   96 (194)
T PRK12531         18 MEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLR   96 (194)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHH
Confidence            344445678999999999999999999999999899999999999999999999997554 6999999999999999998


Q ss_pred             hccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC
Q 007404          436 DQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA  515 (605)
Q Consensus       436 ~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~  515 (605)
                      +..+....                                                    ...+.... + . .......
T Consensus        97 k~~~~~~~----------------------------------------------------~~~~~~~~-~-~-~~~~~~~  121 (194)
T PRK12531         97 KQKGKDLH----------------------------------------------------IHADDIWP-S-D-YYPPDLV  121 (194)
T ss_pred             Hhcccccc----------------------------------------------------cchhhccc-c-c-ccccccc
Confidence            86531100                                                    00000000 0 0 0000000


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          516 DPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       516 D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      +  ...++..    .....+..+|..||+++|+||.|+|..+    +|++|||+.||||.++|+.+++||+++||+.+..
T Consensus       122 ~--~~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~eg----~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~  191 (194)
T PRK12531        122 D--HYSPEQD----MLKEQVMKFLDRLPKAQRDVLQAVYLEE----LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDA  191 (194)
T ss_pred             c--ccCHHHH----HHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhh
Confidence            0  1123322    2335688899999999999999999987    9999999999999999999999999999998875


Q ss_pred             hh
Q 007404          596 KH  597 (605)
Q Consensus       596 ~~  597 (605)
                      ..
T Consensus       192 ~~  193 (194)
T PRK12531        192 ES  193 (194)
T ss_pred             cc
Confidence            43

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

Probab=99.84  E-value=8.7e-20  Score=166.28  Aligned_cols=157  Identities=23%  Similarity=0.346  Sum_probs=132.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404          366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  445 (605)
Q Consensus       366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~  445 (605)
                      |++.|+..|.++|+++++++.+++.+.+|++||+++++|++++.|++.  .+|.+|+.+++++.+.++++++.+   .+.
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  589999999999999999998765   111


Q ss_pred             cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404          446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  525 (605)
Q Consensus       446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~  525 (605)
                      ..                                                   ...   .       ... ...+.+++.
T Consensus        77 ~~---------------------------------------------------~~~---~-------~~~-~~~~~~~~~   94 (158)
T TIGR02937        77 EL---------------------------------------------------DLL---E-------ELL-DSDPSPEEE   94 (158)
T ss_pred             ch---------------------------------------------------hhh---h-------hcc-cccCCHHHH
Confidence            00                                                   000   0       000 112256666


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      .........|..+++.||++++.||.++|..+    +|+.|||+.||+|+.+|+++..++++|||+.+
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            77777788899999999999999999998877    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.

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.84  E-value=8.2e-20  Score=176.22  Aligned_cols=165  Identities=16%  Similarity=0.136  Sum_probs=135.6

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      .+..|++.|+..|.+.|+++++++.++..+++|++||+|+.+|+++++|++.  ..|.+|++..+++.+.+++++..+..
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            3478999999999999999999999999999999999999999999999874  36999999999999999998754311


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  521 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s  521 (605)
                      ..+                                                     .+.        ...+...  ..++
T Consensus        91 ~~~-----------------------------------------------------~~~--------~~~~~~~--~~~~  107 (179)
T PRK09415         91 VIV-----------------------------------------------------TED--------IFTYMES--QKES  107 (179)
T ss_pred             ccc-----------------------------------------------------ccc--------ccccccc--cccC
Confidence            000                                                     000        0000001  1125


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      |++.+...+....|..+|..||+++|+||.|+|+.|    +|++|||+.||||.++|++++.||+++||+.+..
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            666666677778899999999999999999999988    9999999999999999999999999999997753

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.84  E-value=5.2e-20  Score=175.95  Aligned_cols=165  Identities=15%  Similarity=0.140  Sum_probs=131.0

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404          357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  436 (605)
Q Consensus       357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~  436 (605)
                      .....++..|++.|+..|.+.|+.+|++|.++..+++|++||+|+++|++++.|++.  .+|.+|++..+++.+.+++++
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            444556789999999999999999999999999999999999999999999999874  479999999999999999987


Q ss_pred             ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404          437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  516 (605)
Q Consensus       437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D  516 (605)
                      ..+.....                           +.+                       .+             ...+
T Consensus        88 ~~~~~~~~---------------------------~~~-----------------------~~-------------~~~~  104 (176)
T PRK09638         88 QKREKLRL---------------------------QRA-----------------------KE-------------ETLR  104 (176)
T ss_pred             hccccchh---------------------------hhc-----------------------cc-------------ccCC
Confidence            65311000                           000                       00             0000


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ..  .. +..........|..+|..||+++|+||.++|..|    +|++|||+.||+|..+|++.++||+++||+.+
T Consensus       105 ~~--~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l  174 (176)
T PRK09638        105 KE--KW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYG----YTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEW  174 (176)
T ss_pred             cc--ch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehhhcC----CCHHHHHHHHCCChhHHHHHHHHHHHHHHHHh
Confidence            00  00 1122233445689999999999999999999877    99999999999999999999999999999976

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

Probab=99.84  E-value=1.9e-19  Score=183.23  Aligned_cols=182  Identities=13%  Similarity=0.155  Sum_probs=141.2

Q ss_pred             CCHHHHHH-HHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHH-------hhhccCCcCCCcchhHH
Q 007404          351 VDQRELRR-RLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVR-------GAEKFDASKGFKFSTYA  422 (605)
Q Consensus       351 ~d~~~L~~-~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLir-------A~ekFDp~kG~rFSTYA  422 (605)
                      .++..|.. ...++..|++.|+..|.+.|+.+++++.++..+++|++||+|+.+|.       .+.+|++.  ..|.||+
T Consensus        24 ~~d~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL  101 (244)
T TIGR03001        24 AADLYLACACAQGEPAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWV  101 (244)
T ss_pred             ccHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHH
Confidence            34444444 45566899999999999999999999999999999999999999994       78889864  3699999


Q ss_pred             HHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccc
Q 007404          423 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKI  502 (605)
Q Consensus       423 ~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i  502 (605)
                      +.+++|.++++++++.+...+                                                       +   
T Consensus       102 ~~Ia~N~~id~lRk~~r~~~~-------------------------------------------------------~---  123 (244)
T TIGR03001       102 RIVATRIALELQAQERRHSPV-------------------------------------------------------E---  123 (244)
T ss_pred             HHHHHHHHHHHHHHhcccCcc-------------------------------------------------------c---
Confidence            999999999999875431100                                                       0   


Q ss_pred             cccCCCCCCcccCCCCCCCHHHHHHH----HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHH
Q 007404          503 GINQNLKPSEVIADPEAETAEDLLIK----KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERI  578 (605)
Q Consensus       503 ~~d~~~~l~d~l~D~~~~spEe~l~~----~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerV  578 (605)
                        +.+ ...+. .+. ..+|++.+..    .+....|..+|++||+++|+||.|+|..|    +|++|||++||||.++|
T Consensus       124 --~~~-~~~~~-~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~~eg----~S~~EIA~~Lgis~~TV  194 (244)
T TIGR03001       124 --EPT-ELAAL-PAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDG----LSMDRIGAMYQVHRSTV  194 (244)
T ss_pred             --ccc-ccccc-cCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHH
Confidence              000 00000 011 1234444432    23567799999999999999999999988    99999999999999999


Q ss_pred             HHHHHHHHHHHHhHHhhhhHhhh
Q 007404          579 RQIESSAFRKLKNKKRTKHLMQY  601 (605)
Q Consensus       579 Rqie~RALkKLR~~l~~~~L~~y  601 (605)
                      +.+++||+++||+.+.+.....|
T Consensus       195 k~rl~RAr~~Lr~~l~~~~~~~~  217 (244)
T TIGR03001       195 SRWVAQARERLLERTRRRLAERL  217 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999987765554

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=1.1e-19  Score=176.70  Aligned_cols=181  Identities=15%  Similarity=0.162  Sum_probs=137.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404          366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  445 (605)
Q Consensus       366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~  445 (605)
                      +++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++.  .+|.+|++..++|.++++++++.+....+.
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~--~~~~~WL~~ia~n~~~d~~Rk~~r~~~~~~   80 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQ--SSLKTYLVGILKHKIIDAIRSGRREVRLSL   80 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--ccHHHHHHHHHHHHHHHHHHhhcCcCcccc
Confidence            689999999999999999999999999999999999999999999865  369999999999999999998764221100


Q ss_pred             cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404          446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  525 (605)
Q Consensus       446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~  525 (605)
                      ..                  .......++                       ++...  +.+ ......++. ..+|++.
T Consensus        81 ~~------------------~~~~~~~~~-----------------------~~~~~--~~~-~~~~~~~~~-~~~~~~~  115 (191)
T PRK12520         81 DD------------------ADEQSDDDL-----------------------FDALF--AAD-GHYREPPSD-WGDPDAA  115 (191)
T ss_pred             cc------------------cccchhhhh-----------------------hhhhc--ccc-cccccCccc-cCCHHHH
Confidence            00                  000000000                       00000  000 000011111 2367777


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      +...+....|..+|..||+++|.||.|+|..+    +|++|||+.||+|.++|+++++||+++||+.+....
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    999999999999999999999999999999998765

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1e-19  Score=174.03  Aligned_cols=167  Identities=11%  Similarity=0.156  Sum_probs=131.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404          365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  444 (605)
Q Consensus       365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP  444 (605)
                      ..+++|+..|.++|+.+|++|.++..+++|++||+++.+|++.++|++..  +|.+|++..++|.+.++++++.+....+
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            35899999999999999999999999999999999999999999999854  7999999999999999998766421100


Q ss_pred             ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404          445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED  524 (605)
Q Consensus       445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe  524 (605)
                      ..                                                 . .+.    +....+  ...+. ...++.
T Consensus        81 ~~-------------------------------------------------~-~~~----~~~~~~--~~~~~-~~~~~~  103 (173)
T PRK12522         81 LD-------------------------------------------------L-FHK----EDGGEI--EFADD-VNISEE  103 (173)
T ss_pred             cc-------------------------------------------------c-cch----hhhhhh--ccccC-CCChHH
Confidence            00                                                 0 000    000000  00011 112333


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          525 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       525 ~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                       ....+..+.|..+|..||+++++||.|+|..|    +|++|||+.||+|.++|+.+++||+++||+.+..
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             44456678899999999999999999999988    9999999999999999999999999999997754

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

Probab=99.84  E-value=5.3e-20  Score=171.43  Aligned_cols=160  Identities=17%  Similarity=0.172  Sum_probs=130.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404          366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  445 (605)
Q Consensus       366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~  445 (605)
                      |+++|+..|.+.|+++++++.++..+.+|++||+++++|+.+.+|++.  .+|.+|++.++|+.+.+++++..+....  
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~--~~~~~wl~~i~r~~~~d~~r~~~~~~~~--   77 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEV--ESFKAYLFTIVKNRSLNYLRHKQVEEKY--   77 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc--ccHHHHHHHHHHHHHHHHHHHHHhHhHH--
Confidence            789999999999999999999998999999999999999999999874  3799999999999999999876531000  


Q ss_pred             cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404          446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  525 (605)
Q Consensus       446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~  525 (605)
                                      ..         .+                            .+...    +   ....+++++.
T Consensus        78 ----------------~~---------~~----------------------------~~~~~----~---~~~~~~~~~~   97 (161)
T TIGR02985        78 ----------------QE---------EI----------------------------LEIEV----D---ELSENDPEEE   97 (161)
T ss_pred             ----------------HH---------HH----------------------------Hhhcc----c---ccCCCCcHHH
Confidence                            00         00                            00000    0   0011245666


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      +...+....|..++..||+++++||.++|..+    +|.+|||+.||+|+++|+++++||+++||+.+
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            66677778899999999999999999999877    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.

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

Probab=99.84  E-value=1.3e-19  Score=172.44  Aligned_cols=163  Identities=20%  Similarity=0.236  Sum_probs=130.4

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404          355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  434 (605)
Q Consensus       355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i  434 (605)
                      .+.....++..|++.|+..|.+.|++++.++.++..+++|++||+|+.+|+..++|++..  +|.+|++..+++.+++++
T Consensus         6 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~   83 (169)
T TIGR02954         6 LVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECIDLL   83 (169)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHHHHH
Confidence            334445567899999999999999999999999999999999999999999999999753  699999999999999999


Q ss_pred             hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404          435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  514 (605)
Q Consensus       435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  514 (605)
                      ++..+...                                                       ++...      .    .
T Consensus        84 R~~~~~~~-------------------------------------------------------~~~~~------~----~   98 (169)
T TIGR02954        84 KKKKKVIP-------------------------------------------------------FDPNT------S----I   98 (169)
T ss_pred             HhcCCcCc-------------------------------------------------------ccccc------c----c
Confidence            87643100                                                       00000      0    0


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      .+.   .++.  .. .....|..+|..||+++|+||.++|+.|    +|++|||+.||||..+|+.+++||+++||+.+.
T Consensus        99 ~~~---~~~~--~~-~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l~  168 (169)
T TIGR02954        99 EKG---ECET--HA-DSRLDLYKAIDTLNDKYQTAIILRYYHD----LTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE  168 (169)
T ss_pred             ccc---hhhh--ch-HHHHHHHHHHHhCCHHHhHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence            000   0110  01 1123688999999999999999999988    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.

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=9.3e-20  Score=175.97  Aligned_cols=168  Identities=20%  Similarity=0.201  Sum_probs=131.7

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404          355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQG-AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  433 (605)
Q Consensus       355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~-~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~  433 (605)
                      .+.....++..|++.|+..|.+.|+.++.++.+ ...+++|++||+|+.||+.++.|++.  ..|.+|++..++|.+.++
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            345556678999999999999999999998764 57899999999999999999999974  369999999999999999


Q ss_pred             HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404          434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV  513 (605)
Q Consensus       434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~  513 (605)
                      ++++.+....                                                   ..+++.    .     .+.
T Consensus        89 ~Rk~~~~~~~---------------------------------------------------~~~~~~----~-----~~~  108 (181)
T PRK12536         89 LRSRARREAL---------------------------------------------------HDPLDD----E-----SEL  108 (181)
T ss_pred             HHHHhccccc---------------------------------------------------cCCccc----h-----hhh
Confidence            9886431000                                                   000000    0     000


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       514 l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ..+... .+      .+....|..+|+.||+++|.||.++|..|    +|++|||+.||+|+++|+.+++||+++||+.+
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-EA------AEARRDLGKLLEQLPDRQRLPIVHVKLEG----LSVAETAQLTGLSESAVKVGIHRGLKALAAKI  177 (181)
T ss_pred             cCCCCc-ch------HHHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            001110 11      12345689999999999999999999888    99999999999999999999999999999987


Q ss_pred             hh
Q 007404          594 RT  595 (605)
Q Consensus       594 ~~  595 (605)
                      ..
T Consensus       178 ~~  179 (181)
T PRK12536        178 RG  179 (181)
T ss_pred             cC
Confidence            64

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

Probab=99.83  E-value=2.9e-19  Score=172.81  Aligned_cols=172  Identities=21%  Similarity=0.277  Sum_probs=137.9

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404          357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  436 (605)
Q Consensus       357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~  436 (605)
                      .....++..++..++..|.+.++.+++++.++..+++||+||+|+.+|+++..| ... ..|.||++.+++|.+++++++
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~~-~~~~~wl~~Ia~n~~iD~~R~   84 (182)
T COG1595           7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RGR-SSFKAWLYRIARNLAIDRLRK   84 (182)
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CCC-CchHHHHHHHHHHHHHHHHHH
Confidence            344556788999999999999999999999988899999999999999999999 433 479999999999999999998


Q ss_pred             ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404          437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  516 (605)
Q Consensus       437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D  516 (605)
                      ..+.....                                                      +     +.+.  .+...+
T Consensus        85 ~~r~~~~~------------------------------------------------------~-----~~~~--~~~~~~  103 (182)
T COG1595          85 RKRRRARV------------------------------------------------------E-----EADL--LPEEAD  103 (182)
T ss_pred             hccccccc------------------------------------------------------c-----cccc--cccccC
Confidence            76522210                                                      0     0000  000011


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      ...+.. +.+...+....|..+|..||+++|++|.|+|+.|    +|++|||+.||||.++|+.+++||+++||+.+...
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 2455667778899999999999999999999988    99999999999999999999999999999988653

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=2.2e-19  Score=173.75  Aligned_cols=166  Identities=13%  Similarity=0.109  Sum_probs=130.1

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHH----HhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHH
Q 007404          356 LRRRLNYGILCKDKMITSNIRLVISIAK----NYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR  431 (605)
Q Consensus       356 L~~~l~~g~~A~e~LI~~nlrLVvsIAk----rY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~  431 (605)
                      +.+...++..|++.|+..|.+.|+.+++    +|.++..+++|++||+++.+|++++.|++..  .|.+|++..++|.+.
T Consensus        12 ~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~   89 (184)
T PRK12539         12 MLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLI   89 (184)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHH
Confidence            3445567789999999999999999987    4557789999999999999999999999753  699999999999999


Q ss_pred             HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404          432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS  511 (605)
Q Consensus       432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~  511 (605)
                      +++++..+.. .+                                                   .+++      +..   
T Consensus        90 d~~R~~~~~~-~~---------------------------------------------------~~~~------~~~---  108 (184)
T PRK12539         90 DHLRRTRASL-AD---------------------------------------------------VPID------DAD---  108 (184)
T ss_pred             HHHHHHhccc-cc---------------------------------------------------cChh------hhc---
Confidence            9998754310 00                                                   0000      000   


Q ss_pred             cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +....    .+   ....+....|..+|..||+++|+||.|+|..|    +|++|||+.||+|..+|+++++||+++||+
T Consensus       109 ~~~~~----~~---~~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~  177 (184)
T PRK12539        109 ELVAH----DD---HAAVESTLDLGRLLARLPEKMRLAIQAVKLEG----LSVAEAATRSGMSESAVKVSVHRGLKALAA  177 (184)
T ss_pred             cccCC----cH---HhhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            00000    01   11223345789999999999999999999887    999999999999999999999999999999


Q ss_pred             HHhh
Q 007404          592 KKRT  595 (605)
Q Consensus       592 ~l~~  595 (605)
                      .+..
T Consensus       178 ~l~~  181 (184)
T PRK12539        178 LIGR  181 (184)
T ss_pred             HHhh
Confidence            8754

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

Probab=99.83  E-value=2.4e-19  Score=172.42  Aligned_cols=167  Identities=22%  Similarity=0.218  Sum_probs=124.1

Q ss_pred             HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHH-hhhccCCcCCCcchhHHHHHHHHHHH
Q 007404          358 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGM-----NLQDLVQEGCRGLVR-GAEKFDASKGFKFSTYAHWWIKQAVR  431 (605)
Q Consensus       358 ~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~-----d~eDLIQEG~IGLir-A~ekFDp~kG~rFSTYA~~wIRqaI~  431 (605)
                      ....++..|++.|+..|.+.|+.+|++|.++..     +++|++||+|+.+|+ ..++|++.  ..|.+|++.+++|.+.
T Consensus        10 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~   87 (183)
T TIGR02999        10 QWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRILV   87 (183)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHHHH
Confidence            334466889999999999999999999998877     899999999999998 78889764  3699999999999999


Q ss_pred             HHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC
Q 007404          432 KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS  511 (605)
Q Consensus       432 r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~  511 (605)
                      ++++++.+..+..                                                   ...+..        +.
T Consensus        88 d~~R~~~~~~~~~---------------------------------------------------~~~~~~--------~~  108 (183)
T TIGR02999        88 DHARRRRAQKRGG---------------------------------------------------GAVRVP--------LD  108 (183)
T ss_pred             HHHHHHHHHhccC---------------------------------------------------Cccccc--------cc
Confidence            9998754310000                                                   000000        00


Q ss_pred             cccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          512 EVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       512 d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +..++... ...+   .......+...|+.||+++|+||.|+|..|    +|++|||+.||||.++|+.+++||+++||+
T Consensus       109 ~~~~~~~~-~~~~---~~~~l~~~~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~  180 (183)
T TIGR02999       109 EVLPDAEA-DLDE---ELLDLDDALDKLAQVDPRQAEVVELRFFAG----LTVEEIAELLGVSVRTVERDWRFARAWLAD  180 (183)
T ss_pred             cccCCCCc-cHHH---HHHHHHHHHHHhhcCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            00001010 1111   111123344456779999999999999988    999999999999999999999999999998


Q ss_pred             HH
Q 007404          592 KK  593 (605)
Q Consensus       592 ~l  593 (605)
                      .+
T Consensus       181 ~l  182 (183)
T TIGR02999       181 EL  182 (183)
T ss_pred             Hh
Confidence            75

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=1.8e-19  Score=173.88  Aligned_cols=165  Identities=12%  Similarity=0.048  Sum_probs=131.5

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhC--CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404          361 NYGILCKDKMITSNIRLVISIAKNYQG--AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  438 (605)
Q Consensus       361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~--~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s  438 (605)
                      .++..+|+.|+..|.+.|+.++..+.+  +..+++|++||.|+.+|+..++|++.....|.||++..++|.+.++++++.
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            466889999999999999998766665  457899999999999999999998544457999999999999999887643


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC
Q 007404          439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE  518 (605)
Q Consensus       439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~  518 (605)
                      +.  .                ..                                    .+. .  .      + ..+..
T Consensus        89 ~~--~----------------~~------------------------------------~~~-~--~------~-~~~~~  104 (178)
T PRK12529         89 LE--L----------------AW------------------------------------LEA-L--A------T-LPEPL  104 (178)
T ss_pred             HH--h----------------hh------------------------------------hhH-h--h------h-ccCcC
Confidence            20  0                00                                    000 0  0      0 00011


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      .++|++.....+....|..+|.+||+++|.||.|+|..|    +|++|||+.||+|.++|+.+++||+.+|++.+
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            135666666666677899999999999999999999987    99999999999999999999999999998864

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=3.9e-19  Score=177.76  Aligned_cols=170  Identities=14%  Similarity=0.134  Sum_probs=137.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404          363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  442 (605)
Q Consensus       363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR  442 (605)
                      ...++..||..|.+.++.+++++.++..+.+|++||+|+.+|+.+++|++.   .|.+|++.+++|.++++++++.+...
T Consensus        16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~   92 (216)
T PRK12533         16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHE   92 (216)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhccccc
Confidence            467999999999999999999999999999999999999999999999853   49999999999999999987653111


Q ss_pred             ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCH
Q 007404          443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA  522 (605)
Q Consensus       443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~sp  522 (605)
                      ..                                                     .+..+. + .... +.+. +...+|
T Consensus        93 ~~-----------------------------------------------------~~~~~~-~-~~~~-~~~~-~~~~~~  115 (216)
T PRK12533         93 VA-----------------------------------------------------APDTLD-D-ADSL-DDWQ-PAGEDP  115 (216)
T ss_pred             cc-----------------------------------------------------cccccc-c-cccc-cccc-cCCCCH
Confidence            00                                                     000000 0 0000 0011 112357


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      ++.+...+....|..+|..||+++|+||.|+|..+    +|++|||+.||||.++|+++++||+++||+.+...
T Consensus       116 e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y~eg----~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~  185 (216)
T PRK12533        116 LALLLRAEDVRLVNAALAKLPVEYREVLVLRELED----MSYREIAAIADVPVGTVMSRLARARRRLAALLGGA  185 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence            77777778888999999999999999999999987    99999999999999999999999999999998653

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=4.1e-19  Score=171.34  Aligned_cols=165  Identities=17%  Similarity=0.215  Sum_probs=129.5

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhC----CCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHH
Q 007404          357 RRRLNYGILCKDKMITSNIRLVISIAKNYQG----AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  432 (605)
Q Consensus       357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~----~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r  432 (605)
                      .....++..|++.|+..|.+.|+.+|+++++    ...+++|++||+++.+|+..+.|++.  ..|.+|++..+|+.+.+
T Consensus        14 ~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~d   91 (184)
T PRK12512         14 RSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLID   91 (184)
T ss_pred             HHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHHH
Confidence            3344567999999999999999999999886    24689999999999999999999874  47999999999999999


Q ss_pred             HHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCc
Q 007404          433 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE  512 (605)
Q Consensus       433 ~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d  512 (605)
                      +++++.+....                                                     +++.         ..+
T Consensus        92 ~~Rr~~~~~~~-----------------------------------------------------~~~~---------~~~  109 (184)
T PRK12512         92 ALRRRGRRVFV-----------------------------------------------------DIDD---------FAE  109 (184)
T ss_pred             HHHhhcccccC-----------------------------------------------------Cchh---------ccc
Confidence            99876531111                                                     0000         000


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          513 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       513 ~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .+++..   +.+    ......+..+|+.||+++|+||.++|..+    +|++|||+.||+|..+|+..++||+++||..
T Consensus       110 ~~~~~~---~~~----~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~  178 (184)
T PRK12512        110 TLPAEP---ATE----TLPAGDVGRHLETLPPRQRDVVQSISVEG----ASIKETAAKLSMSEGAVRVALHRGLAALAAK  178 (184)
T ss_pred             cccccc---hhh----HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            111110   011    12234578899999999999999999887    9999999999999999999999999999998


Q ss_pred             Hhhh
Q 007404          593 KRTK  596 (605)
Q Consensus       593 l~~~  596 (605)
                      +.+.
T Consensus       179 l~~~  182 (184)
T PRK12512        179 FRSE  182 (184)
T ss_pred             hhcC
Confidence            8653

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=2.1e-19  Score=171.58  Aligned_cols=168  Identities=17%  Similarity=0.129  Sum_probs=130.0

Q ss_pred             HHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhc
Q 007404          358 RRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  437 (605)
Q Consensus       358 ~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~  437 (605)
                      ....++..+++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++.  ..|.+|++..+++.+.+++++.
T Consensus         4 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~   80 (175)
T PRK12518          4 RCQRGDRQSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQF   80 (175)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHh
Confidence            344567899999999999999999999875 4789999999999999999999974  4699999999999999998865


Q ss_pred             cccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCC
Q 007404          438 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP  517 (605)
Q Consensus       438 sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~  517 (605)
                      .+.-..                                                      ++..   ....   . ... 
T Consensus        81 ~~~~~~------------------------------------------------------~~~~---~~~~---~-~~~-   98 (175)
T PRK12518         81 AQRPSR------------------------------------------------------IQDD---SLND---Q-PSR-   98 (175)
T ss_pred             hccccc------------------------------------------------------hhcc---cccc---c-ccC-
Confidence            321000                                                      0000   0000   0 000 


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          518 EAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       518 ~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      ....++  ....+....+..+|+.||+++|.||.|+|+.|    +|++|||+.||+|..+|++.++||+++||+.+...
T Consensus        99 ~~~~~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~  171 (175)
T PRK12518         99 PSDTPD--LMQLHYQDLVQQGLQTLSLEHRAVLVLHDLED----LPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQ  171 (175)
T ss_pred             CCCcHH--HHHHHHHHHHHHHHHhCCHHHeeeeeehHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            011122  22223445688999999999999999999988    99999999999999999999999999999988764

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

Probab=99.82  E-value=1.2e-19  Score=170.25  Aligned_cols=157  Identities=18%  Similarity=0.244  Sum_probs=125.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404          366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  445 (605)
Q Consensus       366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~  445 (605)
                      +++.++..|.+.|+.+|+++.++..+++|++||+++.+|+++++|++..  .|.+|++..+++.++++++++.+.-.. .
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~~-~   78 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRLV-F   78 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccccc-c
Confidence            7899999999999999999999999999999999999999999999764  599999999999999999987542110 0


Q ss_pred             cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404          446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  525 (605)
Q Consensus       446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~  525 (605)
                                               .+++.                                    +.+.+..  ++.+.
T Consensus        79 -------------------------~~~~~------------------------------------~~~~~~~--~~~~~   95 (159)
T TIGR02989        79 -------------------------DDELL------------------------------------EALAAEA--EATEA   95 (159)
T ss_pred             -------------------------CHHHH------------------------------------HHHHhhc--ccchH
Confidence                                     00000                                    0000000  01111


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .........|..+++.||++++.||.++|..|    +|++|||+.||||.++|+..++||+++||+.
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            22233456789999999999999999999887    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).

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.82  E-value=3.8e-19  Score=172.77  Aligned_cols=167  Identities=13%  Similarity=0.066  Sum_probs=128.6

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404          357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  436 (605)
Q Consensus       357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~  436 (605)
                      .+...++..|++.||..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++.  ..|.+|++.+++|.+.+++++
T Consensus        16 ~~~~~gd~~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~~Rk   92 (185)
T PRK09649         16 LSAAKGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRH   92 (185)
T ss_pred             HHHHccCHHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHHHHH
Confidence            344456789999999999999999995 67888899999999999999999999864  369999999999999999987


Q ss_pred             ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404          437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  516 (605)
Q Consensus       437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D  516 (605)
                      +.+..+..                                                     .+.    .     .+...+
T Consensus        93 ~~~~~~~~-----------------------------------------------------~~~----~-----~~~~~~  110 (185)
T PRK09649         93 VRSRPRTT-----------------------------------------------------RGA----R-----PEHLID  110 (185)
T ss_pred             hccccccc-----------------------------------------------------ccc----c-----hhhccC
Confidence            54311100                                                     000    0     000000


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      .     +......+....|..+|..||+++|+||.|+|+.+    +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus       111 ~-----~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~~~~  181 (185)
T PRK09649        111 G-----DRHARGFEDLVEVTTMIADLTTDQREALLLTQLLG----LSYADAAAVCGCPVGTIRSRVARARDALLADAEPD  181 (185)
T ss_pred             h-----hhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCcc
Confidence            0     00001112234588899999999999999999988    99999999999999999999999999999966544


Q ss_pred             h
Q 007404          597 H  597 (605)
Q Consensus       597 ~  597 (605)
                      .
T Consensus       182 ~  182 (185)
T PRK09649        182 D  182 (185)
T ss_pred             c
Confidence            3

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.82  E-value=7e-19  Score=174.05  Aligned_cols=165  Identities=18%  Similarity=0.269  Sum_probs=136.8

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      ++..+++.|+..|.+.++.++.+|.++..+.+|++||+|+.+|+...+|++  + .|.+|++..+|+.+.+++++..+ .
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            357899999999999999999999999999999999999999999999985  3 69999999999999999987643 1


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  521 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s  521 (605)
                      +.                                                    ..++     + +  . +.... ..++
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             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      |+..+...++...|..+|..||++++.||.|+|+.|    ++++|||+.||||.++|++.++||+++||+.+...
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            666677777778899999999999999999999888    99999999999999999999999999999988754

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.82  E-value=3.1e-19  Score=168.32  Aligned_cols=156  Identities=17%  Similarity=0.123  Sum_probs=126.6

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHH
Q 007404          372 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT  451 (605)
Q Consensus       372 ~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i  451 (605)
                      +.|.+.|+.+|+++.++..+++|++||+|+.+|+++++|++.   .|.+|++..++|.+.++++++.+..+.        
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~--------   70 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE--------   70 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc--------
Confidence            578999999999999999999999999999999999999863   499999999999999999876531100        


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHH
Q 007404          452 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM  531 (605)
Q Consensus       452 ~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el  531 (605)
                                                                  ..+..    + .   .+...  ...++++.+...+.
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   00000  11245666666677


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       532 ~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      ...|..+|+.||+++|.||.|+|..|    +|++|||+.||+|.++|+++++||+++||+.+...
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

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

Probab=99.82  E-value=2.4e-19  Score=174.57  Aligned_cols=173  Identities=13%  Similarity=0.135  Sum_probs=132.4

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404          363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  442 (605)
Q Consensus       363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR  442 (605)
                      +..+|+.|+..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|++.  ..|.+|++..++|.+.++++++.+...
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            367999999999999999999999999999999999999999999999864  369999999999999999987654111


Q ss_pred             ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCH
Q 007404          443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA  522 (605)
Q Consensus       443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~sp  522 (605)
                      ..                         ..+++.           ..            ... +    ..+ ........+
T Consensus        87 ~~-------------------------~~~~~~-----------~~------------~~~-~----~~~-~~~~~~~~~  112 (193)
T TIGR02947        87 QS-------------------------DDDDIE-----------DW------------QLA-K----AAS-HTSNGLRSA  112 (193)
T ss_pred             cc-------------------------cchhhh-----------hh------------hhc-c----ccc-cccccccch
Confidence            00                         000000           00            000 0    000 000011133


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      +...........|..+|..||+++|+||.|+|..|    +|++|||+.||||.++|+.+++||+++||+.+..
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            33344444567789999999999999999999888    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=4.1e-19  Score=173.24  Aligned_cols=162  Identities=14%  Similarity=0.155  Sum_probs=129.6

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      ++..++..|+..|.+.++.+|+++.++..+++|++||.|+.+|+..++|+...  .|.+|++..++|.++++++++.+..
T Consensus         7 ~~~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~   84 (187)
T PRK12516          7 EGTPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREV   84 (187)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCc
Confidence            35789999999999999999999999999999999999999999999998643  5999999999999999998765411


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  521 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s  521 (605)
                      ..                                                      .+..        +.+.... . +.
T Consensus        85 ~~------------------------------------------------------~~~~--------~~~~~~~-~-~~  100 (187)
T PRK12516         85 QD------------------------------------------------------TDGM--------FTEQLAV-H-PS  100 (187)
T ss_pred             cc------------------------------------------------------cccc--------cccccCC-C-cc
Confidence            00                                                      0000        0000000 0 01


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      ..    .......|..+|..||+++|+||.|+|..|    +|++|||+.||||.++|+++++||+++||+.+....
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    112235689999999999999999999988    999999999999999999999999999999987654

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.81  E-value=5.7e-19  Score=168.96  Aligned_cols=163  Identities=13%  Similarity=0.092  Sum_probs=129.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      ++..++..|+..|.+.|+.++.++.++..+++|++||+|+.+|+. ..|+..  ..|.+|++.+++|.+.++++++.+..
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            557899999999999999999999999999999999999999987 446543  36999999999999999998764200


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  521 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s  521 (605)
                                        ...         .++                        .     .        .......+
T Consensus        84 ------------------~~~---------~~~------------------------~-----~--------~~~~~~~~   99 (172)
T PRK12523         84 ------------------AYL---------AEL------------------------A-----L--------VPEAEQPS   99 (172)
T ss_pred             ------------------HHH---------HHH------------------------h-----h--------cccccCCC
Confidence                              000         000                        0     0        00001124


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      |++.....+....|..+|..||+++|+||.|+|..|    +|++|||+.||+|.++|+++++||+++||..+..
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            555444444556799999999999999999999988    9999999999999999999999999999987753

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.81  E-value=1e-18  Score=165.27  Aligned_cols=160  Identities=18%  Similarity=0.180  Sum_probs=130.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  443 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl  443 (605)
                      ..+++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|++  .|+.  +..|.+|++..+++.+.+++++..+..+.
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            4589999999999999999999999999999999999999999  6764  34799999999999999999876542111


Q ss_pred             cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404          444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  523 (605)
Q Consensus       444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE  523 (605)
                      ..                                                      ...  +    ..+.  + ....|+
T Consensus        78 ~~------------------------------------------------------~~~--~----~~~~--~-~~~~~e   94 (166)
T PRK09639         78 IL------------------------------------------------------GEF--Q----WQEV--D-NEPSPE   94 (166)
T ss_pred             cc------------------------------------------------------chh--h----hhhc--c-CCCChH
Confidence            00                                                      000  0    0000  1 123567


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      +.....+....|..+|..||+++|.||.++| .|    +|++|||+.||+|..+|+..+.||+++||+.+..
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            7777777777899999999999999999999 77    9999999999999999999999999999998864

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.81  E-value=7.3e-19  Score=166.93  Aligned_cols=157  Identities=17%  Similarity=0.146  Sum_probs=131.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404          367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  446 (605)
Q Consensus       367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~  446 (605)
                      ++.|+..|.+.|+.+|++|.++..+++|++||+|+.+|+.+++|++.   .|.+|++..++|.+.+++++..+....   
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   599999999999999999886541100   


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHH
Q 007404          447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  526 (605)
Q Consensus       447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l  526 (605)
                                             +.+++                                     +.+.+   .+|++.+
T Consensus        77 -----------------------~~~~~-------------------------------------~~~~~---~~~~~~~   93 (165)
T PRK09644         77 -----------------------GTDEI-------------------------------------EAIQA---ESTEEYV   93 (165)
T ss_pred             -----------------------chhHH-------------------------------------hhhcc---cChHHHH
Confidence                                   00000                                     00000   2455656


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       527 ~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      ...+....|..+|..||+++|+||.|+|..|    +|++|||+.||+|.++|+++++||+++||+.+...
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            6666778899999999999999999999988    99999999999999999999999999999988754

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

Probab=99.81  E-value=6.4e-19  Score=166.25  Aligned_cols=157  Identities=16%  Similarity=0.175  Sum_probs=127.6

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      |+..+++.|+..|.+.|+.++..+.++..+++|++||+|+.+|+..++|+. . ..|.+|++..+++.+.++++++.+. 
T Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~-~-~~~~~wl~~i~~n~~~d~~rk~~~~-   79 (162)
T TIGR02983         3 ATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD-P-DAPDAYVRRVLVNLARSRWRRRRLL-   79 (162)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC-c-ccHHHHHHHHHHHHHHHHHHhhccc-
Confidence            568899999999999999999999999999999999999999999999964 3 4799999999999999998865430 


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  521 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s  521 (605)
                      .++                                                      +...        .+.  +..  .
T Consensus        80 ~~~------------------------------------------------------~~~~--------~~~--~~~--~   93 (162)
T TIGR02983        80 ELP------------------------------------------------------TREL--------PDA--AAP--D   93 (162)
T ss_pred             ccc------------------------------------------------------cccc--------Ccc--cCC--c
Confidence            000                                                      0000        000  000  0


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                         ........+.|..+|..||+++|+||.|+|..|    +|++|||+.||+|.++|++++.||+++||+.+.
T Consensus        94 ---~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~  159 (162)
T TIGR02983        94 ---PAPDVALRAALARALRRLPARQRAVVVLRYYED----LSEAQVAEALGISVGTVKSRLSRALARLRELLE  159 (162)
T ss_pred             ---cchhHHHHHHHHHHHHhCCHHHHHHhhhHHHhc----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence               111233456788999999999999999999877    999999999999999999999999999999775

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.

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.1e-18  Score=164.96  Aligned_cols=157  Identities=13%  Similarity=0.100  Sum_probs=125.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404          365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  444 (605)
Q Consensus       365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP  444 (605)
                      .|++.|+..|.+.|+.++.++.++..+++|++||+|+.+|+..+.|++.   .|.+|++.+++|.+.+++++..+..   
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~---   77 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQDLER---   77 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHHHHH---
Confidence            5899999999999999999999999999999999999999999888652   6999999999999999988753200   


Q ss_pred             ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404          445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED  524 (605)
Q Consensus       445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe  524 (605)
                                     ..         ..++                        +            + .++.....+++
T Consensus        78 ---------------~~---------~~~~------------------------~------------~-~~~~~~~~~~~   96 (161)
T PRK12528         78 ---------------AY---------LEAL------------------------A------------Q-LPERVAPSEEE   96 (161)
T ss_pred             ---------------hh---------HHHh------------------------h------------c-cccccCCCHHH
Confidence                           00         0000                        0            0 00001123444


Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          525 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       525 ~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .....+....|..+|..||+++|+||.|+|..|    +|++|||+.||+|.++|+++++||+++||..
T Consensus        97 ~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~~~g----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~  160 (161)
T PRK12528         97 RAIILETLVELDQLLDGLPPLVKRAFLLAQVDG----LGYGEIATELGISLATVKRYLNKAAMRCYFA  160 (161)
T ss_pred             HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence            444444556799999999999999999999988    9999999999999999999999999999964

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=99.81  E-value=1.5e-18  Score=169.10  Aligned_cols=178  Identities=16%  Similarity=0.103  Sum_probs=134.4

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404          369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  448 (605)
Q Consensus       369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~  448 (605)
                      +++..|.+.|+.+++++.++..+++|++||+|+.+|+...+|++.  .+|.+|++..++|.++++++++.+....+.-  
T Consensus         6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~--   81 (188)
T TIGR02943         6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDL--   81 (188)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccc--
Confidence            578899999999999999999999999999999999999999875  4799999999999999999877642111000  


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404          449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  528 (605)
Q Consensus       449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~  528 (605)
                                            .++.      .             .-.++.... ..+....+..++ ..++|++.+..
T Consensus        82 ----------------------~~~~------~-------------~~~~~~~~~-~~~~~~~~~~~~-~~~~~e~~~~~  118 (188)
T TIGR02943        82 ----------------------DDEL------D-------------DEAFNALFT-QNGHWAQHGQPQ-HWNTPEKQLEN  118 (188)
T ss_pred             ----------------------cccc------c-------------cchhhhhhc-cccchhcccccc-ccCCHHHHHHH
Confidence                                  0000      0             000000000 000000011111 22367777777


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      ++....|..+|..||+++|+||.|+|..+    +|++|||+.||+|.++|++++.||+++||+.+....
T Consensus       119 ~e~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~  183 (188)
T TIGR02943       119 KEFWEVFEACLYHLPEQTARVFMMREVLG----FESDEICQELEISTSNCHVLLYRARLSLRACLSINW  183 (188)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            77788899999999999999999999988    999999999999999999999999999999987553

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=1.6e-18  Score=169.12  Aligned_cols=181  Identities=17%  Similarity=0.150  Sum_probs=134.2

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCC-HHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404          368 DKMITSNIRLVISIAKNYQGAGMN-LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  446 (605)
Q Consensus       368 e~LI~~nlrLVvsIAkrY~~~g~d-~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~  446 (605)
                      +..+..|.+.|+.+|+++.++..+ ++|++||+|+.+|+++++|++.  .+|.+|++..++|.++++++++.+.......
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            457888999999999999998888 9999999999999999999864  3799999999999999999986542111000


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHH
Q 007404          447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  526 (605)
Q Consensus       447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l  526 (605)
                      .                   ......+..                    .+.   .. .+.....+..+ ....+|++.+
T Consensus        86 ~-------------------~~~~~~~~~--------------------~~~---~~-~~~~~~~~~~~-~~~~~~e~~~  121 (195)
T PRK12532         86 L-------------------DDELLDEAF--------------------ESH---FS-QNGHWTPEGQP-QHWNTPEKSL  121 (195)
T ss_pred             c-------------------cccccchhh--------------------hhh---hc-cccccccccCc-cccCCHHHHH
Confidence            0                   000000000                    000   00 00000000011 1123677777


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404          527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  598 (605)
Q Consensus       527 ~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  598 (605)
                      ...+....+..+|..||+++|+||.|+|..|    +|++|||+.||+|..+|+++++||+++||+.+....+
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            7777888899999999999999999999988    9999999999999999999999999999999876544

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=1.7e-18  Score=163.58  Aligned_cols=157  Identities=13%  Similarity=0.158  Sum_probs=125.2

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404          363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  442 (605)
Q Consensus       363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR  442 (605)
                      +..+++.++..|.+.|+.++.++.++..+++|++||+++.+|+..++|++.   .|.||++..++|.+.++++++.+...
T Consensus         3 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~   79 (161)
T PRK12541          3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKT   79 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcccccc
Confidence            467999999999999999999999999999999999999999999999863   59999999999999999988654110


Q ss_pred             ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCH
Q 007404          443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA  522 (605)
Q Consensus       443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~sp  522 (605)
                      +                                                     ..+.       ..   .  +.....+
T Consensus        80 ~-----------------------------------------------------~~~~-------~~---~--~~~~~~~   94 (161)
T PRK12541         80 T-----------------------------------------------------TIEE-------FH---L--PNVPSTE   94 (161)
T ss_pred             c-----------------------------------------------------chhh-------hh---c--cCCCCcH
Confidence            0                                                     0000       00   0  0000112


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      ++....++. ..+..+|..||+++|.||.|+|..|    +|++|||+.||+|.++|++.++||+++||+.
T Consensus        95 ~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541         95 HEYFIKHEI-ASWLDSLSSLPLERRNVLLLRDYYG----FSYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             HHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHHhcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            222333333 4456789999999999999999988    9999999999999999999999999999974

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.5e-18  Score=167.56  Aligned_cols=176  Identities=17%  Similarity=0.136  Sum_probs=132.5

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccH
Q 007404          368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM  447 (605)
Q Consensus       368 e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~  447 (605)
                      +..|..|.+.++.+|.+|.++..+++|++||+|+.+|+..++|++..  +|.+|++..++|.+.++++++.+..... ..
T Consensus        10 ~~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~   86 (189)
T PRK12530         10 SLEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES-EL   86 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc-cc
Confidence            34678889999999999999999999999999999999999998753  6999999999999999999765421110 00


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHH
Q 007404          448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI  527 (605)
Q Consensus       448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~  527 (605)
                                        .     ++                   ........    .......+........+|++.+.
T Consensus        87 ------------------~-----~~-------------------~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~  120 (189)
T PRK12530         87 ------------------I-----EE-------------------DSPNSFFD----EKGHWKPEYYEPSEWQEVENTVY  120 (189)
T ss_pred             ------------------c-----cc-------------------ccchhhhc----ccccccccccCCccccCHHHHHH
Confidence                              0     00                   00000000    00000000111111235677777


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       528 ~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      ..+....|..+|+.||+++|+||.|+|..|    +|++|||+.||+|.++|+.+++||+++||+++...
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            777888899999999999999999999988    99999999999999999999999999999988654

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.5e-18  Score=163.54  Aligned_cols=158  Identities=11%  Similarity=0.140  Sum_probs=126.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  443 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl  443 (605)
                      ...|..++..|.+.|+.+|+++.++..+++|++||+|+.+|+..++|++..  .|.+|++..++|.+.+++++..+....
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~~~   82 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREVQD   82 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            467999999999999999999999999999999999999999999998643  599999999999999999876431000


Q ss_pred             cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404          444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  523 (605)
Q Consensus       444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE  523 (605)
                                                  .                          +...  ..     .  .+.   .++
T Consensus        83 ----------------------------~--------------------------~~~~--~~-----~--~~~---~~~   96 (164)
T PRK12547         83 ----------------------------S--------------------------DGVF--TA-----R--VAV---HPA   96 (164)
T ss_pred             ----------------------------c--------------------------cccc--cc-----c--CCC---Cch
Confidence                                        0                          0000  00     0  000   111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      .  ........|..+|..||+++|+||.|+|..|    +|++|||+.||||.++|+++++||+++||..+..
T Consensus        97 ~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  162 (164)
T PRK12547         97 Q--YGSLDLQDFKKALNLLSADQREAIILIGASG----FSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV  162 (164)
T ss_pred             h--hhHHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            1  0112245688999999999999999999887    9999999999999999999999999999998754

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.3e-18  Score=169.54  Aligned_cols=181  Identities=16%  Similarity=0.141  Sum_probs=132.3

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404          369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  448 (605)
Q Consensus       369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~  448 (605)
                      .++..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++..  .|.+|++.+++|.++++++++.+...++..  
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~--   87 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSAL--   87 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccc--
Confidence            3589999999999999999999999999999999999999999763  699999999999999999987642111000  


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404          449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  528 (605)
Q Consensus       449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~  528 (605)
                                            ..++..                  ...++............+..++ ...++++....
T Consensus        88 ----------------------~~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  126 (201)
T PRK12545         88 ----------------------DAELDG------------------EALLDRELFKDNGHWAAHAKPR-PWPKPETILQQ  126 (201)
T ss_pred             ----------------------ccccch------------------hhhhhhhhhcccccccccccCc-CCCCHHHHHHH
Confidence                                  000000                  0000000000000000001111 12256666666


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404          529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  598 (605)
Q Consensus       529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  598 (605)
                      .+....|..+|..||+++|+||.|+|+.|    +|++|||+.||+|.++|++++.||+++||+.+...++
T Consensus       127 ~~~~~~l~~~L~~Lp~~~r~v~~L~~~eg----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~  192 (201)
T PRK12545        127 QQFWTLFETCLDHLPEQIGRVFMMREFLD----FEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL  192 (201)
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            66667899999999999999999999988    9999999999999999999999999999999975443

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=99.80  E-value=1.9e-18  Score=181.03  Aligned_cols=183  Identities=18%  Similarity=0.155  Sum_probs=135.9

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      |+..+++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++.  ..|.+|++.+++|.++++++++.+..
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  36999999999999999998765411


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccC------
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIA------  515 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~------  515 (605)
                      ... .                 ...  +                        .....+.. ..+......+.+.      
T Consensus        80 ~~~-~-----------------~~~--~------------------------~~~~~~~~-~~~~~~~~~~~~~~~~~~~  114 (324)
T TIGR02960        80 RPV-G-----------------LGA--P------------------------SADGTAAA-SEAAEVTWLEPLPDLTLDL  114 (324)
T ss_pred             Ccc-c-----------------cCC--C------------------------CCcccccc-cccccccccCCCCcccccc
Confidence            100 0                 000  0                        00000000 0000000000000      


Q ss_pred             -CCCCCCHHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          516 -DPEAETAEDLLIKKF-MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       516 -D~~~~spEe~l~~~e-l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                       .....+|++.+...+ +...|..+|.+||+++|.||.|+|..+    +|++|||+.||+|.++|+++++||+++||+.+
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             111235666655554 456789999999999999999999988    99999999999999999999999999999988


Q ss_pred             hh
Q 007404          594 RT  595 (605)
Q Consensus       594 ~~  595 (605)
                      ..
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.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.80  E-value=3.3e-18  Score=180.73  Aligned_cols=187  Identities=18%  Similarity=0.156  Sum_probs=137.7

Q ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404          354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  433 (605)
Q Consensus       354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~  433 (605)
                      +.+.+...++..+++.|+..|.+.|+.+|+++.++..+++|++||.|+.+|+.+++|++.  ..|.+|++..++|.++++
T Consensus         8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~   85 (339)
T PRK08241          8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDA   85 (339)
T ss_pred             HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHH
Confidence            345555667789999999999999999999999999999999999999999999999853  369999999999999999


Q ss_pred             HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404          434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV  513 (605)
Q Consensus       434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~  513 (605)
                      ++++.+.... ..                  ... +.                         .........+......+.
T Consensus        86 ~Rk~~~~~~~-~~------------------~~~-~~-------------------------~~~~~~~~~~~~~~~~~~  120 (339)
T PRK08241         86 LEGRARRPLP-TD------------------LGA-PA-------------------------ADPVDELVERPEVPWLEP  120 (339)
T ss_pred             HHhhccccCc-cc------------------cCC-Cc-------------------------CcccccccccccccccCC
Confidence            9876541000 00                  000 00                         000000000000001111


Q ss_pred             cCCC----CCCCHHHHHHHHH-HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 007404          514 IADP----EAETAEDLLIKKF-MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK  588 (605)
Q Consensus       514 l~D~----~~~spEe~l~~~e-l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkK  588 (605)
                      +.+.    ...+|++.+...+ ....|..+|.+||+++|+||.|+|..+    +|++|||+.||+|.++|+++++||+++
T Consensus       121 ~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~~~g----~s~~EIA~~lgis~~tVk~~l~RAr~~  196 (339)
T PRK08241        121 YPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLG----WSAAEVAELLDTSVAAVNSALQRARAT  196 (339)
T ss_pred             CCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHHhhC----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            1111    1235666655544 455689999999999999999999988    999999999999999999999999999


Q ss_pred             HHh
Q 007404          589 LKN  591 (605)
Q Consensus       589 LR~  591 (605)
                      ||+
T Consensus       197 Lr~  199 (339)
T PRK08241        197 LAE  199 (339)
T ss_pred             Hhh
Confidence            999

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=4.1e-18  Score=167.48  Aligned_cols=169  Identities=16%  Similarity=0.069  Sum_probs=130.3

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhh
Q 007404          357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSD  436 (605)
Q Consensus       357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~  436 (605)
                      .....++..+++.|+..|.+.++.+++ +.++..+++|++||.|+.+|+..++|++.  .+|.+|++..+||.+++++++
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            444456789999999999999999975 67888899999999999999999999864  369999999999999999997


Q ss_pred             ccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCC
Q 007404          437 QSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD  516 (605)
Q Consensus       437 ~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D  516 (605)
                      +.+..+.                                                     ..+ ..     ....+.   
T Consensus        94 ~~~~~~~-----------------------------------------------------~~~-~~-----~~~~~~---  111 (196)
T PRK12535         94 DMARPRK-----------------------------------------------------SAT-EY-----EDAAAT---  111 (196)
T ss_pred             hccCCCc-----------------------------------------------------ccc-cc-----cccccc---
Confidence            6531110                                                     000 00     000000   


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          517 PEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       517 ~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                       . ..++.... ......|..+|+.||+++|+||.|+|..|    +|++|||+.||+|.++|+++++||+++||+.+...
T Consensus       112 -~-~~~~~~~~-~~~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~  184 (196)
T PRK12535        112 -T-ASNETTGS-WSEWIDVRTLIDALPPERREALILTQVLG----YTYEEAAKIADVRVGTIRSRVARARADLIAATATG  184 (196)
T ss_pred             -c-CCcchhHH-HHHHHHHHHHHHcCCHHHHHHhhhHHHhC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence             0 01111111 11234689999999999999999999988    99999999999999999999999999999988654


Q ss_pred             h
Q 007404          597 H  597 (605)
Q Consensus       597 ~  597 (605)
                      .
T Consensus       185 ~  185 (196)
T PRK12535        185 Q  185 (196)
T ss_pred             c
Confidence            3

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=5.4e-18  Score=168.09  Aligned_cols=179  Identities=17%  Similarity=0.144  Sum_probs=134.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404          367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  446 (605)
Q Consensus       367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~  446 (605)
                      -..++..|.+.|+.+|+++.++..+++|++||+|+.+|+.+.+|++.  .+|.+|++.+++|.+++++++..+....+..
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            35789999999999999999999999999999999999999999864  4699999999999999999987652211100


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCC-CcccCCCCCCCHHHH
Q 007404          447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKP-SEVIADPEAETAEDL  525 (605)
Q Consensus       447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l-~d~l~D~~~~spEe~  525 (605)
                                        ........           .+..+.               +..... .+...+ ...+|++.
T Consensus        98 ------------------~~~~~~~~-----------~~~~~~---------------~~~~~~~~~~~~~-~~~~~e~~  132 (206)
T PRK12544         98 ------------------LRDEEEEE-----------DFEELF---------------DESGHWQKDERPQ-AWGNPEES  132 (206)
T ss_pred             ------------------ccccchhh-----------HHHHhh---------------ccccccccccccc-ccCCHHHH
Confidence                              00000000           000000               000000 000111 12367777


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      +...+....+..+|..||+++|+||.|+|+.+    +|++|||+.||+|..+|+++++||+++||+.+...
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            77777778899999999999999999999988    99999999999999999999999999999998754

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.79  E-value=7.6e-18  Score=159.07  Aligned_cols=158  Identities=16%  Similarity=0.197  Sum_probs=126.6

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404          369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  448 (605)
Q Consensus       369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~  448 (605)
                      .++..|.+.++.+|.++.++..+++|++||+++.+|+....|++.   .|.+|++..+|+.+.++++++.+....     
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            367889999999999999999999999999999999998888763   478999999999999999876531100     


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404          449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  528 (605)
Q Consensus       449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~  528 (605)
                                                                      + +     .+.... +. .+. ..+|++.+..
T Consensus        74 ------------------------------------------------~-~-----~~~~~~-~~-~~~-~~~~~~~~~~   96 (163)
T PRK07037         74 ------------------------------------------------H-G-----DEEDGL-DV-PSP-EASPEAALIN   96 (163)
T ss_pred             ------------------------------------------------c-c-----cccccc-cc-CCC-CCCHHHHHHH
Confidence                                                            0 0     000000 00 111 1246666666


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      .+..+.|..+|..||+++|.||.++|..+    +|++|||+.||+|.++|++.+.||+++||+.+..
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            66678899999999999999999999988    9999999999999999999999999999998764

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.78  E-value=6.6e-18  Score=159.26  Aligned_cols=155  Identities=14%  Similarity=0.120  Sum_probs=125.3

Q ss_pred             HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHH
Q 007404          371 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA  450 (605)
Q Consensus       371 I~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~  450 (605)
                      +..|.+.++.++.++.++..+++|++||+|+.+|+..+.|++.   +|.||++..++|.++++++++.+....       
T Consensus         1 ~~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~~-------   70 (159)
T PRK12527          1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQAE-------   70 (159)
T ss_pred             ChhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhccccc-------
Confidence            3578899999999999998999999999999999999998752   799999999999999999865421000       


Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHH
Q 007404          451 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF  530 (605)
Q Consensus       451 i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~e  530 (605)
                                                                    +++. .. +.     .   ....++|++.+..++
T Consensus        71 ----------------------------------------------~~~~-~~-~~-----~---~~~~~~~~~~~~~~~   94 (159)
T PRK12527         71 ----------------------------------------------PLEV-LD-EE-----E---RLHSPSPQTRLDLGQ   94 (159)
T ss_pred             ----------------------------------------------chhh-hh-cc-----c---cccCCCHHHHHHHHH
Confidence                                                          0000 00 00     0   001225677777777


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      ....|..+|..||+++++||.|+|+.+    +|++|||+.||+|.++|+..+.||+++||+.+..
T Consensus        95 ~~~~l~~~l~~L~~~~r~v~~l~~~~~----~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~  155 (159)
T PRK12527         95 RLALLQRALAELPPACRDSFLLRKLEG----LSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ  155 (159)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            778899999999999999999999988    9999999999999999999999999999998764

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.78  E-value=1.4e-18  Score=162.20  Aligned_cols=153  Identities=17%  Similarity=0.150  Sum_probs=123.8

Q ss_pred             HHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHH
Q 007404          371 ITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEA  450 (605)
Q Consensus       371 I~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~  450 (605)
                      +..|.+.|+.+++++.++..+++|++||+++.+|+.+++|++   .+|.+|++..+++.+.++++++.+....+      
T Consensus         1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------   71 (154)
T TIGR02950         1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------   71 (154)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc------
Confidence            357899999999999999899999999999999999999997   37999999999999999998765311000      


Q ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHH
Q 007404          451 TYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKF  530 (605)
Q Consensus       451 i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~e  530 (605)
                                          .+.                                    +.+...+ ....|++.+...+
T Consensus        72 --------------------~~~------------------------------------~~~~~~~-~~~~~~~~~~~~~   94 (154)
T TIGR02950        72 --------------------DDA------------------------------------IGDLEQH-PVESPEHHLLIKI   94 (154)
T ss_pred             --------------------Hhh------------------------------------hhhcccc-ccCChhHHHHHHH
Confidence                                000                                    0000001 1124566666666


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ....|..+|..||+++++||.++|+.|    +|++|||+.||+|..+|++..+||+++||+.+
T Consensus        95 ~~~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l  153 (154)
T TIGR02950        95 EQEEITHHLSRLPENYRTVLILREFKE----FSYKEIAELLNLSLAKVKSNLFRARKELKKLL  153 (154)
T ss_pred             HHHHHHHHHHhCCHhheeeeeehhhcc----CcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            677899999999999999999999877    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.

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=1e-17  Score=163.49  Aligned_cols=162  Identities=14%  Similarity=0.100  Sum_probs=127.8

Q ss_pred             HhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccc
Q 007404          360 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  439 (605)
Q Consensus       360 l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr  439 (605)
                      +..+..+++.++..|.+.|+.+|+++.++..+++|++||+|+.+|+.++.|++.  ..|.+|++..+++.+.+.++++.+
T Consensus        18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~   95 (188)
T PRK12517         18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQF   95 (188)
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhcc
Confidence            345688999999999999999999999999999999999999999999999865  369999999999987665543221


Q ss_pred             cccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCC
Q 007404          440 TIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEA  519 (605)
Q Consensus       440 ~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~  519 (605)
                      .  .                                                    ...+       ..    ...+...
T Consensus        96 ~--~----------------------------------------------------~~~~-------~~----~~~~~~~  110 (188)
T PRK12517         96 D--L----------------------------------------------------VDIE-------DD----SIEDDAS  110 (188)
T ss_pred             C--c----------------------------------------------------cCcc-------cc----cccCccc
Confidence            0  0                                                    0000       00    0111111


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       520 ~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      .+++..    .....|..+|..||+++|.||.++|..|    ++++|||+.||||..+|+.+++||+++||+.+...
T Consensus       111 ~~~e~~----~~~~~l~~~l~~Lp~~~r~v~~l~~~~g----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  179 (188)
T PRK12517        111 HSSEEE----MEQEWLRRQIAKLDPEYREPLLLQVIGG----FSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP  179 (188)
T ss_pred             cChhHH----HHHHHHHHHHHhCCHHHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            133332    2235689999999999999999999988    99999999999999999999999999999998754

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=8.4e-18  Score=163.34  Aligned_cols=160  Identities=14%  Similarity=0.156  Sum_probs=127.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404          365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  444 (605)
Q Consensus       365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP  444 (605)
                      .++..++..|.+.|+.+|.++.++..+++|++||.|+.+|+..++|++..  .|.+|++..++|.++++++++.+.... 
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            46888999999999999999999999999999999999999999998653  699999999999999999876531100 


Q ss_pred             ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404          445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED  524 (605)
Q Consensus       445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe  524 (605)
                                                                           .+.        ...+... +   .++.
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             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404          525 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  598 (605)
Q Consensus       525 ~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  598 (605)
                      ..  ......|..+|+.||+++|+||.|+|..+    +|++|||+.||+|..+|+++++||+++||+.+.....
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    9999999999999999999999999999999886553

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.77  E-value=1.2e-17  Score=162.02  Aligned_cols=154  Identities=14%  Similarity=0.120  Sum_probs=127.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404          367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  446 (605)
Q Consensus       367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~  446 (605)
                      ++.|++.|.+.|+.++.++.++..+++|++||.++.+|+.+..|++.  .+|.+|++..+++.+.++++++.+...++  
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  37999999999999999998765411100  


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHH
Q 007404          447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  526 (605)
Q Consensus       447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l  526 (605)
                                                                                ++.     ...+    .+++..
T Consensus        79 ----------------------------------------------------------~~~-----~~~~----~~~~~~   91 (181)
T PRK09637         79 ----------------------------------------------------------DDL-----LFED----EEREEN   91 (181)
T ss_pred             ----------------------------------------------------------hhh-----hccC----CChhHH
Confidence                                                                      000     0000    111223


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       527 ~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      ...+....+..+|+.||+++|.||.|+|..|    ++++|||+.||+|..+|+.++.||+++||+.+..
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=1.1e-17  Score=160.37  Aligned_cols=162  Identities=14%  Similarity=0.081  Sum_probs=126.9

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccc
Q 007404          363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIR  442 (605)
Q Consensus       363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IR  442 (605)
                      +..|+..++..|.+.++.++.++.++..+++||+||.|+.+|+. ..|++..  .|.+|++..++|.+.++++++.+...
T Consensus         8 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~~~   84 (172)
T PRK09651          8 ASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALEKA   84 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            36799999999999999999999999999999999999999998 3565432  58999999999999999986532000


Q ss_pred             ccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCH
Q 007404          443 LPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETA  522 (605)
Q Consensus       443 lP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~sp  522 (605)
                      .                           ...+                              .   .+    .+...++|
T Consensus        85 ~---------------------------~~~~------------------------------~---~~----~~~~~~~~  100 (172)
T PRK09651         85 Y---------------------------LEML------------------------------A---LM----PEGGAPSP  100 (172)
T ss_pred             h---------------------------hhHH------------------------------h---hc----cccCCCCh
Confidence            0                           0000                              0   00    00011134


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      +......+....|..+|+.||+++|+||.|+|+.+    +|++|||+.||+|.++|+..++||+++|+...-.
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            44444445557799999999999999999999988    9999999999999999999999999999986543

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.77  E-value=1.6e-17  Score=166.52  Aligned_cols=115  Identities=16%  Similarity=0.187  Sum_probs=104.0

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc-
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAG--MNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS-  438 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g--~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s-  438 (605)
                      |+.. +++||..|.++|.++|++|.++.  .+.+|++|+|++|||+|+++|||++|.+|.|||.+|||+.|.+++|+.. 
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            4455 99999999999999999998764  5899999999999999999999999999999999999999999999887 


Q ss_pred             --ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHh
Q 007404          439 --RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA  477 (605)
Q Consensus       439 --r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~  477 (605)
                        +.+++|....+....+..+...+..+.++.|+.+||+..
T Consensus        86 ~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~  126 (218)
T TIGR02895        86 YQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY  126 (218)
T ss_pred             ccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence              678999776666778888888999999999999999864

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).

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=2.7e-17  Score=160.77  Aligned_cols=157  Identities=12%  Similarity=0.137  Sum_probs=122.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  443 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl  443 (605)
                      ..+++.|+. |.+.|+.+|+.+.++..+++|++||.|+.+|+.+..|+..  ..|.+|++..++|.+.++++++.+....
T Consensus         7 ~~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~~   83 (188)
T PRK12546          7 RDPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVPD   83 (188)
T ss_pred             hhHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcccccC
Confidence            456666766 7799999999999999999999999999999999999864  3699999999999999998876531000


Q ss_pred             cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404          444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  523 (605)
Q Consensus       444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE  523 (605)
                                                                            .+.        ...+...+..  ..+
T Consensus        84 ------------------------------------------------------~~~--------~~~~~~~~~~--~~~   99 (188)
T PRK12546         84 ------------------------------------------------------PEG--------VHAASLAVKP--AHD   99 (188)
T ss_pred             ------------------------------------------------------ccc--------ccccccccCC--cch
Confidence                                                                  000        0000000000  111


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      .    ......|..+|..||+++|+||.|+|..+    +|++|||+.||||..+|+++++||+++||+.+..
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    12234688999999999999999999987    9999999999999999999999999999998864

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.76  E-value=2.4e-17  Score=157.89  Aligned_cols=148  Identities=18%  Similarity=0.206  Sum_probs=121.5

Q ss_pred             HHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHH
Q 007404          372 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEAT  451 (605)
Q Consensus       372 ~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i  451 (605)
                      ..|.+.++.+++++.++..+++|++||+|+.+|+++++|++.  .+|.+|++..+++.+.+++++..+...++       
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            468899999999999999999999999999999999999863  47999999999999999998875411110       


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHHHHH
Q 007404          452 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFM  531 (605)
Q Consensus       452 ~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el  531 (605)
                                                                     +     .       .... .  ++++.....+.
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  11222334445


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       532 ~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ...|..+|..||+++|.||.|+|..+    +|++|||+.||+|..+|+++++||+++||..+.
T Consensus        91 ~~~l~~~l~~L~~~~r~v~~l~~~~g----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  149 (170)
T TIGR02959        91 SQCIPPMIKELPDEYREAIRLTELEG----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE  149 (170)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            66789999999999999999999988    999999999999999999999999999999876

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=159.46  Aligned_cols=156  Identities=13%  Similarity=0.133  Sum_probs=122.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404          367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  446 (605)
Q Consensus       367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~  446 (605)
                      .+..+..+++.|+.++.++.++..+++|++||.|+.+|+....|++.  .+|.+|++..+++.+.++++++.+.....  
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            44568889999999999999999999999999999999999999864  36999999999999999998865411000  


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHH
Q 007404          447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  526 (605)
Q Consensus       447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l  526 (605)
                                               +++                        .            +. .+...+.+.+  
T Consensus        82 -------------------------~~~------------------------~------------~~-~~~~~~~~~~--   97 (182)
T PRK12511         82 -------------------------DEL------------------------A------------VL-ADASLPAAQE--   97 (182)
T ss_pred             -------------------------cch------------------------h------------hc-cccCCCcchH--
Confidence                                     000                        0            00 0000001111  


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       527 ~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                       .......|..+|..||+++|+||.|+|..+    +|++|||+.||||.++|+++++||+++||+.+..
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             122345688999999999999999999987    9999999999999999999999999999998864

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=5.9e-17  Score=154.63  Aligned_cols=159  Identities=15%  Similarity=0.108  Sum_probs=127.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccc
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRL  443 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRl  443 (605)
                      ..++.+++..|.+.++.++.+|.++..+++|++||.|+.+|+..+.++.   ..|.+|++..++|.+.+++++....   
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            4689999999999999999999999999999999999999987665542   2699999999999999988764310   


Q ss_pred             cccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHH
Q 007404          444 PFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAE  523 (605)
Q Consensus       444 P~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spE  523 (605)
                                     +.....                                 ++     +        .+.....+|+
T Consensus        82 ---------------~~~~~~---------------------------------~~-----~--------~~~~~~~~~~  100 (168)
T PRK12525         82 ---------------RAYLQS---------------------------------LA-----E--------APEAVQPSPE  100 (168)
T ss_pred             ---------------HHHHHH---------------------------------Hh-----c--------ccccccCChH
Confidence                           000000                                 00     0        0001113566


Q ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       524 e~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      +.....+....|..+|..||+++|+||.|+|..|    +|++|||+.||+|..+|+..+.||+++||..+
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            6666666678899999999999999999999888    99999999999999999999999999999865

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.74  E-value=7e-17  Score=167.88  Aligned_cols=160  Identities=16%  Similarity=0.141  Sum_probs=124.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404          365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  444 (605)
Q Consensus       365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP  444 (605)
                      ..+..++..|.+.++.+|+++.++..+++|++||.|+. |.....|+.   ..|.+|++..++|.++++++++.+.... 
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~~-   78 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRET-   78 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccccc-
Confidence            34678999999999999999999999999999999999 666677762   4799999999999999999875431000 


Q ss_pred             ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404          445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED  524 (605)
Q Consensus       445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe  524 (605)
                                                                          ..    +    ..+.+...+.. .+|++
T Consensus        79 ----------------------------------------------------~~----~----~~~~e~~~~~~-~~~~~   97 (293)
T PRK09636         79 ----------------------------------------------------YV----G----PWLPEPVVEEL-DDPLE   97 (293)
T ss_pred             ----------------------------------------------------cc----C----CcCCcCCCCCC-CChHH
Confidence                                                                00    0    00000011111 13444


Q ss_pred             H-HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          525 L-LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       525 ~-l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      . .....+...+..+|+.||+++|.||.|+|..+    +|++|||+.||+|..+|+++++||+++||+...
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 33445566789999999999999999999988    999999999999999999999999999999754

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.72  E-value=1.1e-16  Score=150.56  Aligned_cols=155  Identities=16%  Similarity=0.180  Sum_probs=113.0

Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcC
Q 007404          387 GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENG  466 (605)
Q Consensus       387 ~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elg  466 (605)
                      ++..+++|++||+|+.+|+....+ +  +..|.+|++..++|.++++++++.+..+....                    
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            344678999999999999998863 3  34799999999999999999876531111000                    


Q ss_pred             CCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC--CCCHHHHHHHHHHHHHHHHHHhcCCH
Q 007404          467 RHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE--AETAEDLLIKKFMKEDLEKVLDTLNP  544 (605)
Q Consensus       467 r~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~--~~spEe~l~~~el~~~L~~aL~~L~~  544 (605)
                                                  ..++..... +++....+.+.+..  ..+|++.+...+....|..+|..||+
T Consensus        59 ----------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~  109 (161)
T PRK09047         59 ----------------------------FSSFSDDDD-DDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPA  109 (161)
T ss_pred             ----------------------------ccccccccc-cccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCH
Confidence                                        000000000 00011111122111  24677777777888889999999999


Q ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      ++|+||.|+|+.|    +|++|||+.||||..+|+.+++||+++||+.+...+
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

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.70  E-value=5.7e-16  Score=156.41  Aligned_cols=159  Identities=13%  Similarity=0.137  Sum_probs=124.4

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404          355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  434 (605)
Q Consensus       355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i  434 (605)
                      .|++.+.++..+++.+++.| +.++.++.++.++..+++||+||.|+.+|+.   |+..  ..|.+|++.+++|.+++++
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            34555667778898888877 7899999999999999999999999999986   5543  2599999999999999999


Q ss_pred             hhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCccc
Q 007404          435 SDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVI  514 (605)
Q Consensus       435 r~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l  514 (605)
                      +++.+.-.+                                                       .     + ...    .
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            876531000                                                       0     0 000    0


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          515 ADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       515 ~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                           ..+.+..  .+..+.+..+|+.||+++|.||.|+|..+    +|++|||+.||+|.++|+++++||+++||+.+.
T Consensus        97 -----~~~~~~~--~~~~~~l~~~L~~Lp~~~R~v~lL~~~eg----~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~  165 (228)
T PRK06704         97 -----EEPHEKI--ADLHEMVGKVLSSLNVQQSAILLLKDVFQ----YSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE  165 (228)
T ss_pred             -----CChHHHH--HHHHHHHHHHHHhCCHHHhhHhhhHHhhC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence                 0111111  12345688999999999999999999887    999999999999999999999999999999886


Q ss_pred             h
Q 007404          595 T  595 (605)
Q Consensus       595 ~  595 (605)
                      .
T Consensus       166 ~  166 (228)
T PRK06704        166 E  166 (228)
T ss_pred             h
Confidence            4

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=99.69  E-value=5.9e-16  Score=160.34  Aligned_cols=156  Identities=18%  Similarity=0.161  Sum_probs=120.3

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHH
Q 007404          369 KMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV  448 (605)
Q Consensus       369 ~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~  448 (605)
                      +++..|.+.++.+|+++.++..++||++||+|+.+++.  .|+..  ..|.+|++.+++|.+++++++..+....     
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~~--~~~~awL~~Ia~n~~ld~lR~~~~~~~~-----   71 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQI--ENPKAYLTKVVTRRCIDVLRSARARREV-----   71 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccccc--cCHHHHHHHHHHHHHHHHHHHhhhcccc-----
Confidence            37899999999999999999999999999999998775  45432  3699999999999999999875421000     


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHHH
Q 007404          449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIK  528 (605)
Q Consensus       449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~  528 (605)
                                                                       ..       +..+.+...+. ..+|++....
T Consensus        72 -------------------------------------------------~~-------~~~~~e~~~~~-~~~~~~~~~~   94 (281)
T TIGR02957        72 -------------------------------------------------YV-------GPWLPEPLLTT-SADPAESVEL   94 (281)
T ss_pred             -------------------------------------------------cC-------CCCCCcccCCC-CCChHHHHHH
Confidence                                                             00       00000001111 1245554443


Q ss_pred             -HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          529 -KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       529 -~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                       +.+...+..+|++||++||.||.|+|..+    +|++|||+.||+|..+|+++++||+++||+...
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.

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.68  E-value=1.3e-15  Score=158.91  Aligned_cols=161  Identities=16%  Similarity=0.133  Sum_probs=124.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccc
Q 007404          365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLP  444 (605)
Q Consensus       365 ~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP  444 (605)
                      ..+..+++.|.+.++.+|+++.++..++||++||.|+.+|++...+ .   ..|.+|++...+|.+++++++..+.-..+
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~~   80 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRERP   80 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcCc
Confidence            4678899999999999999999999999999999999999987653 1   25999999999999999998754210000


Q ss_pred             ccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHH
Q 007404          445 FHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAED  524 (605)
Q Consensus       445 ~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe  524 (605)
                                                                         ...+...       ..+..++  ..+|++
T Consensus        81 ---------------------------------------------------~~~~~~~-------~~~~~~~--~~~~~~  100 (290)
T PRK09635         81 ---------------------------------------------------QDIAAWH-------DGDASVS--SVDPAD  100 (290)
T ss_pred             ---------------------------------------------------ccccccC-------ccccCCC--CCCcHH
Confidence                                                               0000000       0000111  113333


Q ss_pred             -HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          525 -LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       525 -~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                       ....++....+..+|..|||++|.||.|+|..+    +|++|||+.||+|..+|+++++||+++||+..
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             344556667899999999999999999999998    99999999999999999999999999999854

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.55  E-value=5.8e-14  Score=130.16  Aligned_cols=136  Identities=11%  Similarity=0.164  Sum_probs=100.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhc-----cCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK-----FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ek-----FDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      ++.|+..|.++++.++++|...    +| +||.++.+|+.+.+     |++.  ..|.||++..+||.++++++++.+..
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            4679999999999999999762    34 49999999999865     5543  46999999999999999998764310


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  521 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s  521 (605)
                      +.                 . ..       .+                        +      .          +.. ..
T Consensus        74 ~~-----------------~-~~-------~~------------------------~------~----------~~~-~~   87 (142)
T TIGR03209        74 KI-----------------I-YN-------SE------------------------I------T----------DIK-LS   87 (142)
T ss_pred             hh-----------------h-hh-------hh------------------------h------h----------ccc-cc
Confidence            00                 0 00       00                        0      0          000 01


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHH
Q 007404          522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIR  579 (605)
Q Consensus       522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVR  579 (605)
                      +.+.....+....|..+|+.||+++|+||.|+|..|    +|++|||+.||+|.+||+
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            122333444556789999999999999999999988    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=99.52  E-value=1.1e-13  Score=139.12  Aligned_cols=136  Identities=14%  Similarity=0.143  Sum_probs=111.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccc
Q 007404          366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPF  445 (605)
Q Consensus       366 A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~  445 (605)
                      ++..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+...+|++.  ..|.+|++.++++.....    .       
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~----~-------   68 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA----G-------   68 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc----c-------
Confidence            578899999999999999999999999999999999999999999874  358999998775432100    0       


Q ss_pred             cHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404          446 HMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  525 (605)
Q Consensus       446 ~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~  525 (605)
                                                                              .  . ..       ...  .+.. 
T Consensus        69 --------------------------------------------------------~--~-~~-------~~~--~~~~-   79 (261)
T PRK09191         69 --------------------------------------------------------A--N-DP-------EPG--SPFE-   79 (261)
T ss_pred             --------------------------------------------------------c--c-CC-------CCC--CCch-
Confidence                                                                    0  0 00       000  0110 


Q ss_pred             HHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          526 LIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       526 l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                             ..+..+|+.||+++|+||.|+|..+    +|++|||+.||+|.++|+.+.+||+++||..+.
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                   1688999999999999999999888    999999999999999999999999999998664

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.41  E-value=1.3e-11  Score=125.58  Aligned_cols=86  Identities=15%  Similarity=0.209  Sum_probs=76.5

Q ss_pred             HHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCC--CHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHH
Q 007404          357 RRRLNYGILCKDKMITSNIRLVISIAKNYQGAGM--NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL  434 (605)
Q Consensus       357 ~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~--d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~i  434 (605)
                      .....++..|++.|+..|.++|+++|.+|.++..  +.+|++|||++++|+++++|++++|.+|.+|++.+|++.+.+++
T Consensus        10 ~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDyl   89 (237)
T PRK08311         10 EKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYF   89 (237)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            3344566889999999999999999999998765  58999999999999999999999988899999999999999999


Q ss_pred             hhcccccc
Q 007404          435 SDQSRTIR  442 (605)
Q Consensus       435 r~~sr~IR  442 (605)
                      |++.+...
T Consensus        90 Rk~~~~~~   97 (237)
T PRK08311         90 RKESKHNL   97 (237)
T ss_pred             HHhhcccc
Confidence            98766433

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.39  E-value=2.4e-11  Score=118.66  Aligned_cols=173  Identities=25%  Similarity=0.310  Sum_probs=119.7

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCC---CCCHHH--HHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHH
Q 007404          355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGA---GMNLQD--LVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQA  429 (605)
Q Consensus       355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~---g~d~eD--LIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqa  429 (605)
                      .|.+...||..|++.|+..|+.-++.+|+++...   +.+.+|  |++|.|+.+++.-...+.+.-..|-.|+...+++.
T Consensus         7 ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~   86 (185)
T PF07638_consen    7 LLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRK   86 (185)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHH
Confidence            3455556779999999999999999999987643   344554  57788888877433323332236888888999999


Q ss_pred             HHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCC
Q 007404          430 VRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLK  509 (605)
Q Consensus       430 I~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~  509 (605)
                      +.++.+++....|-                      |..                         ...+||...       
T Consensus        87 lid~~R~~~a~KRg----------------------~~~-------------------------~~~~l~~~~-------  112 (185)
T PF07638_consen   87 LIDHARRRQAQKRG----------------------GDQ-------------------------VRVELDERA-------  112 (185)
T ss_pred             HHHHHHHHHHHhcC----------------------CCC-------------------------cccchhhhh-------
Confidence            98888876542221                      000                         011222111       


Q ss_pred             CCcccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 007404          510 PSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL  589 (605)
Q Consensus       510 l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKL  589 (605)
                           .+...+.|++.+.   +.+.+..+.. |+|+++++|.++|+.|    +|.+|||+.||||..||+.....|..+|
T Consensus       113 -----~~~~~~~~~~~~~---l~e~l~~L~~-l~~~~~~~v~l~~~~G----ls~~EIA~~lgiS~~tV~r~l~~aR~~l  179 (185)
T PF07638_consen  113 -----DSGDEPSPEELLE---LEEALERLLA-LDPRQRRVVELRFFEG----LSVEEIAERLGISERTVRRRLRRARAWL  179 (185)
T ss_pred             -----ccccCCCHHHHHH---HHHHHHHHHc-cCHHHHHHHHHHHHCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence                 0111235555433   3344555444 9999999999999877    9999999999999999999999999999


Q ss_pred             HhHHh
Q 007404          590 KNKKR  594 (605)
Q Consensus       590 R~~l~  594 (605)
                      +..+.
T Consensus       180 ~~~l~  184 (185)
T PF07638_consen  180 RRELR  184 (185)
T ss_pred             HHHhc
Confidence            98664

>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=99.24  E-value=1.8e-11  Score=99.57  Aligned_cols=70  Identities=23%  Similarity=0.377  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccc
Q 007404          370 MITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  439 (605)
Q Consensus       370 LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr  439 (605)
                      |++.|.++|++++++|.+++.+.+|++||++++||+++++||++++..|.+|++..+++.+.++++++.|
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            7899999999999999999999999999999999999999999999899999999999999999998765

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=99.21  E-value=3.7e-11  Score=93.05  Aligned_cols=50  Identities=46%  Similarity=0.726  Sum_probs=46.0

Q ss_pred             HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       538 aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +|+.||++|++||.++|+.+    +|++|||+.||+|+++|++++.+|++|||+
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            58899999999999999887    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=99.06  E-value=2e-10  Score=96.51  Aligned_cols=77  Identities=31%  Similarity=0.538  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHH
Q 007404          449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDL  525 (605)
Q Consensus       449 ~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~  525 (605)
                      +.+++|.+++++|.+++||.||.+|||+.||+++++|..++.....++|||.+++.+++.++.+++.|+...+|++.
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            36789999999999999999999999999999999999999999999999999998888899999999988888875

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=98.91  E-value=3.8e-09  Score=82.74  Aligned_cols=54  Identities=28%  Similarity=0.465  Sum_probs=46.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 007404          532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL  589 (605)
Q Consensus       532 ~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKL  589 (605)
                      ++.|..+|..||+++|.||.++|..|    +|++|||+.+|+|.++|++++.||+++|
T Consensus         1 r~~l~~~l~~L~~~~r~i~~l~~~~g----~s~~eIa~~l~~s~~~v~~~l~ra~~~L   54 (54)
T PF08281_consen    1 REALQQALAQLPERQREIFLLRYFQG----MSYAEIAEILGISESTVKRRLRRARKKL   54 (54)
T ss_dssp             HHHHHHHHHCS-HHHHHHHHHHHTS-------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHC----cCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence            35789999999999999999999988    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=98.64  E-value=1.5e-07  Score=91.42  Aligned_cols=70  Identities=19%  Similarity=0.332  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       523 Ee~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      .+..........|..+|..||+++|+||.|+|+.|    +|++|||+.||+|.++|++++.||+++|++.+...
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            33444455677899999999999999999999888    99999999999999999999999999999988654

>PRK00118 putative DNA-binding protein; Validated

Probab=98.43  E-value=1.1e-06  Score=78.72  Aligned_cols=61  Identities=18%  Similarity=0.163  Sum_probs=54.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      ..+.-....||+++++||.++|..+    +|++|||+.+|+|+.+|+.++.||+++||+++..-+
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            3445566799999999999999987    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=98.27  E-value=2.8e-06  Score=64.28  Aligned_cols=54  Identities=44%  Similarity=0.701  Sum_probs=49.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      ..+..++..|++.++.++.++|..+    +|..+||+.+|+|..+|+++.+++..+||
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~~~----~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            3577889999999999999999766    99999999999999999999999988875

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

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.07  E-value=1.1e-05  Score=75.68  Aligned_cols=57  Identities=19%  Similarity=0.335  Sum_probs=50.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYA  602 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl  602 (605)
                      -|+++|++||.|++ .|    +|++|||+.||+|+.+|++++++|+++||+......+-.++
T Consensus         6 ~Lte~qr~VL~Lr~-~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~   62 (137)
T TIGR00721         6 FLTERQIKVLELRE-KG----LSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFI   62 (137)
T ss_pred             CCCHHHHHHHHHHH-cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHh
Confidence            59999999999963 44    99999999999999999999999999999877666665554

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PRK04217 hypothetical protein; Provisional

Probab=98.06  E-value=9e-06  Score=73.68  Aligned_cols=57  Identities=23%  Similarity=0.119  Sum_probs=51.5

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ  600 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~  600 (605)
                      ..|++.|++||.++|..+    +|++|||+.||||+.||++++.+|+++|++.+.......
T Consensus        41 ~~Lt~eereai~l~~~eG----lS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~~   97 (110)
T PRK04217         41 IFMTYEEFEALRLVDYEG----LTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRELI   97 (110)
T ss_pred             ccCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcccee
Confidence            579999999999999887    999999999999999999999999999999987655443

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=97.99  E-value=2.1e-05  Score=74.24  Aligned_cols=51  Identities=31%  Similarity=0.464  Sum_probs=46.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      ..|+++|++||.++ ..+    +|++|||+.||+|+.+|++++++++++||+....
T Consensus         5 ~~Lt~rqreVL~lr-~~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t   55 (141)
T PRK03975          5 SFLTERQIEVLRLR-ERG----LTQQEIADILGTSRANVSSIEKRARENIEKARET   55 (141)
T ss_pred             cCCCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            46999999999995 355    9999999999999999999999999999997764

>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=68.83  Aligned_cols=59  Identities=22%  Similarity=0.317  Sum_probs=46.0

Q ss_pred             HHHHHHh-cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          534 DLEKVLD-TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       534 ~L~~aL~-~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      .|.+... -|+++|+.++.++|..|    +|+.|||+.+|||+..|...+.||.++|...-..-
T Consensus         9 ~L~d~Yg~LLT~kQ~~~l~lyy~eD----lSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL   68 (101)
T PF04297_consen    9 LLFDFYGELLTEKQREILELYYEED----LSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKL   68 (101)
T ss_dssp             HHHHHHGGGS-HHHHHHHHHHCTS-------HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHccC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444444 49999999999999888    99999999999999999999999999998765543

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.

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=97.95  E-value=3.3e-06  Score=61.96  Aligned_cols=31  Identities=45%  Similarity=0.620  Sum_probs=27.8

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 007404          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL  322 (605)
Q Consensus       291 ~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~  322 (605)
                      +|+++ ||++| +++||||++||++|+++|+..
T Consensus         1 ~D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g   32 (37)
T PF00140_consen    1 SDSLRLYLKEI-GRYPLLTAEEEIELARRIRKG   32 (37)
T ss_dssp             HHHHHHHHHHH-HHS-EETTHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHh
Confidence            37899 99999 999999999999999999974

2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=97.86  E-value=6.6e-05  Score=70.21  Aligned_cols=62  Identities=11%  Similarity=0.205  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      .....|..+|+.|++.+|.||.++|+..  ..+|..+||..||+|+.+|+++..+++.+|+..+
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            4567789999999999999999999754  2379999999999999999999999999999864

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=97.75  E-value=6e-05  Score=58.05  Aligned_cols=47  Identities=36%  Similarity=0.525  Sum_probs=41.1

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|+.|+.+ +..+    +|.+|||+.||+|+.+|+++..++++||+-
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            4689999999877 4444    899999999999999999999999998864

lux regulon (activates the bioluminescence operon

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.65  E-value=0.00015  Score=61.02  Aligned_cols=47  Identities=19%  Similarity=0.196  Sum_probs=40.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          534 DLEKVLDTLNPRERQVVRWRF-GLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       534 ~L~~aL~~L~~rER~VL~LRy-Gl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      .+.+-|+.||++.+.++.|.+ ..+    +|++|||+.||+|..+|++++++
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            456678999999999999964 455    99999999999999999988775

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.

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=97.59  E-value=0.00035  Score=62.15  Aligned_cols=55  Identities=27%  Similarity=0.491  Sum_probs=49.6

Q ss_pred             HHHHHHHHHhcCC-HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 007404          531 MKEDLEKVLDTLN-PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL  589 (605)
Q Consensus       531 l~~~L~~aL~~L~-~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKL  589 (605)
                      .+..+..+++.|. +.+|.||.++|..+    ++..+|++.||+|+.++..+..+|++.|
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            4456888888886 79999999999976    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.

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=97.59  E-value=0.004  Score=71.98  Aligned_cols=32  Identities=34%  Similarity=0.583  Sum_probs=30.1

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 007404          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL  322 (605)
Q Consensus       290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~  322 (605)
                      ..||++ ||+++ |..||||+|+|++++++|...
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 999999999999999999864

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=97.54  E-value=0.00032  Score=55.63  Aligned_cols=48  Identities=33%  Similarity=0.517  Sum_probs=42.5

Q ss_pred             CCHHHHHHHHHHHhcC--C-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLE--D-GRMKTLQEIGELMGVSRERIRQIESSAFRKL  589 (605)
Q Consensus       542 L~~rER~VL~LRyGl~--d-g~~~Tl~EIAe~LGISrerVRqie~RALkKL  589 (605)
                      |+++|++||..-|-.|  + .+..|+.|||+.||||+.+|..++.+|.+||
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            7899999999887665  2 3468999999999999999999999999987

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=97.53  E-value=0.00023  Score=54.98  Aligned_cols=46  Identities=37%  Similarity=0.571  Sum_probs=40.2

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      |+++|+.|+.+. ..+    +|.+|||+.||+|+.+|+++.++++++|+..
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            689999999874 344    8999999999999999999999998888763

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=97.44  E-value=0.00032  Score=55.83  Aligned_cols=47  Identities=26%  Similarity=0.354  Sum_probs=39.5

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|.+||.+.. .|    ++.+|||+.||||..||+.+..+.++||.-
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 ....

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.09  E-value=0.00089  Score=67.41  Aligned_cols=51  Identities=8%  Similarity=0.067  Sum_probs=45.6

Q ss_pred             HHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          536 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       536 ~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .++...|+++|++||.+. ..|    +|.+|||+.|++|..||+.+..+.++||.-
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            556688999999999985 455    999999999999999999999999999964

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.09  E-value=0.0009  Score=66.68  Aligned_cols=46  Identities=17%  Similarity=0.258  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++||++||.+. ..|    +|.+|||+.||||..||+.+..+.++||.-
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            4999999999985 344    999999999999999999999999999974

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.06  E-value=0.00096  Score=67.68  Aligned_cols=50  Identities=30%  Similarity=0.501  Sum_probs=44.4

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ...|+++|++||.+. ..|    +|.+|||++||||..||+.++.++++||+..-
T Consensus       169 ~~~Lt~re~evl~~~-a~G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~  218 (232)
T TIGR03541       169 AGVLSEREREVLAWT-ALG----RRQADIAAILGISERTVENHLRSARRKLGVAT  218 (232)
T ss_pred             hccCCHHHHHHHHHH-HCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCC
Confidence            347999999999995 444    99999999999999999999999999998543

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.

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.06  E-value=0.001  Score=65.49  Aligned_cols=46  Identities=28%  Similarity=0.299  Sum_probs=41.7

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      ..|++||++||.+.- .|    +|.+|||+.|+||..||+.+..+.++||-
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            359999999999853 44    99999999999999999999999999995

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.04  E-value=0.0011  Score=66.25  Aligned_cols=46  Identities=24%  Similarity=0.364  Sum_probs=41.9

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      ..|++||++||.+.- .|    +|.+|||+.|+||..||+.+..+.++||.
T Consensus       133 ~~LT~RE~eVL~ll~-~G----~snkeIA~~L~iS~~TV~~h~~~I~~KLg  178 (207)
T PRK11475        133 RMLSPTEREILRFMS-RG----YSMPQIAEQLERNIKTIRAHKFNVMSKLG  178 (207)
T ss_pred             CCCCHHHHHHHHHHH-CC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            469999999999853 44    99999999999999999999999999995

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.03  E-value=0.0011  Score=58.50  Aligned_cols=48  Identities=25%  Similarity=0.367  Sum_probs=41.4

Q ss_pred             HHHHHHHh-cCCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHHH
Q 007404          533 EDLEKVLD-TLNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIRQ  580 (605)
Q Consensus       533 ~~L~~aL~-~L~~rER~VL~LRyGl~d---g~~~Tl~EIAe~LGISrerVRq  580 (605)
                      +.+..+|. -|+|+|+.+|.+||++-+   ..++|++|||+.+|||+.+|..
T Consensus        23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR   74 (94)
T TIGR01321        23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITR   74 (94)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhH
Confidence            45667774 599999999999999876   4569999999999999999984

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.

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.03  E-value=0.0011  Score=68.23  Aligned_cols=50  Identities=24%  Similarity=0.436  Sum_probs=44.4

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      +..|+++|++||.+.. .|    +|.+|||++||||..||+.+..++++||.-.-
T Consensus       188 ~~~LT~RE~evl~l~a-~G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n  237 (247)
T TIGR03020       188 AGLITAREAEILAWVR-DG----KTNEEIAAILGISSLTVKNHLQHIFKKLDVRN  237 (247)
T ss_pred             ccCCCHHHHHHHHHHH-CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence            4579999999999854 55    99999999999999999999999999997543

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.

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=97.03  E-value=0.0013  Score=64.16  Aligned_cols=46  Identities=24%  Similarity=0.374  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++||.+. ..|    +|.+|||+.|++|..||+....++++||.-
T Consensus       133 ~LSpRErEVLrLL-AqG----kTnKEIAe~L~IS~rTVkth~srImkKLgV  178 (198)
T PRK15201        133 HFSVTERHLLKLI-ASG----YHLSETAALLSLSEEQTKSLRRSIMRKLHV  178 (198)
T ss_pred             CCCHHHHHHHHHH-HCC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            5999999999985 344    999999999999999999999999999975

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=96.96  E-value=0.0013  Score=65.94  Aligned_cols=47  Identities=30%  Similarity=0.393  Sum_probs=42.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|++||++|+++- ..|    +|.+|||+.|++|..||+.+.++.++||.-
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            46999999999874 444    999999999999999999999999999964

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=96.95  E-value=0.0014  Score=65.91  Aligned_cols=47  Identities=17%  Similarity=0.189  Sum_probs=43.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|++||.+... |    +|.+|||+.|++|..||+.+..++++||.-
T Consensus       154 ~~Lt~rE~~Vl~l~~~-G----~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v  200 (216)
T PRK10100        154 ALLTHREKEILNKLRI-G----ASNNEIARSLFISENTVKTHLYNLFKKIAV  200 (216)
T ss_pred             CCCCHHHHHHHHHHHc-C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            4699999999999874 4    999999999999999999999999999975

>PRK13870 transcriptional regulator TraR; Provisional

Probab=96.93  E-value=0.0015  Score=66.66  Aligned_cols=46  Identities=28%  Similarity=0.549  Sum_probs=41.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++||++||.+- -.|    +|..|||.+||||..||..++.+|++||--
T Consensus       173 ~LT~RE~E~L~W~-A~G----KT~~EIa~ILgISe~TV~~Hl~na~~KLga  218 (234)
T PRK13870        173 WLDPKEATYLRWI-AVG----KTMEEIADVEGVKYNSVRVKLREAMKRFDV  218 (234)
T ss_pred             CCCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            5999999999885 333    999999999999999999999999999954

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=96.90  E-value=0.0017  Score=66.36  Aligned_cols=46  Identities=20%  Similarity=0.453  Sum_probs=42.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++||++||.+- ..|    +|..|||++||||..||+.++.++++||--
T Consensus       179 ~LT~rE~evl~~~-a~G----~t~~eIa~~l~is~~TV~~h~~~~~~KL~~  224 (240)
T PRK10188        179 NFSKREKEILKWT-AEG----KTSAEIAMILSISENTVNFHQKNMQKKFNA  224 (240)
T ss_pred             CCCHHHHHHHHHH-HcC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            5999999999987 344    999999999999999999999999999964

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=96.86  E-value=0.0052  Score=60.75  Aligned_cols=65  Identities=20%  Similarity=0.261  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHh
Q 007404          530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLM  599 (605)
Q Consensus       530 el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~  599 (605)
                      .....+...+++|++|||+|+..-- .|    +..++||..||||..||..+..+.++||+..-...-++
T Consensus       131 ~~~~~~~~~l~tLT~RERqVl~~vV-~G----~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr  195 (202)
T COG4566         131 DRQAAIRARLATLTPRERQVLDLVV-RG----LMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVR  195 (202)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH-cC----cccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHH
Confidence            4456788999999999999998764 45    89999999999999999999999999998755444433

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=96.86  E-value=0.0028  Score=57.24  Aligned_cols=53  Identities=26%  Similarity=0.225  Sum_probs=49.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      .|+..|-+.|+|.++++    +|++|-|+.||||+.|+..++..|.+|+-..+....
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            57888999999999988    999999999999999999999999999999887654

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.69  E-value=0.0036  Score=58.90  Aligned_cols=47  Identities=28%  Similarity=0.397  Sum_probs=42.2

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|++||.+ +..+    ++.+|||+.|++|..||+.+..++++||.-
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

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=96.68  E-value=0.0022  Score=48.73  Aligned_cols=41  Identities=22%  Similarity=0.337  Sum_probs=23.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      ..|++.||..|...+-.+    +|+.+||+.||+|++||...+.|
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            468999999998776555    99999999999999999977665

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.67  E-value=0.0042  Score=62.35  Aligned_cols=53  Identities=25%  Similarity=0.398  Sum_probs=46.4

Q ss_pred             cCCHHHHHHHHHHHhcC--C-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          541 TLNPRERQVVRWRFGLE--D-GRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~--d-g~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      .|+++|++||+.-|-.|  | .+..+++|||+.||||+.++.+++.||.+||=...
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            69999999999988765  2 25589999999999999999999999999996644

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=96.65  E-value=0.0059  Score=48.59  Aligned_cols=51  Identities=33%  Similarity=0.573  Sum_probs=43.2

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      ..|+++|.+|+.+. ..+    ++..|||..+|+|..+|+.+..+.++||.-.-+.
T Consensus         3 ~~Lt~rE~~v~~l~-~~G----~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~   53 (65)
T COG2771           3 ADLTPREREILRLV-AQG----KSNKEIARILGISEETVKTHLRNIYRKLGVKNRV   53 (65)
T ss_pred             ccCCHHHHHHHHHH-HCC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHH
Confidence            36899999999774 333    8999999999999999999999999999764433

>PRK09483 response regulator; Provisional

Probab=96.65  E-value=0.0033  Score=60.67  Aligned_cols=46  Identities=24%  Similarity=0.336  Sum_probs=41.2

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      ..|+++|++||.+. ..|    +|.+|||+.|++|..||+.+.++.++||-
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

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.59  E-value=0.014  Score=54.16  Aligned_cols=63  Identities=16%  Similarity=0.142  Sum_probs=54.1

Q ss_pred             HHHHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          530 FMKEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       530 el~~~L~~aL-~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      .....+..++ +.|++.+|+||.++|...++  ++..+|+..||+|+.+...+..+|+.++-..+.
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            4455677778 99999999999999987332  899999999999999999999999999877553

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.

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=96.56  E-value=0.053  Score=57.94  Aligned_cols=159  Identities=11%  Similarity=0.058  Sum_probs=99.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccH
Q 007404          368 DKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHM  447 (605)
Q Consensus       368 e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~  447 (605)
                      +..+..-.+.++.---+|+++-.-.||.+||.|+.-.+.-.+=-|-++  -..|++..-|+.-++.++++.+.-..|.+ 
T Consensus         8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~~--PaAWL~~v~R~~aiD~~Rr~~~~~~~~~e-   84 (415)
T COG4941           8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPRN--PAAWLIAVGRNRAIDRVRRRARRDAAPPE-   84 (415)
T ss_pred             HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCCC--hHHHHHHHHhhhHHHHHHHHHHhccCChh-
Confidence            334444444444444556676667899999999866655554444333  46788888999999988887653322211 


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHHH
Q 007404          448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI  527 (605)
Q Consensus       448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~  527 (605)
                                                +.                    ++.+     |.+....+...|        ...
T Consensus        85 --------------------------l~--------------------~~~e-----~~e~~~a~~~~d--------~~i  105 (415)
T COG4941          85 --------------------------LL--------------------LSDE-----DEEMEEAEALDD--------EHI  105 (415)
T ss_pred             --------------------------hc--------------------cccc-----chhhhccccccc--------ccc
Confidence                                      00                    0000     000000011111        111


Q ss_pred             HHHHHHHHHHH-HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          528 KKFMKEDLEKV-LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       528 ~~el~~~L~~a-L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .++....|.-+ =-.|++.+|--|.||...|    +|..|||..|=++..++-|++.||.++|+..
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            11122222222 2369999999999998877    9999999999999999999999999999974

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.51  E-value=0.0075  Score=53.66  Aligned_cols=49  Identities=20%  Similarity=0.239  Sum_probs=44.0

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .-|+.+|+..+.++|..|    +|+.|||+.++||+..|...+.|+-+.|-+.
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            348999999999999888    9999999999999999999999987776554

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.31  E-value=0.011  Score=55.38  Aligned_cols=56  Identities=18%  Similarity=0.243  Sum_probs=47.6

Q ss_pred             HHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       534 ~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      .+...+..|+++|++||.+ +..+    ++.++||+.+|+|..+|+.+..++++||+..-.
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    899999999999999999999999999976443

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.22  E-value=0.0081  Score=57.27  Aligned_cols=47  Identities=17%  Similarity=0.329  Sum_probs=41.7

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|++|+.+. ..+    ++.++||+.|++|..||+.+..+.++||.-
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

>PRK01381 Trp operon repressor; Provisional

Probab=96.10  E-value=0.0077  Score=53.65  Aligned_cols=51  Identities=24%  Similarity=0.298  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHhc-CCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHH
Q 007404          529 KFMKEDLEKVLDT-LNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIR  579 (605)
Q Consensus       529 ~el~~~L~~aL~~-L~~rER~VL~LRyGl~d---g~~~Tl~EIAe~LGISrerVR  579 (605)
                      ....+.+..+|.. |+|+|+..|..||+.-.   ...+|+.||++.+|||..+|.
T Consensus        19 a~~~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT   73 (99)
T PRK01381         19 AFEEDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT   73 (99)
T ss_pred             hccHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence            3334556677765 99999999999998864   335999999999999999887

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=96.04  E-value=0.0082  Score=42.83  Aligned_cols=27  Identities=30%  Similarity=0.559  Sum_probs=21.7

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |+|.+|||+.+|+|+|+|.    |++++|++
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    88888876

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 ....

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=95.92  E-value=0.021  Score=50.41  Aligned_cols=53  Identities=23%  Similarity=0.166  Sum_probs=47.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      .|+..|-+.|+|...++    ++.+|-|.+||||+.|+-..++.|++|+-..+....
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            46777889999999988    999999999999999999999999999998886543

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.31  E-value=0.033  Score=64.30  Aligned_cols=54  Identities=26%  Similarity=0.221  Sum_probs=46.1

Q ss_pred             HhcCCHHHHHHHHHHHhcC---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          539 LDTLNPRERQVVRWRFGLE---DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~---dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      ...|+++|+++|..-|..|   -.+.-|++|||+.||||+.|+.+++.+|.+||=..
T Consensus       605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~  661 (665)
T PRK13558        605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGA  661 (665)
T ss_pred             hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            4679999999999999876   01223999999999999999999999999998653

>PRK10403 transcriptional regulator NarP; Provisional

Probab=95.09  E-value=0.041  Score=52.27  Aligned_cols=48  Identities=19%  Similarity=0.276  Sum_probs=41.8

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      ..|+++|.+|+.+. ..+    +|.+|||+.+|+|..||+.+..+.++||.-.
T Consensus       152 ~~Lt~~e~~vl~~~-~~g----~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~  199 (215)
T PRK10403        152 SVLTERELDVLHEL-AQG----LSNKQIASVLNISEQTVKVHIRNLLRKLNVR  199 (215)
T ss_pred             ccCCHHHHHHHHHH-HCC----CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence            35999999999875 344    9999999999999999999999999999543

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.03  E-value=0.047  Score=51.96  Aligned_cols=46  Identities=22%  Similarity=0.304  Sum_probs=39.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|..|+.+ +..+    +|.+|||+.|++|..||+.+..++++||.-
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            488888888865 3344    999999999999999999999999999953

>PRK15320 transcriptional activator SprB; Provisional

Probab=95.00  E-value=0.046  Score=54.57  Aligned_cols=66  Identities=11%  Similarity=0.088  Sum_probs=48.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       520 ~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ++||+.+..-.. -....+--.|+++|.+|+.+-- .|    +|.+|||+.|++|.+||+....+.+.||.-
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            356665443211 1122333579999999998742 33    999999999999999999999999999853

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=94.98  E-value=0.048  Score=51.67  Aligned_cols=47  Identities=28%  Similarity=0.330  Sum_probs=41.6

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|++|+.+.. .+    +|.++||+.|++|..+|+.+..+.++||.-
T Consensus       136 ~~Lt~~E~~il~~l~-~g----~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~  182 (196)
T PRK10360        136 DPLTKRERQVAEKLA-QG----MAVKEIAAELGLSPKTVHVHRANLMEKLGV  182 (196)
T ss_pred             cCCCHHHHHHHHHHH-CC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            369999999999843 34    899999999999999999999999999864

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=94.90  E-value=0.04  Score=45.47  Aligned_cols=44  Identities=23%  Similarity=0.467  Sum_probs=29.6

Q ss_pred             HhcCCHHHHHHHHH--HHhcCCCCCCCHHHHHHHHCCC-HHHHHHHH
Q 007404          539 LDTLNPRERQVVRW--RFGLEDGRMKTLQEIGELMGVS-RERIRQIE  582 (605)
Q Consensus       539 L~~L~~rER~VL~L--RyGl~dg~~~Tl~EIAe~LGIS-rerVRqie  582 (605)
                      |..|+++|++||..  .|....|-|-|+.|||+.||++ ..+|.+++
T Consensus         1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L   47 (65)
T PF01726_consen    1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHL   47 (65)
T ss_dssp             -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHH
Confidence            45799999999876  4445567778999999999997 99999554

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=94.85  E-value=0.074  Score=41.82  Aligned_cols=49  Identities=14%  Similarity=0.176  Sum_probs=41.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      +|+..++-++.+.|.-.+   .++++||..+|||+++|.++.+..+.-|-..
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            588889988888776654   8999999999999999999998888777653

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=94.79  E-value=0.06  Score=51.36  Aligned_cols=47  Identities=30%  Similarity=0.398  Sum_probs=41.2

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      +..|+++|++|+.+.. .+    .+.+|||+.+++|..||+.+..+.++||.
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

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=94.65  E-value=0.035  Score=51.40  Aligned_cols=49  Identities=20%  Similarity=0.316  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      -|+++|-.||.||- .|    .|.+|||++||-|+..|+-++.+|+.++.+.-.
T Consensus         8 flte~qikvl~lRe-kG----~tQ~eIA~~L~TTraNvSaIEkrA~enIekarn   56 (143)
T COG1356           8 FLTEQQIKVLVLRE-KG----LTQSEIARILKTTRANVSAIEKRALENIEKARN   56 (143)
T ss_pred             eeehhheeeeehhh-cc----ccHHHHHHHHccchhhHHHHHHHHHHHHHHHHH
Confidence            38899999999984 23    899999999999999999999999999987654

>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=94.57  E-value=0.11  Score=39.55  Aligned_cols=39  Identities=21%  Similarity=0.351  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      |++.++.||..-+-.+   ..|..|||+.+|+|..+|++++.
T Consensus         1 l~~~~~~Il~~l~~~~---~~t~~ela~~~~is~~tv~~~l~   39 (48)
T PF13412_consen    1 LDETQRKILNYLRENP---RITQKELAEKLGISRSTVNRYLK   39 (48)
T ss_dssp             --HHHHHHHHHHHHCT---TS-HHHHHHHHTS-HHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcC---CCCHHHHHHHhCCCHHHHHHHHH
Confidence            5778888987765422   39999999999999999995543

...

>PRK04841 transcriptional regulator MalT; Provisional

Probab=94.50  E-value=0.06  Score=64.14  Aligned_cols=47  Identities=21%  Similarity=0.257  Sum_probs=42.1

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|++|+.+.. .+    +|.+|||+.|+||..||+.++++.++||.-
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            349999999999854 44    999999999999999999999999999964

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=94.49  E-value=0.15  Score=47.87  Aligned_cols=52  Identities=21%  Similarity=0.418  Sum_probs=44.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      ....|..+++.|.+.++.||.+||+...+  +|..+||..|+||..+++.....
T Consensus        71 ~k~~id~~~~~l~de~k~Ii~lry~~r~~--~TW~~IA~~l~i~erta~r~~~~  122 (130)
T PF05263_consen   71 QKEAIDRWLETLIDEEKRIIKLRYDRRSR--RTWYQIAQKLHISERTARRWRDR  122 (130)
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHHccccc--chHHHHHHHhCccHHHHHHHHHH
Confidence            34567888899999999999999986633  99999999999999999955443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>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=94.15  E-value=0.19  Score=41.52  Aligned_cols=57  Identities=14%  Similarity=0.119  Sum_probs=46.8

Q ss_pred             HHHHHHhccHHHHHHHHHHHHHHHHHHHHHhh----C--CCCCHHHHHHHHHHHHHHhhhccC
Q 007404          355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQ----G--AGMNLQDLVQEGCRGLVRGAEKFD  411 (605)
Q Consensus       355 ~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~----~--~g~d~eDLIQEG~IGLirA~ekFD  411 (605)
                      .+.++.+||..|.++++..|.+++.+.+.+-.    +  .+.-=+|+-|+--..|++++.+|+
T Consensus         3 vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen    3 VIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            45667778899999999999999999988722    1  123338999999999999999996

Some proteins with this domain are annotated as conjugative transposon proteins.

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=93.85  E-value=0.067  Score=40.90  Aligned_cols=31  Identities=23%  Similarity=0.308  Sum_probs=21.6

Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      ||.+.. .+    +|..+||+.||||+.||+++.++
T Consensus        10 ii~l~~-~G----~s~~~ia~~lgvs~~Tv~~w~kr   40 (50)
T PF13384_consen   10 IIRLLR-EG----WSIREIAKRLGVSRSTVYRWIKR   40 (50)
T ss_dssp             HHHHHH-HT------HHHHHHHHTS-HHHHHHHHT-
T ss_pred             HHHHHH-CC----CCHHHHHHHHCcCHHHHHHHHHH
Confidence            555544 34    99999999999999999987665

>PF13730 HTH_36: Helix-turn-helix domain

Probab=93.73  E-value=0.25  Score=38.47  Aligned_cols=47  Identities=21%  Similarity=0.435  Sum_probs=34.1

Q ss_pred             cCCHHHHHHHHHHHhc--CCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGL--EDGRM-KTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl--~dg~~-~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++.++.|+..-...  +++.. .|.+.||+.+|+|+.||+    ++++.|.+
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            5888888776543322  22222 389999999999999999    77777765

>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=93.29  E-value=0.2  Score=33.67  Aligned_cols=36  Identities=25%  Similarity=0.420  Sum_probs=27.4

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      +++.++..+...|..+    .+..+|++.+|+|+.+|..+
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

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=93.27  E-value=0.48  Score=43.92  Aligned_cols=52  Identities=15%  Similarity=0.136  Sum_probs=47.5

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      |.+-.+.+-+||.++|..+    +|...||..+++|...||+.+.+|-.-+..++.
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=93.02  E-value=0.29  Score=36.88  Aligned_cols=39  Identities=23%  Similarity=0.405  Sum_probs=26.1

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      |++-.+.||..--.  | ...|+.+||+.+|+|..+|.+++.
T Consensus         1 lD~~D~~Il~~Lq~--d-~r~s~~~la~~lglS~~~v~~Ri~   39 (42)
T PF13404_consen    1 LDELDRKILRLLQE--D-GRRSYAELAEELGLSESTVRRRIR   39 (42)
T ss_dssp             --HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--c-CCccHHHHHHHHCcCHHHHHHHHH
Confidence            34566777776433  2 238999999999999999996554

...

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=92.85  E-value=0.15  Score=54.45  Aligned_cols=36  Identities=19%  Similarity=0.364  Sum_probs=31.7

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404          548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR  587 (605)
Q Consensus       548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALk  587 (605)
                      .|=.|||..+    +|.+|||++|||||.+|.+++.+|++
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            4667777776    99999999999999999999998876

>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=92.81  E-value=0.21  Score=40.76  Aligned_cols=35  Identities=26%  Similarity=0.301  Sum_probs=26.5

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      ..+.++...+|.  +++.+||+.||||..+||....+
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            455555443333  99999999999999999987654

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 [].

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=92.74  E-value=0.24  Score=43.41  Aligned_cols=38  Identities=26%  Similarity=0.351  Sum_probs=29.8

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      ++.|++| ..|+.+. ..+    +|..|||+.+|||+.||..+.
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.

>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=92.56  E-value=0.29  Score=38.11  Aligned_cols=42  Identities=29%  Similarity=0.461  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      |++.||.+-+-.  +.+.|.+|||+.||||+.||+    +-++.|+..
T Consensus         1 R~~~il~~L~~~--~~~it~~eLa~~l~vS~rTi~----~~i~~L~~~   42 (55)
T PF08279_consen    1 RQKQILKLLLES--KEPITAKELAEELGVSRRTIR----RDIKELREW   42 (55)
T ss_dssp             HHHHHHHHHHHT--TTSBEHHHHHHHCTS-HHHHH----HHHHHHHHT
T ss_pred             CHHHHHHHHHHc--CCCcCHHHHHHHhCCCHHHHH----HHHHHHHHC
Confidence            456777764333  334999999999999999999    555666553

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 ....

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=92.32  E-value=0.18  Score=38.32  Aligned_cols=32  Identities=19%  Similarity=0.250  Sum_probs=22.1

Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      ..+|+.|+ -.+    +|..+||+.+|||+.||..++
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            34566664 333    999999999999999999664

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 ....

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=92.26  E-value=0.29  Score=49.12  Aligned_cols=47  Identities=13%  Similarity=0.105  Sum_probs=35.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR  587 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALk  587 (605)
                      .|+++|.+++........+..+|.+|||+.||+|..||+.+..++..
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            48889987775443221223399999999999999999998887743

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=92.16  E-value=0.41  Score=43.84  Aligned_cols=49  Identities=20%  Similarity=0.337  Sum_probs=41.5

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +..|++.+..-|... ....|   +++|+++.||||-.|||.++.+.+++|..
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            678998888877664 44433   99999999999999999999999999876

>PHA00675 hypothetical protein

Probab=91.38  E-value=0.41  Score=40.80  Aligned_cols=40  Identities=18%  Similarity=0.085  Sum_probs=32.1

Q ss_pred             hcCCHHHHHHHHHHH-hcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          540 DTLNPRERQVVRWRF-GLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       540 ~~L~~rER~VL~LRy-Gl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      .+|++.+-+.|+.++ -.+    .|+.+||..||||+++|.+|.+
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            467777777776666 344    7999999999999999998865

>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=91.33  E-value=0.37  Score=40.18  Aligned_cols=38  Identities=32%  Similarity=0.414  Sum_probs=28.9

Q ss_pred             HHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHH
Q 007404          323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL  360 (605)
Q Consensus       323 ~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l  360 (605)
                      .++.+.+.+|...+|+.||..+.|..+|++.+.+...+
T Consensus         4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l   41 (78)
T PF04539_consen    4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELL   41 (78)
T ss_dssp             HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence            35667888999999999999999999999987765543

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 ....

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=91.04  E-value=2.2  Score=46.44  Aligned_cols=126  Identities=21%  Similarity=0.187  Sum_probs=69.6

Q ss_pred             HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH-HHH
Q 007404          324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEG-CRG  402 (605)
Q Consensus       324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG-~IG  402 (605)
                      ++.+...+|...+|+.||..+.|...|++.+.+...+...                   ..    ..++++.+.++ -..
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            3455677788889999999999999999987765432211                   00    01111111100 001


Q ss_pred             HHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHc----CCCCCHHHHHHhc
Q 007404          403 LVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSEN----GRHPNNEEVAEAT  478 (605)
Q Consensus       403 LirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~el----gr~PT~eEIAe~l  478 (605)
                      |..-+.  |+.............++..+.+++..      +|..-.          .-+....    |.+-|.+|||+.+
T Consensus       274 l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~------L~~rEr----------~Vl~lrygl~~~~~~tl~EIa~~l  335 (367)
T PRK09210        274 LGDFIE--DQDATSPADHAAYELLKEQLEDVLDT------LTDREE----------NVLRLRFGLDDGRTRTLEEVGKVF  335 (367)
T ss_pred             hhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh------CCHHHH----------HHHHHHhccCCCCCccHHHHHHHH
Confidence            111111  11112233444555666666666642      222211          1112222    3678999999999


Q ss_pred             CCCHHHHHHHHh
Q 007404          479 GLSMKRLHAVLL  490 (605)
Q Consensus       479 gis~e~V~~~l~  490 (605)
                      |+|.++|+.+..
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=90.80  E-value=2.8  Score=42.47  Aligned_cols=35  Identities=26%  Similarity=0.353  Sum_probs=28.0

Q ss_pred             HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404          324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  358 (605)
Q Consensus       324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~  358 (605)
                      ++.+....|....|++||..+.|...|++.+.+..
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~  122 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVRE  122 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            34455677778889999999999999999876653

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.

>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=90.79  E-value=0.59  Score=37.89  Aligned_cols=46  Identities=22%  Similarity=0.400  Sum_probs=30.5

Q ss_pred             CCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          542 LNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       542 L~~rER~VL~LRyGl~-dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |++....-|..-|.+. ++.+.+..+||+.||+|+.+|.    .+++||.+
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            3343333333333332 5667999999999999999999    66777765

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 ....

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=90.69  E-value=1.2  Score=49.39  Aligned_cols=38  Identities=34%  Similarity=0.492  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHH
Q 007404          452 YRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL  489 (605)
Q Consensus       452 ~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l  489 (605)
                      ..+.+.+..|..++|+.||.+|.|...|+++..++..+
T Consensus       111 ~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l  148 (415)
T PRK07598        111 LRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL  148 (415)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence            35666778899999999999999988887766666554

>PF13518 HTH_28: Helix-turn-helix domain

Probab=89.87  E-value=0.61  Score=35.51  Aligned_cols=24  Identities=21%  Similarity=0.361  Sum_probs=21.1

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          562 KTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       562 ~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      .|+.+||..+|||+.+|+++..+-
T Consensus        13 ~s~~~~a~~~gis~~tv~~w~~~y   36 (52)
T PF13518_consen   13 ESVREIAREFGISRSTVYRWIKRY   36 (52)
T ss_pred             CCHHHHHHHHCCCHhHHHHHHHHH
Confidence            699999999999999999776553

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=89.85  E-value=3.3  Score=47.25  Aligned_cols=35  Identities=26%  Similarity=0.373  Sum_probs=29.2

Q ss_pred             HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404          324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  358 (605)
Q Consensus       324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~  358 (605)
                      ++.+.+.+|...+|+.||..+.|+..|++.+.+..
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~  393 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVRE  393 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            45567788888899999999999999999876654

>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=89.66  E-value=0.72  Score=37.27  Aligned_cols=24  Identities=25%  Similarity=0.392  Sum_probs=22.2

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          562 KTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       562 ~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      ++..|||+.||+++.||.+...+-
T Consensus        14 ~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   14 WSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             CCHHHHHHHHCCChHHHHHHHHhh
Confidence            999999999999999999988763

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=89.53  E-value=3.6  Score=44.23  Aligned_cols=35  Identities=20%  Similarity=0.368  Sum_probs=28.7

Q ss_pred             HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404          324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  358 (605)
Q Consensus       324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~  358 (605)
                      ++.+.+..|...+|++||..+.|+..|++.+.+..
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~  208 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIAD  208 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHH
Confidence            45566777888889999999999999999876654

>smart00351 PAX Paired Box domain

Probab=89.42  E-value=0.96  Score=41.82  Aligned_cols=41  Identities=20%  Similarity=0.094  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  586 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL  586 (605)
                      |+..+|.=|...|-.+    .|..+||+.||||+.+|..++.+..
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            5555555455555444    8999999999999999998888754

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=89.40  E-value=1.3  Score=41.38  Aligned_cols=53  Identities=21%  Similarity=0.262  Sum_probs=41.8

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..+..++-.|++.+-+|+..-.-.  +.|+|..|||+.||++++||.    ||+++|-.
T Consensus        16 ~dvl~c~~GLs~~Dv~v~~~LL~~--~~~~tvdelae~lnr~rStv~----rsl~~L~~   68 (126)
T COG3355          16 EDVLKCVYGLSELDVEVYKALLEE--NGPLTVDELAEILNRSRSTVY----RSLQNLLE   68 (126)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHhh--cCCcCHHHHHHHHCccHHHHH----HHHHHHHH
Confidence            346677778999999998765422  346999999999999999998    77777754

>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=89.35  E-value=0.97  Score=35.64  Aligned_cols=41  Identities=24%  Similarity=0.319  Sum_probs=31.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      .|++.|..||..-+..+ +...|..||++.+++++.+|.+++
T Consensus         2 glt~~q~~vL~~l~~~~-~~~~t~~~la~~l~~~~~~vs~~v   42 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHP-GEELTQSELAERLGISKSTVSRIV   42 (62)
T ss_dssp             TSTHHHHHHHHHHHHST-TSGEEHHHHHHHHTS-HHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCcCHHHHHHHH
Confidence            37788888887766554 334899999999999999999443

...

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=89.10  E-value=0.56  Score=45.15  Aligned_cols=50  Identities=18%  Similarity=0.185  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVS-----RERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGIS-----rerVRqie~RALkKLR~  591 (605)
                      .|+++|.+||.+.. .+.|..+|.+||++.++.+     ..||+.+..+.++||..
T Consensus       154 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (228)
T PRK11083        154 TLTRYEFLLLKTLL-LSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA  208 (228)
T ss_pred             ecCHHHHHHHHHHH-hCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence            59999999998765 3456679999999999996     78999999999999974

>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=88.86  E-value=0.56  Score=37.04  Aligned_cols=40  Identities=23%  Similarity=0.309  Sum_probs=26.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      .|+..|+.=|.-+|-.|    .+..+||..|||+++||+.|...
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            46666666444455444    69999999999999999988765

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.

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=88.62  E-value=0.61  Score=50.09  Aligned_cols=35  Identities=23%  Similarity=0.261  Sum_probs=29.8

Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404          549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR  587 (605)
Q Consensus       549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALk  587 (605)
                      +-.+||..+    +|..|||++||||+.+|+..+.+|.+
T Consensus        18 ~A~lYY~~g----ltQ~eIA~~LgiSR~~v~rlL~~Ar~   52 (321)
T COG2390          18 AAWLYYVEG----LTQSEIAERLGISRATVSRLLAKARE   52 (321)
T ss_pred             HHHHHHhcC----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            556677666    99999999999999999988888765

>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=88.48  E-value=1.2  Score=38.26  Aligned_cols=41  Identities=27%  Similarity=0.344  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHHHHH--hcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          541 TLNPRERQVVRWRF--GLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       541 ~L~~rER~VL~LRy--Gl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      .|+++|++||..--  +...++|..-++||+.+++|..|||+.
T Consensus         1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~   43 (78)
T PF03444_consen    1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNE   43 (78)
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHH
Confidence            38899999876532  233678999999999999999999954

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

>PRK12423 LexA repressor; Provisional

Probab=88.44  E-value=0.85  Score=45.45  Aligned_cols=48  Identities=27%  Similarity=0.424  Sum_probs=36.6

Q ss_pred             hcCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWR--FGLEDGRMKTLQEIGELMG-VSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LR--yGl~dg~~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~  591 (605)
                      ..|++++++|+..-  |...+|-+-|..|||+.|| .|+.+|+    ++|++|++
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            34899999998753  2233455579999999999 5999999    56777766

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=88.28  E-value=0.76  Score=44.01  Aligned_cols=49  Identities=27%  Similarity=0.246  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLK  590 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR  590 (605)
                      .|+++|.+|+.+.. .+-|.+.|.++|++.+.     +|..+|+.+..+.++||.
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 44466789999999996     999999999999999985

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=88.19  E-value=1.5  Score=36.19  Aligned_cols=41  Identities=10%  Similarity=0.278  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +..||.+-. ..++++.|..|||+.+||++.+|+    +.|.+|.+
T Consensus         8 ~~~IL~~L~-~~g~~~~ta~eLa~~lgl~~~~v~----r~L~~L~~   48 (68)
T smart00550        8 EEKILEFLE-NSGDETSTALQLAKNLGLPKKEVN----RVLYSLEK   48 (68)
T ss_pred             HHHHHHHHH-HCCCCCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            344554433 223335999999999999999999    55566654

Helix-turn-helix-containing domain. Also known as Zab.

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

Probab=88.02  E-value=5.4  Score=41.43  Aligned_cols=123  Identities=17%  Similarity=0.185  Sum_probs=68.5

Q ss_pred             HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHH
Q 007404          325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLV  404 (605)
Q Consensus       325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLi  404 (605)
                      ++.+..+|+..+|++||..+.|...|++.+++..          .+...+-...+++-......+...            
T Consensus       112 i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~----------~~~~~~~~~~~sld~~~~~~~d~~------------  169 (247)
T COG1191         112 IEEAIDELEQELGREPTDEEIAEELGIDKEEYIE----------ALLAINGSQLLSLDEDVLKDDDDD------------  169 (247)
T ss_pred             HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHH----------HHHHhccccccchhhhhccccccc------------
Confidence            4456778888999999999999999999866543          333333222222222222111110            


Q ss_pred             HhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHH
Q 007404          405 RGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKR  484 (605)
Q Consensus       405 rA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~  484 (605)
                           -+...+..+..+-.|-.++.+..++..      +|..-          +.-+.-....+-|..||++.||+|..+
T Consensus       170 -----~~~~~~~~~~~~~~~~~~~~l~~ai~~------L~ERE----------k~Vl~l~y~eelt~kEI~~~LgISes~  228 (247)
T COG1191         170 -----VDDQIENPDDGVEKEELLEILKEAIEP------LPERE----------KLVLVLRYKEELTQKEIAEVLGISESR  228 (247)
T ss_pred             -----hhhccccchhHHHHHHHHHHHHHHHHc------cCHHH----------HHHHHHHHHhccCHHHHHHHhCccHHH
Confidence                 011122234445556666666666542      11110          000111123456788999999999999


Q ss_pred             HHHHHh
Q 007404          485 LHAVLL  490 (605)
Q Consensus       485 V~~~l~  490 (605)
                      |..+..
T Consensus       229 VSql~k  234 (247)
T COG1191         229 VSRLHK  234 (247)
T ss_pred             HHHHHH
Confidence            987753

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=88.00  E-value=1.4  Score=38.70  Aligned_cols=49  Identities=29%  Similarity=0.342  Sum_probs=37.3

Q ss_pred             HhcCCHHHHHHHHHH----HhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          539 LDTLNPRERQVVRWR----FGLE-DGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       539 L~~L~~rER~VL~LR----yGl~-dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ...|++++..+|..-    ||.+ ...+.|..|||+.+|+++++|.    |++++|.+
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            457899999877633    3322 2356999999999999999999    77777765

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PHA02591 hypothetical protein; Provisional

Probab=87.86  E-value=1.1  Score=38.43  Aligned_cols=22  Identities=32%  Similarity=0.527  Sum_probs=20.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Q 007404          562 KTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       562 ~Tl~EIAe~LGISrerVRqie~  583 (605)
                      +|.++||+.||+|.++||+..+
T Consensus        60 lSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         60 FTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHh
Confidence            9999999999999999998765

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=87.79  E-value=0.77  Score=44.00  Aligned_cols=49  Identities=24%  Similarity=0.230  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLK  590 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR  590 (605)
                      .|+++|.+||.+. ..+.|..+|.++|++.+.     ++..+|+.+..+.++||.
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            4999999999864 445567799999999996     999999999999999885

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=87.77  E-value=1.1  Score=38.94  Aligned_cols=42  Identities=29%  Similarity=0.473  Sum_probs=31.4

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH--CCCHHHHHHHHH
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELM--GVSRERIRQIES  583 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L--GISrerVRqie~  583 (605)
                      ++.||+..+++..+|--.-+   .|+.|+|+.|  .||++.|.-+..
T Consensus        35 ~~~l~~~l~~~a~lRl~~Pd---~SL~EL~~~~~~~iSKSgvnhrlr   78 (85)
T PF02650_consen   35 LDKLPEKLREFAELRLENPD---ASLKELGELLEPPISKSGVNHRLR   78 (85)
T ss_dssp             GGGS-HHHHHHHHHHHH-TT---S-HHHHHHTT--T--HHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHHCcc---ccHHHHHHHHcCcCcHHHHHHHHH
Confidence            57899999999999975544   9999999999  999999985543

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=87.75  E-value=0.83  Score=44.53  Aligned_cols=50  Identities=20%  Similarity=0.226  Sum_probs=44.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++|+.+... +.|+..|.++|++.+.     ++..+|+.+..+.++||..
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            599999999998664 4567799999999998     9999999999999999963

>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=87.65  E-value=0.63  Score=37.95  Aligned_cols=44  Identities=27%  Similarity=0.323  Sum_probs=33.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++.|..|+..-.-.+   +.|..|||+.+|+++.+|+    +++++|.+
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            46777888876543222   3999999999999999999    66666654

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.

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=87.64  E-value=2  Score=37.38  Aligned_cols=42  Identities=24%  Similarity=0.231  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHhHHh
Q 007404          545 RERQVVRWRFGLEDGRMKTLQEIGELMG-VSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       545 rER~VL~LRyGl~dg~~~Tl~EIAe~LG-ISrerVRqie~RALkKLR~~l~  594 (605)
                      |+--+...+...+    +|+.+||..|| .+..+|.    .|++|+.+.+.
T Consensus        32 R~ia~yl~~~~~~----~s~~~Ig~~fg~r~hStV~----~a~~ri~~~~~   74 (90)
T cd06571          32 RQIAMYLARELTG----LSLPEIGRAFGGRDHSTVL----HAVRKIEELLE   74 (90)
T ss_pred             HHHHHHHHHHHhC----CCHHHHHHHhCCCCHhHHH----HHHHHHHHHHH
Confidence            3333444444455    99999999999 9999999    45555555444

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.

>TIGR00498 lexA SOS regulatory protein LexA

Probab=87.64  E-value=1  Score=44.46  Aligned_cols=48  Identities=17%  Similarity=0.305  Sum_probs=37.2

Q ss_pred             hcCCHHHHHHHHHHHh--cCCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFG--LEDGRMKTLQEIGELMGVS-RERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyG--l~dg~~~Tl~EIAe~LGIS-rerVRqie~RALkKLR~  591 (605)
                      ..|+++|++||..-.-  ..++.+.|..|||+.+|++ +.+|+    +.+++|.+
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            3589999999887542  3356778999999999998 99999    55555554

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.

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=87.55  E-value=0.84  Score=44.29  Aligned_cols=50  Identities=18%  Similarity=0.129  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHH--HHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEI--GELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EI--Ae~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|.+||.+.. .+-|..+|.++|  +..++++..+|+.+..|.++||..
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 444666799999  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.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=87.55  E-value=1.5  Score=38.60  Aligned_cols=43  Identities=16%  Similarity=0.341  Sum_probs=31.8

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |++.++.||..... +  .+.|+.+||+.+|+|+.+|+    +.+++|.+
T Consensus         1 ld~~D~~il~~L~~-~--~~~~~~~la~~l~~s~~tv~----~~l~~L~~   43 (108)
T smart00344        1 LDEIDRKILEELQK-D--ARISLAELAKKVGLSPSTVH----NRVKRLEE   43 (108)
T ss_pred             CCHHHHHHHHHHHH-h--CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            46678888876543 2  24899999999999999999    44455544

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=87.07  E-value=1  Score=34.71  Aligned_cols=28  Identities=29%  Similarity=0.488  Sum_probs=24.1

Q ss_pred             CCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          560 RMK-TLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       560 ~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ... |..|||+.+|+|+.+|+    +++++|.+
T Consensus        18 ~~l~s~~~la~~~~vs~~tv~----~~l~~L~~   46 (60)
T smart00345       18 DKLPSERELAAQLGVSRTTVR----EALSRLEA   46 (60)
T ss_pred             CcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            345 89999999999999999    77777775

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=87.05  E-value=0.74  Score=54.72  Aligned_cols=46  Identities=20%  Similarity=0.190  Sum_probs=41.8

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      |+.||++|+.+.|- |    +|.+|||++|.||-.||+.+.++...||.-.
T Consensus       832 Ls~RE~eVL~Lia~-G----~SN~eIa~~L~isl~TVKtH~rniy~KLgV~  877 (894)
T COG2909         832 LSQRELEVLGLIAQ-G----LSNEEIAQELFISLTTVKTHIRNIYQKLGVA  877 (894)
T ss_pred             ccHHHHHHHHHHHc-c----CCHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence            89999999999873 3    8999999999999999999999999998643

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=86.74  E-value=0.97  Score=35.07  Aligned_cols=35  Identities=20%  Similarity=0.265  Sum_probs=25.0

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      -+-.+.+.-..+.++|+.||++.+|+++.+|..++
T Consensus         5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L   39 (52)
T PF09339_consen    5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLL   39 (52)
T ss_dssp             HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            33344445555666899999999999999999443

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.

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=86.71  E-value=2.2  Score=43.89  Aligned_cols=35  Identities=23%  Similarity=0.315  Sum_probs=28.4

Q ss_pred             HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404          324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  358 (605)
Q Consensus       324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~  358 (605)
                      ++.+.+.+|...+|++|+..+.|...|++.+.+..
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~  148 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE  148 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHH
Confidence            34556777888899999999999999999876543

>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=86.40  E-value=1.7  Score=34.12  Aligned_cols=39  Identities=26%  Similarity=0.434  Sum_probs=29.7

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      |+..|-.||..-+-.++   .|..|||+.+++++.+|.++..
T Consensus         1 lt~~q~~iL~~l~~~~~---~~~~~la~~~~~~~~~~t~~i~   39 (59)
T PF01047_consen    1 LTPSQFRILRILYENGG---ITQSELAEKLGISRSTVTRIIK   39 (59)
T ss_dssp             STHHHHHHHHHHHHHSS---EEHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCC---CCHHHHHHHHCCChhHHHHHHH
Confidence            56677778877765543   9999999999999999994443

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 ....

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=85.56  E-value=1.5  Score=35.09  Aligned_cols=44  Identities=23%  Similarity=0.337  Sum_probs=27.4

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |+..|..||..-.  ..+.+++..+|++.+++++.+|.    +++++|..
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs----~~i~~L~~   44 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVS----RIIKKLEE   44 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHH----HHHHHHHH
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            4566666665443  34456999999999999999999    55555543

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=85.17  E-value=4.5  Score=41.83  Aligned_cols=56  Identities=29%  Similarity=0.428  Sum_probs=42.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          532 KEDLEKVLDTLNPRERQVVRWRFGLEDG--RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       532 ~~~L~~aL~~L~~rER~VL~LRyGl~dg--~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +..++-++.+|+--|.+.+...+-.=++  .-.+..+||+.+|||+..|+    +|+++|..
T Consensus       167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~  224 (251)
T TIGR02787       167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES  224 (251)
T ss_pred             HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4457788999998887766655443222  34899999999999999999    77787765

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.

>cd00131 PAX Paired Box domain

Probab=84.99  E-value=2.4  Score=39.43  Aligned_cols=41  Identities=17%  Similarity=0.054  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  586 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL  586 (605)
                      |+...|.=|...|..+    +|..+||+.||||+.+|..+.++-.
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            5554555444445444    8999999999999999998877644

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=84.43  E-value=2.2  Score=40.59  Aligned_cols=38  Identities=16%  Similarity=0.253  Sum_probs=30.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      .|++.++.||..---  || ..|+.|||+.+|+|+.+|+.+
T Consensus         6 ~lD~~D~~Il~~Lq~--d~-R~s~~eiA~~lglS~~tV~~R   43 (153)
T PRK11179          6 QIDNLDRGILEALME--NA-RTPYAELAKQFGVSPGTIHVR   43 (153)
T ss_pred             ccCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHHH
Confidence            477888888876432  22 389999999999999999943

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=84.41  E-value=2.5  Score=33.30  Aligned_cols=39  Identities=31%  Similarity=0.343  Sum_probs=27.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      .|++-|+--|....-++    +++.|||..+|-|+..|+..+.
T Consensus         4 ~Lt~~Eqaqid~m~qlG----~s~~~isr~i~RSr~~Ir~yl~   42 (50)
T PF11427_consen    4 TLTDAEQAQIDVMHQLG----MSLREISRRIGRSRTCIRRYLK   42 (50)
T ss_dssp             ---HHHHHHHHHHHHTT------HHHHHHHHT--HHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhc----hhHHHHHHHhCccHHHHHHHhc
Confidence            47888888888877787    9999999999999999996643

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=84.31  E-value=1.1  Score=44.67  Aligned_cols=39  Identities=21%  Similarity=0.232  Sum_probs=28.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      .|+++  +|+.+.-  +|...+|.+|||+.||||+.||+.+..
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  5665532  222238999999999999999997764

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=84.02  E-value=4.5  Score=38.50  Aligned_cols=67  Identities=25%  Similarity=0.358  Sum_probs=39.5

Q ss_pred             HHHHHhcCCHHHHHHHHHH----HhcCCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHhHHhhhhHhhh
Q 007404          535 LEKVLDTLNPRERQVVRWR----FGLEDGRMKTLQEIGELMGVSRERIRQIES--SAFRKLKNKKRTKHLMQY  601 (605)
Q Consensus       535 L~~aL~~L~~rER~VL~LR----yGl~dg~~~Tl~EIAe~LGISrerVRqie~--RALkKLR~~l~~~~L~~y  601 (605)
                      +..+=.+|++.|+....+.    |...+|+.+|+.|||+.+||++.+.-++.+  +++-...+.+....+.++
T Consensus         4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~~~   76 (142)
T PF13022_consen    4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLSSH   76 (142)
T ss_dssp             HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHh
Confidence            4455578999988833322    222244669999999999999999999874  455555555555544444

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=84.00  E-value=11  Score=39.17  Aligned_cols=34  Identities=35%  Similarity=0.479  Sum_probs=27.1

Q ss_pred             HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404          325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  358 (605)
Q Consensus       325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~  358 (605)
                      +.+...+|...+|+.||..+.|...|++.+.+..
T Consensus       129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~  162 (264)
T PRK07122        129 LGRATAELSQRLGRAPTASELAAELGMDREEVVE  162 (264)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            3445666777889999999999999999876644

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=83.69  E-value=8.1  Score=39.88  Aligned_cols=32  Identities=22%  Similarity=0.285  Sum_probs=25.3

Q ss_pred             hHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404          327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRR  358 (605)
Q Consensus       327 ~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~  358 (605)
                      .....|...+|++|+..+.|+..|++.+.+..
T Consensus       114 ~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~  145 (257)
T PRK05911        114 DAMDSLRQSLGKEPTDGELCEYLNISQQELSG  145 (257)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHH
Confidence            34455667789999999999999999876643

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=83.36  E-value=1.9  Score=40.19  Aligned_cols=40  Identities=25%  Similarity=0.333  Sum_probs=31.7

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      ..|++.++.||...-  .|++ .|+.|||+.+|+|+.+|+.+.
T Consensus         4 ~~lD~~D~~IL~~L~--~d~r-~~~~eia~~lglS~~~v~~Ri   43 (154)
T COG1522           4 MKLDDIDRRILRLLQ--EDAR-ISNAELAERVGLSPSTVLRRI   43 (154)
T ss_pred             ccccHHHHHHHHHHH--HhCC-CCHHHHHHHHCCCHHHHHHHH
Confidence            457888899988743  3333 999999999999999999443

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=83.26  E-value=0.9  Score=43.56  Aligned_cols=50  Identities=14%  Similarity=0.212  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEI-----GELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EI-----Ae~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|.+||.+-.. +-|..+|.++|     |..+++|..||+.+..+.++||..
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            599999999988654 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.

>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=83.13  E-value=3.3  Score=31.50  Aligned_cols=22  Identities=23%  Similarity=0.330  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHH
Q 007404          561 MKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       561 ~~Tl~EIAe~LGISrerVRqie  582 (605)
                      +++..||++.+|+|+.+|++++
T Consensus        15 ~~~~~el~~~l~~s~~~vs~hL   36 (47)
T PF01022_consen   15 PLTVSELAEELGLSQSTVSHHL   36 (47)
T ss_dssp             SEEHHHHHHHHTS-HHHHHHHH
T ss_pred             CCchhhHHHhccccchHHHHHH
Confidence            5999999999999999999654

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 ....

>PRK00215 LexA repressor; Validated

Probab=83.11  E-value=2.1  Score=42.31  Aligned_cols=42  Identities=19%  Similarity=0.297  Sum_probs=32.8

Q ss_pred             CCHHHHHHHHHHH--hcCCCCCCCHHHHHHHHCC-CHHHHHHHHH
Q 007404          542 LNPRERQVVRWRF--GLEDGRMKTLQEIGELMGV-SRERIRQIES  583 (605)
Q Consensus       542 L~~rER~VL~LRy--Gl~dg~~~Tl~EIAe~LGI-SrerVRqie~  583 (605)
                      |+++|++||.+-.  ...++.+.|+.|||+.+|+ ++.+|..++.
T Consensus         2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~   46 (205)
T PRK00215          2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLK   46 (205)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            7889999986543  2345667899999999999 9999995443

>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=83.06  E-value=1.7  Score=35.76  Aligned_cols=27  Identities=37%  Similarity=0.661  Sum_probs=24.0

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ++|.++||..+|+|+++|.    +.+++|++
T Consensus        28 ~lt~~~iA~~~g~sr~tv~----r~l~~l~~   54 (76)
T PF13545_consen   28 PLTQEEIADMLGVSRETVS----RILKRLKD   54 (76)
T ss_dssp             ESSHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            5899999999999999998    77777776

...

>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=83.04  E-value=2.7  Score=33.51  Aligned_cols=39  Identities=26%  Similarity=0.371  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          546 ERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       546 ER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +..|+.+-.-   ....|.+|+|+.||||..|||    |=|..|.+
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            4455555322   234899999999999999999    44555543

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

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=82.93  E-value=3.1  Score=36.31  Aligned_cols=43  Identities=21%  Similarity=0.177  Sum_probs=36.1

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      ..|++.-|..|..+...++   .++.++|+.||||+.|++++..|=
T Consensus         7 A~Lt~~gR~~lv~~vv~~g---~~~a~aA~~~gVS~~Ta~kW~~Ry   49 (85)
T PF13011_consen    7 ARLTPRGRLRLVRRVVEQG---WPVAHAAAEFGVSRRTAYKWLARY   49 (85)
T ss_pred             CCCCHHHHHHHHHHHHHcC---CcHHHHHHHhCCCHHHHHHHHHHH
Confidence            3589999998888875543   899999999999999999877663

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=82.84  E-value=18  Score=38.06  Aligned_cols=100  Identities=20%  Similarity=0.204  Sum_probs=51.9

Q ss_pred             CCCCCHHHHHHhcC--CCHHHHHHHHhCCCCCCCccccccccCCCCC-CcccCCCCCCCHHH-HHHHHHHHHHHHHHHhc
Q 007404          466 GRHPNNEEVAEATG--LSMKRLHAVLLSPKAPRSLDQKIGINQNLKP-SEVIADPEAETAED-LLIKKFMKEDLEKVLDT  541 (605)
Q Consensus       466 gr~PT~eEIAe~lg--is~e~V~~~l~~~~~~~SLD~~i~~d~~~~l-~d~l~D~~~~spEe-~l~~~el~~~L~~aL~~  541 (605)
                      +..+++++||+.++  ||.++|++.+......-=|. ..+ ++.-.. ...+.......+.. .-...++.+.-.++|+.
T Consensus       135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glik-k~~-~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~~  212 (271)
T TIGR02147       135 PFADDPEELAKRCFPKISAEQVKESLDLLERLGLIK-KNE-DGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALDA  212 (271)
T ss_pred             CCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCee-ECC-CCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHHHh
Confidence            44567889999998  99999999876322111111 001 110000 11122111111221 11223344455677888


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGEL  570 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~  570 (605)
                      .|+.+|.+=.+-++.+.   ..+++|.+.
T Consensus       213 ~p~~eR~~S~lT~~i~~---~~~~~i~~~  238 (271)
T TIGR02147       213 LPPSERDVSTVTFGISE---EAYKEIVKK  238 (271)
T ss_pred             CCccccccceeeEecCH---HHHHHHHHH
Confidence            99999998777666552   455554443

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.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=82.80  E-value=2  Score=31.80  Aligned_cols=27  Identities=37%  Similarity=0.639  Sum_probs=23.0

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +.|..|||+.+|+|+.+|+    +.+++|.+
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    66677665

>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=82.77  E-value=4.8  Score=32.14  Aligned_cols=41  Identities=22%  Similarity=0.399  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |.-+.||.+-..   +.++|..|||+.+|++..+|+.+    +++|++
T Consensus        10 p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~h----L~~L~~   50 (61)
T PF12840_consen   10 PTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYH----LKKLEE   50 (61)
T ss_dssp             HHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHH----HHHHHH
T ss_pred             HHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHH----HHHHHH
Confidence            555566665422   23599999999999999999944    445543

...

>PF12728 HTH_17: Helix-turn-helix domain

Probab=82.49  E-value=1.4  Score=33.77  Aligned_cols=23  Identities=30%  Similarity=0.469  Sum_probs=20.9

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
Q 007404          562 KTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       562 ~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      +|.+|+|+.||||+.+|+++..+
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~   24 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQ   24 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            68999999999999999988754

>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=82.44  E-value=4  Score=32.39  Aligned_cols=28  Identities=29%  Similarity=0.515  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .++|..|||+.+|+|+.+|+    +.+++|++
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            45899999999999999998    66677765

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=82.17  E-value=11  Score=38.55  Aligned_cols=35  Identities=23%  Similarity=0.186  Sum_probs=27.3

Q ss_pred             HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHH
Q 007404          325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRR  359 (605)
Q Consensus       325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~  359 (605)
                      +.+...++...+|++||..+.|+..|++.+.+...
T Consensus       122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~  156 (254)
T TIGR02850       122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFA  156 (254)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence            33445667777899999999999999998776543

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.

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=82.05  E-value=4.3  Score=39.75  Aligned_cols=64  Identities=14%  Similarity=0.252  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHHhhCCCCC---HHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404          372 TSNIRLVISIAKNYQGAGMN---LQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  435 (605)
Q Consensus       372 ~~nlrLVvsIAkrY~~~g~d---~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir  435 (605)
                      .+-+..+..+.++|.-++..   -+|+|.+|.-..++.+..|||++...+-.|++..+-++..+.|.
T Consensus        44 ~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~  110 (179)
T PHA02547         44 LAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIK  110 (179)
T ss_pred             HHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHH
Confidence            34445555566665545555   48999999999999999999999877766666666555555443

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=81.98  E-value=1.6  Score=41.81  Aligned_cols=29  Identities=28%  Similarity=0.346  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      -++|.+|||..+|+|+++|.    |++++|++.
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            36899999999999999999    888888874

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.

>PRK05949 RNA polymerase sigma factor; Validated

Probab=81.88  E-value=14  Score=39.71  Aligned_cols=34  Identities=24%  Similarity=0.330  Sum_probs=26.9

Q ss_pred             HHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404          325 LEGLREVLSERCGGSPTFAQWAAAAGVDQRELRR  358 (605)
Q Consensus       325 le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~  358 (605)
                      +.+.+.++...+|++|+..+.|+..|++.+.+..
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            4445566777789999999999999999876544

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=81.82  E-value=1.4  Score=33.90  Aligned_cols=22  Identities=23%  Similarity=0.483  Sum_probs=19.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q 007404          563 TLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       563 Tl~EIAe~LGISrerVRqie~R  584 (605)
                      |++|||+..|+|..||+..++.
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 ....

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=81.65  E-value=2.2  Score=41.07  Aligned_cols=37  Identities=19%  Similarity=0.235  Sum_probs=28.7

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      |++.++.||..-  ..|| ..|+.|||+.+|+|+.+|+.+
T Consensus        12 lD~~D~~IL~~L--q~d~-R~s~~eiA~~lglS~~tv~~R   48 (164)
T PRK11169         12 LDRIDRNILNEL--QKDG-RISNVELSKRVGLSPTPCLER   48 (164)
T ss_pred             HHHHHHHHHHHh--ccCC-CCCHHHHHHHHCcCHHHHHHH
Confidence            566778888753  2233 399999999999999999944

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=81.49  E-value=6.8  Score=43.01  Aligned_cols=37  Identities=32%  Similarity=0.546  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh
Q 007404          454 VKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL  490 (605)
Q Consensus       454 i~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~  490 (605)
                      +.+.+.+|..++|+.|+..+.|...|++...+...+.
T Consensus        96 ~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~  132 (373)
T PRK07406         96 LEELREQFESELGREPSDKEWAELVDMPLPKFRRRLM  132 (373)
T ss_pred             HHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHh
Confidence            3455677888899999999999999998877665543

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=81.46  E-value=4.8  Score=40.42  Aligned_cols=32  Identities=34%  Similarity=0.460  Sum_probs=25.3

Q ss_pred             hHHHHHHhhcCCCCchHHHHHhhcCCHHHHHH
Q 007404          327 GLREVLSERCGGSPTFAQWAAAAGVDQRELRR  358 (605)
Q Consensus       327 ~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~  358 (605)
                      +....|...+|+.||..+.|+..|++.+.+..
T Consensus       101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~  132 (231)
T TIGR02885       101 YMKEELSKELGREPTINELAEALGVSPEEIVM  132 (231)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHH
Confidence            34556667789999999999999999876543

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

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=81.39  E-value=21  Score=36.84  Aligned_cols=34  Identities=24%  Similarity=0.371  Sum_probs=27.4

Q ss_pred             HHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHH
Q 007404          324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELR  357 (605)
Q Consensus       324 ~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~  357 (605)
                      .+.+....|+..+|+.||..+.|...|++.+.+.
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~  152 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYN  152 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHH
Confidence            4555667778888999999999999999876554

>CHL00148 orf27 Ycf27; Reviewed

Probab=80.98  E-value=2.2  Score=41.55  Aligned_cols=50  Identities=14%  Similarity=0.086  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-------CCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-------GVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L-------GISrerVRqie~RALkKLR~  591 (605)
                      .|+++|.+|+.+.. .+.|+.+|.+||++.+       +++..+|+.+..+.++||..
T Consensus       161 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~  217 (240)
T CHL00148        161 RLTGMEFSLLELLI-SKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED  217 (240)
T ss_pred             EcCHHHHHHHHHHH-HCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence            49999999998754 3345669999999999       48999999999999999974

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=80.94  E-value=4.2  Score=35.03  Aligned_cols=32  Identities=22%  Similarity=0.451  Sum_probs=27.1

Q ss_pred             cCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          556 LEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       556 l~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +.++.+.|-++||+.||+|+.+|-    +.+++||+
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    77788886

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=80.93  E-value=3  Score=35.14  Aligned_cols=52  Identities=19%  Similarity=0.357  Sum_probs=34.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~-dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      +...|......|++.|+.|...-.-.- +-..+|..|||+..|+|..+|-...
T Consensus         3 l~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~   55 (77)
T PF01418_consen    3 LLEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFC   55 (77)
T ss_dssp             HHHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHH
T ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHH
Confidence            345677778899999999876432211 1134999999999999999998443

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.

>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=80.82  E-value=5.1  Score=35.14  Aligned_cols=44  Identities=30%  Similarity=0.445  Sum_probs=29.9

Q ss_pred             cCCHHHHHHHHHHHhc-----CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGL-----EDGRMKTLQEIGELMGVSRERIRQIESSAFR  587 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl-----~dg~~~Tl~EIAe~LGISrerVRqie~RALk  587 (605)
                      -|+|.|+.-|..|+-.     .+|  +|+.||++.+|+|..||. +.+|+|+
T Consensus        26 L~T~~E~~~l~~R~~va~~lL~~g--~syreIa~~tgvS~aTIt-Rvsr~Lk   74 (87)
T PF01371_consen   26 LCTPDELEALAQRWQVAKELLDEG--KSYREIAEETGVSIATIT-RVSRCLK   74 (87)
T ss_dssp             HSSHHHHHHHHHHHHHHHHHHHTT--SSHHHHHHHHTSTHHHHH-HHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHHhCCCHHHHH-HHHHHHH
Confidence            3677777655554422     233  999999999999999997 2334443

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 ....

>PF00046 Homeobox: Homeobox domain not present here

Probab=80.53  E-value=3.9  Score=31.89  Aligned_cols=51  Identities=14%  Similarity=0.188  Sum_probs=40.9

Q ss_pred             cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg-~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .+++.+..+|.-.|..+.. .....++||..+||+...|.....+-..+.|+
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            4788889999999887532 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 ....

>TIGR01764 excise DNA binding domain, excisionase family

Probab=80.46  E-value=1.9  Score=31.84  Aligned_cols=24  Identities=25%  Similarity=0.479  Sum_probs=21.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          562 KTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       562 ~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      +|.+|+|+.||||+.+|+++....
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            689999999999999999887654

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).

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=80.29  E-value=5.1  Score=29.93  Aligned_cols=27  Identities=37%  Similarity=0.631  Sum_probs=22.0

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +.|..+|++.+|+|+.+|++    .++.|.+
T Consensus        14 ~~s~~~l~~~l~~s~~tv~~----~l~~L~~   40 (53)
T smart00420       14 KVSVEELAELLGVSEMTIRR----DLNKLEE   40 (53)
T ss_pred             CcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence            48999999999999999984    4455543

>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=80.26  E-value=3.1  Score=31.02  Aligned_cols=36  Identities=19%  Similarity=0.294  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      +-|+.+|.-..-..+   -...+.|+.||||+.+++..+
T Consensus         4 ~~E~~~i~~aL~~~~---gn~~~aA~~Lgisr~tL~~kl   39 (42)
T PF02954_consen    4 EFEKQLIRQALERCG---GNVSKAARLLGISRRTLYRKL   39 (42)
T ss_dssp             HHHHHHHHHHHHHTT---T-HHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHhC---CCHHHHHHHHCCCHHHHHHHH
Confidence            446666665554444   378999999999999998443

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 ....

>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators

Probab=80.18  E-value=3.6  Score=32.26  Aligned_cols=26  Identities=38%  Similarity=0.640  Sum_probs=22.6

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          562 KTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       562 ~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|..+||+.+|+|+++|+    +++++|.+
T Consensus        26 ~~~~~la~~~~is~~~v~----~~l~~L~~   51 (66)
T cd07377          26 PSERELAEELGVSRTTVR----EALRELEA   51 (66)
T ss_pred             CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            469999999999999999    77777765

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

>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=80.16  E-value=3.8  Score=33.76  Aligned_cols=39  Identities=33%  Similarity=0.393  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHhcCCC-HHHHHHHHh
Q 007404          452 YRVKEARKQLYSENGRHPNNEEVAEATGLS-MKRLHAVLL  490 (605)
Q Consensus       452 ~ki~ka~~~L~~elgr~PT~eEIAe~lgis-~e~V~~~l~  490 (605)
                      .++-.....+..++|..||..|||+.+|++ ...|...+.
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            344555566778899999999999999997 888877764

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.

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=80.01  E-value=20  Score=28.86  Aligned_cols=23  Identities=30%  Similarity=0.408  Sum_probs=19.6

Q ss_pred             CCCHHHHHHhcCCCHHHHHHHHh
Q 007404          468 HPNNEEVAEATGLSMKRLHAVLL  490 (605)
Q Consensus       468 ~PT~eEIAe~lgis~e~V~~~l~  490 (605)
                      +++.++||+.+|++...+..+..
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f~   23 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFK   23 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Confidence            36889999999999999888765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	605
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		1e-52
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		8e-48
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		9e-48
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		4e-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		1e-17
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		8e-17
1tty_A	87	Solution Structure Of Sigma A Region 4 From Thermot		2e-16
4g94_A	62	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		4e-16
3n97_A	72	Rna Polymerase Alpha C-Terminal Domain (E. Coli) An		2e-11
1ku3_A	73	Crystal Structure Of Thermus Aquaticus Rna Polymera		3e-11
1rio_H	73	Structure Of Bacteriophage Lambda Ci-Ntd In Complex		3e-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		5e-08
2p7v_B	68	Crystal Structure Of The Escherichia Coli Regulator		7e-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: 291 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 338
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 339 SPTFAQWAAAAGVDQRELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDL 395
           +    +         +EL+R L+    G   +  +I +N+RLV+SIAK Y G G++  DL
Sbjct: 62  TARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL 121
Query: 396 VQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVK 455
           +QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++ 
Sbjct: 122 IQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLS 181
Query: 456 EARKQLYSENGRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV 513
              +QL  E GR P+ EE+AEA   G   KR+   L   + P SL+  IG  ++    + 
Sbjct: 182 RTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDF 241
Query: 514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGV 573
           I D    +  +   +  + E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV
Sbjct: 242 IPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGV 301
Query: 574 SRERIRQIESSAFRKLK-NKKRTKHLMQY 601
           +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 (533), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 131/347 (37%), Positives = 194/347 (55%), Gaps = 33/347 (9%)
Query: 288 VDYSDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSER 335
           V  SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +
Sbjct: 90  VSTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAK 149
Query: 336 CGGS------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRL 377
             G+      P   +      V++         +EL+R L+    G   +  +I +N+RL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 378 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 437
           V+SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ 269
Query: 438 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGLSMKRLHAVLLSPKAP 495
           +RTIR+P HMVE   ++    +QL  E GR P+ EE+AEA   G   KR+   L   + P
Sbjct: 270 ARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEP 329
Query: 496 RSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFG 555
            SL+  IG  ++    + I D    +  +   +  + E+LEK L  L+ RE  V++ R G
Sbjct: 330 VSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKG 389
Query: 556 LEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLMQY 601
           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: 363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 422
           G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 423 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGL 480
            WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P  EE+AEA   G 
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 481 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 540
             KR+   L   + P SL+  IG  ++    + I D    +  D   +  + E+LEK L 
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLM 599
            L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK ++ RT+ L 
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLR 419
Query: 600 QY 601
            +
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: 363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 422
           G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 239
Query: 423 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGL 480
            WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P  EE+AEA   G 
Sbjct: 240 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 299
Query: 481 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 540
             KR+   L   + P SL+  IG  ++    + I D    +  D   +  + E+LEK L 
Sbjct: 300 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 359
Query: 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLM 599
            L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK ++ RT+ L 
Sbjct: 360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLR 419
Query: 600 QY 601
            +
Sbjct: 420 DF 421

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score =  204 bits (520), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 107/242 (44%), Positives = 152/242 (62%), Gaps = 3/242 (1%)
Query: 363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 422
           G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYA 259
Query: 423 HWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEA--TGL 480
            WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P  EE+AEA   G 
Sbjct: 260 TWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGW 319
Query: 481 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 540
             KR+   L   + P SL+  IG  ++    + I D    +  D   +  + E+LEK L 
Sbjct: 320 DAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALS 379
Query: 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLM 599
            L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK ++ RT+ L 
Sbjct: 380 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLR 439
Query: 600 QY 601
            +
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 =  188 bits (477), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 97/252 (38%), Positives = 153/252 (60%), Gaps = 4/252 (1%)
Query: 354 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 409
           +++ RR++ G       K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +K
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418
Query: 410 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 469
           F+  +G+KFSTYA WWI+QA+ +S++DQ+RTIR+P HM+E   ++    +Q+  E GR P
Sbjct: 419 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 478
Query: 470 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 529
             EE+AE   +   ++  VL   K P S++  IG +++    + I D   E   D    +
Sbjct: 479 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTE 538
Query: 530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 589
            ++     VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL
Sbjct: 539 SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 598
Query: 590 KNKKRTKHLMQY 601
           ++  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 =  188 bits (477), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 97/252 (38%), Positives = 153/252 (60%), Gaps = 4/252 (1%)
Query: 354 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 409
           +++ RR++ G       K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +K
Sbjct: 359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 418
Query: 410 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 469
           F+  +G+KFSTYA WWI+QA+ +S++DQ+RTIR+P HM+E   ++    +Q+  E GR P
Sbjct: 419 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREP 478
Query: 470 NNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLIKK 529
             EE+AE   +   ++  VL   K P S++  IG +++    + I D   E   D    +
Sbjct: 479 TPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTE 538
Query: 530 FMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKL 589
            ++     VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL
Sbjct: 539 SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKL 598
Query: 590 KNKKRTKHLMQY 601
           ++  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 (364), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 89/240 (37%), Positives = 132/240 (55%), Gaps = 32/240 (13%)
Query: 291 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 338
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 339 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 380
           +      P   +      V++         +EL+R L+    G   +  +I +N+RLV+S
Sbjct: 62  TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 121
Query: 381 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 440
           IAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+RT
Sbjct: 122 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 181
Query: 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSL 498
           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: 291 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 338
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 6   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 65
Query: 339 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 380
           +      P   +      V++         +EL+R L+    G   +  +I +N+RLV+S
Sbjct: 66  TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 125
Query: 381 IAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT 440
           IAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+RT
Sbjct: 126 IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 185
Query: 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEAT--GLSMKRLHAVLLSPKAPRSL 498
           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 = 99.8 bits (247), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 65/89 (73%), Gaps = 3/89 (3%)
Query: 354 RELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 410
           +EL+R L+    G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF
Sbjct: 91  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 150
Query: 411 DASKGFKFSTYAHWWIKQAVRKSLSDQSR 439
           +  +GF FSTYA WWI+QA+ ++++DQ+R
Sbjct: 151 EYKRGFAFSTYATWWIRQAINRAIADQAR 179

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 41/90 (45%), Positives = 64/90 (71%), Gaps = 4/90 (4%)
Query: 354 RELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 409
           +++ RR++ G       K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +K
Sbjct: 250 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 309
Query: 410 FDASKGFKFSTYAHWWIKQAVRKSLSDQSR 439
           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 = 88.2 bits (217), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 42/71 (59%), Positives = 55/71 (77%)
Query: 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           MKE LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 591 NKKRTKHLMQY 601
           +  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 = 85.5 bits (210), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 122/240 (50%), Gaps = 15/240 (6%)
Query: 354 RELRRRLNYGIL-CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA 412
           +EL RR   G    +D++I  N+RLV S+ + +   G    DL Q GC GL++  +KFD 
Sbjct: 16  KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDL 75
Query: 413 SKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNE 472
           S   KFSTYA   I   +++ L D   T+++   + E   ++++A+ +L    GR P   
Sbjct: 76  SYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVT 134
Query: 473 EVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN--LKPSEVIADPEAETAEDLLIKKF 530
           E+A+  G+S + +     + + P S+ + +  N    +   + IAD +  +        F
Sbjct: 135 EIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASW-------F 187
Query: 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
            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 = 84.7 bits (208), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/72 (55%), Positives = 56/72 (77%)
Query: 527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586
           ++  M+E+LEKVL TL+PRE  V+R R+GL DG+ KTL+E+G+   V+RERIRQIE  A 
Sbjct: 4   MRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKAL 63
Query: 587 RKLKNKKRTKHL 598
           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 = 4e-16,   Method: Compositional matrix adjust.
 Identities = 39/61 (63%), Positives = 50/61 (81%)
Query: 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           MKE LE VLDTL  RE  V+R RFGL+DGR +TL+E+G++ GV+RERIRQIE+ A RKL+
Sbjct: 1   MKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 60
Query: 591 N 591
           +
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 = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/69 (50%), Positives = 48/69 (69%)
Query: 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
           E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKL++ 
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLRHP 61
Query: 593 KRTKHLMQY 601
            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 = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/70 (52%), Positives = 49/70 (70%), Gaps = 1/70 (1%)
Query: 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-N 591
           E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK +
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61
Query: 592 KKRTKHLMQY 601
           + 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 = 3e-11,   Method: Compositional matrix adjust.
 Identities = 37/70 (52%), Positives = 49/70 (70%), Gaps = 1/70 (1%)
Query: 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-N 591
           E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK +
Sbjct: 2   EELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61
Query: 592 KKRTKHLMQY 601
           + 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 = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/239 (25%), Positives = 113/239 (47%), Gaps = 35/239 (14%)
Query: 367 KDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAH 423
           ++++I   + LV +IA N +      ++++DL+  G  GL++  +        +   Y  
Sbjct: 14  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73
Query: 424 WWIKQAVR---KSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGL 480
             IK A+    +SL   SR +R      E   R+KE  ++L  + GR P +EEVA+  G+
Sbjct: 74  LRIKGAIYDYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGI 127
Query: 481 SMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIAD---------PEAETAEDLLIKKFM 531
           S + L          ++LD KI  +  L   EV  D         P +   E+ +IK+ +
Sbjct: 128 STEELF---------KTLD-KINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKREL 177
Query: 532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
            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: 538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 15  VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 74
Query: 598 LMQY 601
           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 = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 42/61 (68%)
Query: 538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 16  VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 75
Query: 598 L 598
           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 = 7e-08,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 43/64 (67%)
Query: 538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61
Query: 598 LMQY 601
           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	605
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	2e-82
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	4e-81
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	6e-75
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	8e-71
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	1e-56
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	2e-46
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	6e-26
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	1e-25
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	2e-25
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	3e-23
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	2e-22
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	9e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-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 =  264 bits (676), Expect = 2e-82
 Identities = 125/406 (30%), Positives = 189/406 (46%), Gaps = 23/406 (5%)

Query: 200 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVR-SRRQTERKARR 258
             D  + +     E        +   L+   EE  L   ++S S  VR    +  +    
Sbjct: 35  EPDPDLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLL 94

Query: 259 TRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAG 318
           T   E   A  +     +  +    +  + D                ++ A         
Sbjct: 95  TLEEEVELARKVEEGMEAIKKLSEITGLDPDLIR------------EVVRAKILGSARVR 142

Query: 319 IQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLV 378
               LK     + + E      +  +       + +        G   +  +I +N+RLV
Sbjct: 143 HIPGLKETLDPKTVEEIDQKLKSLPK-------EHKRYLHIAREGEAARQHLIEANLRLV 195

Query: 379 ISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS 438
           +SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+
Sbjct: 196 VSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQA 255

Query: 439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM--KRLHAVLLSPKAPR 496
           RTIR+P HMVE   ++    +QL  E GR P  EE+AEA G     KR+   L   + P 
Sbjct: 256 RTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPV 315

Query: 497 SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGL 556
           SL+  IG  ++    + I D    +  D   +  + E+LEK L  L+ RE  V++ R GL
Sbjct: 316 SLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGL 375

Query: 557 EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK-KRTKHLMQY 601
            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 =  261 bits (667), Expect = 4e-81
 Identities = 121/435 (27%), Positives = 196/435 (45%), Gaps = 7/435 (1%)

Query: 174 KPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEEL 233
           K + S                +    + +    E   +    + + L    +LE   + L
Sbjct: 2   KKSKSKKKAAKAQEVEVKEPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPL 61

Query: 234 KLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDP 293
            L     +  +      + E +         +      +             +       
Sbjct: 62  DLEGPLEADLLPEEGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTLEEEIDLARKV 121

Query: 294 LRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 353
              + A    S     ++E+        +L    ++++   +    P   +         
Sbjct: 122 EEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSL 181

Query: 354 RELRRRLNY----GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 409
            +  +R  +    G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EK
Sbjct: 182 PKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEK 241

Query: 410 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHP 469
           F+  + FKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P
Sbjct: 242 FEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREP 301

Query: 470 NNEEVAEATGLSM--KRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 527
           + EE+AEA G     KR+   L   + P SL+  IG  ++    + I D    +  +   
Sbjct: 302 SYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAA 361

Query: 528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 587
           +  + E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A R
Sbjct: 362 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALR 421

Query: 588 KLKNK-KRTKHLMQY 601
           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 =  249 bits (638), Expect = 6e-75
 Identities = 97/254 (38%), Positives = 153/254 (60%), Gaps = 4/254 (1%)

Query: 352 DQRELRRRLNYG----ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGA 407
             +++ RR++ G       K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  
Sbjct: 357 QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 416

Query: 408 EKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGR 467
           +KF+  +G+KFSTYA WWI+QA+ +S++DQ+RTIR+P HM+E   ++    +Q+  E GR
Sbjct: 417 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR 476

Query: 468 HPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLLI 527
            P  EE+AE   +   ++  VL   K P S++  IG +++    + I D   E   D   
Sbjct: 477 EPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSAT 536

Query: 528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFR 587
            + ++     VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A R
Sbjct: 537 TESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 588 KLKNKKRTKHLMQY 601
           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 =  227 bits (581), Expect = 8e-71
 Identities = 66/242 (27%), Positives = 123/242 (50%), Gaps = 15/242 (6%)

Query: 352 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 410
           + +EL RR   G    +D++I  N+RLV S+ + +   G    DL Q GC GL++  +KF
Sbjct: 14  EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKF 73

Query: 411 DASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN 470
           D S   KFSTYA   I   +++ L D   T+++   + E   ++++A+ +L    GR P 
Sbjct: 74  DLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPT 132

Query: 471 NEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGIN--QNLKPSEVIADPEAETAEDLLIK 528
             E+A+  G+S + +     + + P S+ + +  N    +   + IAD +  +  D    
Sbjct: 133 VTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADEASWFD---- 188

Query: 529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRK 588
              K  L+K ++ L+ RER +V  R+  +    +T  E+   +G+S+ ++ ++E    + 
Sbjct: 189 ---KIALKKAIEELDERERLIVYLRYYKD----QTQSEVASRLGISQVQMSRLEKKILQH 241

Query: 589 LK 590
           +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 =  189 bits (483), Expect = 1e-56
 Identities = 52/232 (22%), Positives = 105/232 (45%), Gaps = 17/232 (7%)

Query: 367 KDKMITSNIRLVISIA---KNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAH 423
           ++++I   + LV +IA   K +    ++++DL+  G  GL++  +        +   Y  
Sbjct: 14  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73

Query: 424 WWIKQAVRKSLSDQSRTI-RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM 482
             IK A+     D  R++      + E   R+KE  ++L  + GR P +EEVA+  G+S 
Sbjct: 74  LRIKGAIY----DYLRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGIST 129

Query: 483 KRLHAVLLSPKAPR--SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLD 540
           + L   L         SL++                P +   E+ +IK+ + E +++ + 
Sbjct: 130 EELFKTLDKINFSYILSLEEVFRDFAR---DYSELIPSSTNVEEEVIKRELTEKVKEAVS 186

Query: 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
            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 =  162 bits (412), Expect = 2e-46
 Identities = 64/149 (42%), Positives = 93/149 (62%), Gaps = 2/149 (1%)

Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 411
           + +        G   +  +I +N+RLV+SIAK Y G G++  DL+QEG +GL+R  EKF+
Sbjct: 97  ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFE 156

Query: 412 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNN 471
             + FKFSTYA WWI+QA+ ++++DQ+RTIR+P HMVE   ++    +QL  E GR P+ 
Sbjct: 157 YKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSY 216

Query: 472 EEVAE--ATGLSMKRLHAVLLSPKAPRSL 498
           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 =  108 bits (270), Expect = 6e-26
 Identities = 38/73 (52%), Positives = 56/73 (76%)

Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426
           K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +KF+  +G+KFSTYA WWI
Sbjct: 267 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 326

Query: 427 KQAVRKSLSDQSR 439
           +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 = 99.8 bits (249), Expect = 1e-25
 Identities = 40/78 (51%), Positives = 56/78 (71%)

Query: 524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583
              ++  M+E+LEKVL TL+PRE  V+R R+GL DG+ KTL+E+G+   V+RERIRQIE 
Sbjct: 1   KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEV 60

Query: 584 SAFRKLKNKKRTKHLMQY 601
            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 = 99.8 bits (249), Expect = 2e-25
 Identities = 30/78 (38%), Positives = 46/78 (58%)

Query: 524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583
           D    + ++     VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+
Sbjct: 2   DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 61

Query: 584 SAFRKLKNKKRTKHLMQY 601
            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 = 92.3 bits (230), Expect = 3e-23
 Identities = 29/64 (45%), Positives = 43/64 (67%)

Query: 538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61

Query: 598 LMQY 601
           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 = 90.5 bits (225), Expect = 2e-22
 Identities = 37/70 (52%), Positives = 47/70 (67%), Gaps = 1/70 (1%)

Query: 533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK 592
           E+LEK L  L+ RE  V++ R GL DGR  TL+E+G   GV+RERIRQIE+ A RKLK  
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 61

Query: 593 -KRTKHLMQY 601
             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 = 59.9 bits (145), Expect = 9e-11
 Identities = 34/204 (16%), Positives = 77/204 (37%), Gaps = 49/204 (24%)

Query: 389 GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMV 448
           G   +DLVQEG  GL++  + +D +K   FS++A   I++ +  ++   +    +  +  
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREMISAIRKANTQKHMVLNEA 59

Query: 449 EATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNL 508
             T  + E     + + G + NN + +E                                
Sbjct: 60  LKTNAILE-DSAYFDDEGHNINNYKSSE-------------------------------- 86

Query: 509 KPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIG 568
                 ++PE    E  L+K+ ++E  +   +  +  E++V+ +      G   + +EI 
Sbjct: 87  ------SNPE----EAYLLKEEIEEFKKFSENNFSKFEKEVLTYLI---RG--YSYREIA 131

Query: 569 ELMGVSRERIRQIESSAFRKLKNK 592
            ++  + + 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 = 53.3 bits (127), Expect = 2e-07
 Identities = 66/428 (15%), Positives = 131/428 (30%), Gaps = 134/428 (31%)

Query: 217 QQPLNKSADLEPTHEELK--LLEEQVSQSIAVRSRRQTER------KARRTRAAEKAAAN 268
           +     + D +   +  K  L +E++   I  +              +++    +K    
Sbjct: 26  EDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEE 85

Query: 269 VMS-----VKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANE---EMQLSAGIQ 320
           V+      + S   + +++PS+    Y +            RL   N+   +  +S  +Q
Sbjct: 86  VLRINYKFLMSPIKTEQRQPSMMTRMYIEQR---------DRLYNDNQVFAKYNVSR-LQ 135

Query: 321 DLLKL-EGLREVLSER---------CGGSPTFAQWAAAAGVDQRELRRRLNYGIL----- 365
             LKL + L E+   +          G +     W A       +++ ++++ I      
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKT-----WVALDVCLSYKVQCKMDFKIFWLNLK 190

Query: 366 -CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHW 424
            C           V+            LQ L             + D +           
Sbjct: 191 NCNSP------ETVL----------EMLQKL----LY-------QIDPNW---------- 213

Query: 425 WIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPN---------NEEVA 475
                   S SD S  I+L  H       ++   ++L      + N         N +  
Sbjct: 214 -------TSRSDHSSNIKLRIH------SIQAELRRLLKSK-PYENCLLVLLNVQNAKAW 259

Query: 476 EATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADP--EAETAEDLLIKKF-MK 532
            A  LS K    +LL+ +  +  D            +  +      E  + LL+K    +
Sbjct: 260 NAFNLSCK----ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV-KSLLLKYLDCR 314

Query: 533 -EDLEKVLDTLNP----------RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI 581
            +DL + + T NP          R+  +  W         K L  I   +  S   +  +
Sbjct: 315 PQDLPREVLTTNPRRLSIIAESIRDG-LATWDNWKHVNCDK-LTTI---IESS---LNVL 366

Query: 582 ESSAFRKL 589
           E + +RK+
Sbjct: 367 EPAEYRKM 374

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	605
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	100.0
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.98
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.97
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	99.86
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.7
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.65
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.59
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.53
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.3
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.26
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.24
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.19
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	98.98
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	98.98
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.92
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.82
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.71
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.66
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.52
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.44
3c57_A	95	Two component transcriptional regulatory protein;	98.44
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.33
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.32
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.16
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	97.98
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.89
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.8
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	97.08
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	96.98
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.83
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.21
1yio_A	208	Response regulatory protein; transcription regulat	96.0
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	95.86
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	95.6
3c3w_A	225	Two component transcriptional regulatory protein;	95.14
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	94.73
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	94.53
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	94.21
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	94.05
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	94.05
2gwr_A	238	DNA-binding response regulator MTRA; two-component	93.55
2oqr_A	230	Sensory transduction protein REGX3; response regul	93.43
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	92.97
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	92.5
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	92.32
1ys7_A	233	Transcriptional regulatory protein PRRA; response	92.22
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	92.1
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	91.38
2hqr_A	223	Putative transcriptional regulator; phosporylation	90.96
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	90.9
3q9s_A	249	DNA-binding response regulator; DNA binding protei	90.58
3r0a_A	123	Putative transcriptional regulator; structural gen	90.52
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	90.51
3r0j_A	250	Possible two component system response transcript	90.46
1u78_A	141	TC3 transposase, transposable element TC3 transpos	90.2
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	89.83
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	88.52
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	87.85
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	87.61
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	87.54
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	87.43
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	87.39
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	86.82
1sfx_A	109	Conserved hypothetical protein AF2008; structural	86.71
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	86.69
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	86.56
1y0u_A	96	Arsenical resistance operon repressor, putative; s	86.5
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	86.2
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	85.82
1ku9_A	152	Hypothetical protein MJ223; putative transcription	85.66
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	85.59
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	85.55
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	85.3
2w25_A	150	Probable transcriptional regulatory protein; trans	85.28
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	84.94
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	84.92
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	84.84
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	84.84
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	84.45
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	84.24
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	84.18
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	84.07
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	83.91
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	83.85
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	83.1
3nqo_A	189	MARR-family transcriptional regulator; structural	82.75
3sqn_A	485	Conserved domain protein; structural genomics, PSI	82.72
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	82.47
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	82.24
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	82.12
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	82.03
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	81.88
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	81.8
2k27_A	159	Paired box protein PAX-8; paired domain, solution	81.69
2nnn_A	140	Probable transcriptional regulator; structural gen	81.65
3jth_A	98	Transcription activator HLYU; transcription factor	81.63
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	81.6
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	81.58
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	81.56
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	81.39
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	81.37
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	81.31
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	81.12
3iwf_A	107	Transcription regulator RPIR family; transcription	80.69
2gxg_A	146	146AA long hypothetical transcriptional regulator;	80.35
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	80.33
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	80.28

>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=2e-54  Score=469.31  Aligned_cols=313  Identities=38%  Similarity=0.622  Sum_probs=281.7

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHH------------------HHHHhhcCCCCchHHHHHh--
Q 007404          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLR------------------EVLSERCGGSPTFAQWAAA--  348 (605)
Q Consensus       290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~------------------~~L~~~~G~~pt~~ewA~a--  348 (605)
                      ..|+++ ||++| +++||||++||++|+++|+.++.++...                  .+.....|+.|+..+|+..  
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 9999999999999999999865433211                  1112234677887777432  


Q ss_pred             ----------hcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcc
Q 007404          349 ----------AGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKF  418 (605)
Q Consensus       349 ----------~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rF  418 (605)
                                .|++...|...+++|..|+++||.+|+++|++||++|.++|.+++|||||||||||+|+++|||.+|++|
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                      3556677888888899999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcC--CCHHHHHHHHhCCCCCC
Q 007404          419 STYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPR  496 (605)
Q Consensus       419 STYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lg--is~e~V~~~l~~~~~~~  496 (605)
                      +||++|||||.|.++|+++++++|+|.|+.+.+++++++.+.+.+.+||.|+.+|||+.+|  +++++|..++.....++
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 007404          497 SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRE  576 (605)
Q Consensus       497 SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISre  576 (605)
                      |||.+++++++..+.+.+++....+|++.+....+...|..+|+.||++||.||.+|||++|++++|++|||+.||||++
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            99999987766677787877666688988888889999999999999999999999999988888999999999999999


Q ss_pred             HHHHHHHHHHHHHH-hHHhhhhHhhhhc
Q 007404          577 RIRQIESSAFRKLK-NKKRTKHLMQYAI  603 (605)
Q Consensus       577 rVRqie~RALkKLR-~~l~~~~L~~yl~  603 (605)
                      ||||+++||++||| +.+....|++|+.
T Consensus       411 rVRqi~~RAlkKLR~~~~~~~~l~~yl~  438 (438)
T 1l9z_H          411 RIRQIENKALRKLKYHESRTRKLRDFLE  438 (438)
T ss_pred             HHHHHHHHHHHHHHHhHhhHHHHHHhhC
Confidence            99999999999999 8888899999974

>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=1.4e-54  Score=469.90  Aligned_cols=313  Identities=39%  Similarity=0.631  Sum_probs=274.0

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHH------------------HHHhhcCCCCchHHHHH---
Q 007404          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE------------------VLSERCGGSPTFAQWAA---  347 (605)
Q Consensus       290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~------------------~L~~~~G~~pt~~ewA~---  347 (605)
                      ..|+++ ||++| +++|+||++||++|+++|+....+...-.                  ......|+.|+..+|+.   
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            457999 99999 99999999999999999998643222111                  00112245566554432   


Q ss_pred             ---------hhcCCHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcc
Q 007404          348 ---------AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKF  418 (605)
Q Consensus       348 ---------a~g~d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rF  418 (605)
                               +.+++...|...+++|..|+++||.+|+++|++||++|.++|.+++|||||||||||+|+++|||.+|++|
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                     23566777888888889999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcC--CCHHHHHHHHhCCCCCC
Q 007404          419 STYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPR  496 (605)
Q Consensus       419 STYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lg--is~e~V~~~l~~~~~~~  496 (605)
                      +||++||||+.|.+++++++|++|+|.|+.+.+++++++.+.+.+.+|+.|+.+|||+.+|  +++++|..++.....++
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 007404          497 SLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRE  576 (605)
Q Consensus       497 SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISre  576 (605)
                      |||.+++++++..+.+.+++....+|++.+....+...|..+|+.||++||.||.+|||++||+++|++|||+.||||++
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            99999987777778888887766789998888889999999999999999999999999988889999999999999999


Q ss_pred             HHHHHHHHHHHHHH-hHHhhhhHhhhhc
Q 007404          577 RIRQIESSAFRKLK-NKKRTKHLMQYAI  603 (605)
Q Consensus       577 rVRqie~RALkKLR-~~l~~~~L~~yl~  603 (605)
                      ||||++++|++||| +......|++|++
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 8888888999974

>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=1.3e-42  Score=391.90  Aligned_cols=248  Identities=39%  Similarity=0.645  Sum_probs=232.6

Q ss_pred             HHHHHhccHHH---HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHH
Q 007404          356 LRRRLNYGILC---KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK  432 (605)
Q Consensus       356 L~~~l~~g~~A---~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r  432 (605)
                      +.+...|+..|   |+.||..|+++|+++|++|.+++.+++||+||||||||+++++||+.+|++|+||++|||||.|.+
T Consensus       362 i~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn~i~~  441 (613)
T 3iyd_F          362 NRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR  441 (613)
T ss_dssp             HHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHHHHHH
Confidence            33444555666   999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCc
Q 007404          433 SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSE  512 (605)
Q Consensus       433 ~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d  512 (605)
                      +++++.+.+|+|.|+.+.+++++++.+.+.+++|+.||++|||+.+|+++++|..++.....++||+.+++++++..+.+
T Consensus       442 ~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~~~~~~~~l~d  521 (613)
T 3iyd_F          442 SIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGD  521 (613)
T ss_dssp             HTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCCSSSSSCCGGG
T ss_pred             HHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCCCCCCCccHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999998877778888


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          513 VIADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       513 ~l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .+.+....+|++.+...++...|..+|..||+++|.||.|||++++++.+|++|||+.||||++||+++++||+++||+.
T Consensus       522 ~i~d~~~~~p~~~~~~~e~~~~l~~aL~~Lp~~er~Vl~Lr~~~~~~e~~s~~EIA~~lgis~~tVk~~~~rAl~kLR~~  601 (613)
T 3iyd_F          522 FIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP  601 (613)
T ss_dssp             SCCCSSSCCHHHHHHHHTTSSSHHHHTTSSCHHHHHHHHHHHTSSSCCCCSTTGGGTTTSSCSSHHHHHHHHHHTTTTSC
T ss_pred             HhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhhCc
Confidence            88887777899999888888899999999999999999999997766779999999999999999999999999999999


Q ss_pred             HhhhhHhhhhc
Q 007404          593 KRTKHLMQYAI  603 (605)
Q Consensus       593 l~~~~L~~yl~  603 (605)
                      +....|+.|++
T Consensus       602 ~~~~~l~~~l~  612 (613)
T 3iyd_F          602 SRSEVLRSFLD  612 (613)
T ss_dssp             SSSCSSTTCC-
T ss_pred             chhhHHHHHhc
Confidence            99999999986

>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=4.9e-36  Score=303.17  Aligned_cols=208  Identities=38%  Similarity=0.647  Sum_probs=130.7

Q ss_pred             CCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH-HHhHHHHHHh-------------------------hcCCCCch
Q 007404          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK-LEGLREVLSE-------------------------RCGGSPTF  342 (605)
Q Consensus       290 ~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~-le~~~~~L~~-------------------------~~G~~pt~  342 (605)
                      ..||++ ||++| +++||||++||++|+++|+.++. .+.+......                         ..+.+|+.
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 99999999999999999998654 3333221110                         02467889


Q ss_pred             HHHHHhhcCC----HHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcc
Q 007404          343 AQWAAAAGVD----QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKF  418 (605)
Q Consensus       343 ~ewA~a~g~d----~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rF  418 (605)
                      .+||.+.|++    ...|.+..++|..|++.||..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|
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    345666778899999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcC--CCHHHHHHHHhCCCCCC
Q 007404          419 STYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPR  496 (605)
Q Consensus       419 STYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lg--is~e~V~~~l~~~~~~~  496 (605)
                      +||++||||++|.++++++.+.+++|.++.+.++++.++.+.+.+.+|+.||.+|||+.||  +|+++|...+..+...+
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 007404          497 SL  498 (605)
Q Consensus       497 SL  498 (605)
                      ||
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=99.98  E-value=4.6e-32  Score=265.63  Aligned_cols=222  Identities=23%  Similarity=0.338  Sum_probs=192.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhh---CCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccc
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRT  440 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~---~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~  440 (605)
                      ..|++.||..|.++|+.+|++|.   +++.+++||+|||+++||+++++||+.+|.+|.||+++||++.|.++++++.+ 
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   67899999999999999999999999999999999999999999999998764 


Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCC--CCCCCccccccccCCCCCCcccCCCC
Q 007404          441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSP--KAPRSLDQKIGINQNLKPSEVIADPE  518 (605)
Q Consensus       441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~--~~~~SLD~~i~~d~~~~l~d~l~D~~  518 (605)
                        .|.+......+++++...+...+|+.|+.+++++.+|++.+++..++...  ....|+|.++.++++.. .+. +++ 
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              67777788899999999999999999999999999999999998876532  22346666543322222 333 332 


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      ..+|++.+...+....|..+|..||+++|.||.++|+.+    +|++|||+.||||.++|+++++||+++||+.+..
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            346888888888889999999999999999999999887    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=7.5e-32  Score=263.84  Aligned_cols=217  Identities=28%  Similarity=0.449  Sum_probs=52.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      |+..|++.|+..|.++|+++|++|.++..+++||+||||++||+++++||+.+|.+|.||+++|+++.+.++++++. .+
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            45789999999999999999999999999999999999999999999999999889999999999999999999987 78


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCC--CCCCcccCCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQN--LKPSEVIADPEA  519 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~--~~l~d~l~D~~~  519 (605)
                      ++|.++.....+++++...+.+..++.|+.++++..+|++.+.+...+.......|++.++.++++  .++.+.++    
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~----  179 (243)
T 1l0o_C          104 KVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIA----  179 (243)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC---------------------------
T ss_pred             cCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCcccchhhccC----
Confidence            999999999999999999999999999999999999999999998887655557788777543322  22233222    


Q ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          520 ETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       520 ~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                         ++.+...+....|..+|..||+++|.||.|+|+.+    +|++|||+.||||.++|+++++||+++||
T Consensus       180 ---~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr  243 (243)
T 1l0o_C          180 ---DADEASWFDKIALKKAIEELDERERLIVYLRYYKD----QTQSEVASRLGISQVQMSRLEKKILQHIK  243 (243)
T ss_dssp             -----------------------------------------------------------------------
T ss_pred             ---cchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence               22334445667789999999999999999999887    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=3.7e-23  Score=197.01  Aligned_cols=178  Identities=16%  Similarity=0.190  Sum_probs=136.1

Q ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404          354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  433 (605)
Q Consensus       354 ~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~  433 (605)
                      +.+.+...|+..|++.|+..|.+.|+.+|++|.+ ..+++|++||+|+++|+++++|++..  .|.+|++.+++|.+.++
T Consensus        12 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~d~   88 (194)
T 1or7_A           12 VLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAKNY   88 (194)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHH
Confidence            3444555667999999999999999999999999 99999999999999999999999875  59999999999999999


Q ss_pred             HhhccccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcc
Q 007404          434 LSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEV  513 (605)
Q Consensus       434 ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~  513 (605)
                      ++++.+..+..                            ++..        .. .       ..++.          .+.
T Consensus        89 ~R~~~~~~~~~----------------------------~~~~--------~~-~-------~~~~~----------~~~  114 (194)
T 1or7_A           89 LVAQGRRPPSS----------------------------DVDA--------IE-A-------ENFES----------GGA  114 (194)
T ss_dssp             HHHHTTCCTHH----------------------------HHHH--------HH-H-------HSCCS----------SCC
T ss_pred             HHHHhccCccc----------------------------cccc--------cc-c-------ccccc----------ccc
Confidence            99876532110                            0000        00 0       00000          001


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          514 IADPEAETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       514 l~D~~~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      +.+.  .+|++.+...+....|..+|..||+++|+||.|+|+.+    +|++|||+.||||..+|+++++||+++||+.+
T Consensus       115 ~~~~--~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l  188 (194)
T 1or7_A          115 LKEI--SNPENLMLSEELRQIVFRTIESLPEDLRMAITLRELDG----LSYEEIAAIMDCPVGTVRSRIFRAREAIDNKV  188 (194)
T ss_dssp             ----------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHHTTC----CCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCC--CChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHHHcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            1111  13443344445667789999999999999999999887    99999999999999999999999999999976


Q ss_pred             h
Q 007404          594 R  594 (605)
Q Consensus       594 ~  594 (605)
                      .
T Consensus       189 ~  189 (194)
T 1or7_A          189 Q  189 (194)
T ss_dssp             C
T ss_pred             H
Confidence            4

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=99.86  E-value=1.1e-21  Score=180.79  Aligned_cols=154  Identities=16%  Similarity=0.247  Sum_probs=107.8

Q ss_pred             CCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccccccccHHHHHHHHHHHHHHHHHHcCCC
Q 007404          389 GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRH  468 (605)
Q Consensus       389 g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~~~~~i~ki~ka~~~L~~elgr~  468 (605)
                      |.+++|++||+|++||+++.+||+.+ .+|.||+++++++.+.++++++.+..+.|..                      
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 6899999999999999999987643322211                      


Q ss_pred             CCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCC----cccCCCCCCCHHHHHHHHHHHHHHHHHHh-cCC
Q 007404          469 PNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPS----EVIADPEAETAEDLLIKKFMKEDLEKVLD-TLN  543 (605)
Q Consensus       469 PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~----d~l~D~~~~spEe~l~~~el~~~L~~aL~-~L~  543 (605)
                                               ..++++.+..++....+.    +.+.+ ...+|++.+...+....|..+|. .||
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             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                      +++|.||. +|..|    +|++|||+.||||.++|+++++||+++||+.+...
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 77776    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=1.4e-18  Score=162.63  Aligned_cols=142  Identities=9%  Similarity=0.106  Sum_probs=118.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcccccccccc
Q 007404          367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFH  446 (605)
Q Consensus       367 ~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~IRlP~~  446 (605)
                      |+.|+..|.+.|+.+|+++.++..+++|++||+|+.+|+++++|++..  .|.+|++..++|.+.+++++...       
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~-------   73 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGEA-------   73 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTSC-------
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccCc-------
Confidence            567899999999999999999999999999999999999999999763  69999999999999998875310       


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCCHHHHH
Q 007404          447 MVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAETAEDLL  526 (605)
Q Consensus       447 ~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l  526 (605)
                                            +                             +.      .  . +   ..         
T Consensus        74 ----------------------~-----------------------------~~------~--~-e---~~---------   81 (157)
T 2lfw_A           74 ----------------------Q-----------------------------TS------Q--S-D---AE---------   81 (157)
T ss_dssp             ----------------------C-----------------------------CC------C--C-S---CS---------
T ss_pred             ----------------------c-----------------------------cC------C--c-c---hH---------
Confidence                                  0                             00      0  0 0   00         


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhh
Q 007404          527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTK  596 (605)
Q Consensus       527 ~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~  596 (605)
                         +....|..+|..||+++|+||.|+|..|    +|++|||+.||||..+|++++.||+++||+.+...
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               0112366788999999999999999887    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=99.65  E-value=2.2e-16  Score=165.81  Aligned_cols=83  Identities=48%  Similarity=0.866  Sum_probs=75.7

Q ss_pred             HHHHhccH---HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHH
Q 007404          357 RRRLNYGI---LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKS  433 (605)
Q Consensus       357 ~~~l~~g~---~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~  433 (605)
                      .+...|+.   .|++.||..|+++|+++|++|.+++.+++||+||||||||+++++|++.+|++|+||++|||||.|.++
T Consensus       254 ~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~~~~~  333 (339)
T 1sig_A          254 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS  333 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHH
Confidence            34445556   899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhccc
Q 007404          434 LSDQSR  439 (605)
Q Consensus       434 ir~~sr  439 (605)
                      ++++.+
T Consensus       334 lr~~~r  339 (339)
T 1sig_A          334 IADQAR  339 (339)
T ss_dssp             HHHC--
T ss_pred             HHHhcC
Confidence            998653

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.59  E-value=1.3e-15  Score=156.29  Aligned_cols=143  Identities=13%  Similarity=0.061  Sum_probs=119.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccccc
Q 007404          362 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTI  441 (605)
Q Consensus       362 ~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr~I  441 (605)
                      ++..+|+.||..|.+.++.+|++|.++..+++|++||.|+.+|+...+|++.  ..|.+|++.+++|.+.+++++...  
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            4567899999999999999999999999999999999999999999999875  369999999999999887753110  


Q ss_pred             cccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCCCCC
Q 007404          442 RLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPEAET  521 (605)
Q Consensus       442 RlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~s  521 (605)
                                                 +                                  ...         +..   
T Consensus        94 ---------------------------~----------------------------------~~~---------~~~---  100 (286)
T 3n0r_A           94 ---------------------------G----------------------------------HDQ---------GLH---  100 (286)
T ss_dssp             ---------------------------C----------------------------------CCC---------CCC---
T ss_pred             ---------------------------C----------------------------------CCc---------ccc---
Confidence                                       0                                  000         000   


Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          522 AEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       522 pEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                               ....|..+|+.||+++|+||.|+|..+    +|++|||+.+|+|..+|+....+|+++|+..+.
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    999999999999999999999999999997543

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=99.53  E-value=4e-14  Score=124.22  Aligned_cols=80  Identities=36%  Similarity=0.530  Sum_probs=74.2

Q ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhcc
Q 007404          525 LLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT  604 (605)
Q Consensus       525 ~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~~  604 (605)
                      .+...++...|..+|+.||++||+||.||||++|++++|++|||+.||||++||++++.+|+++||+.+....|++|+..
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            45667788899999999999999999999998777779999999999999999999999999999999999999999864

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=99.30  E-value=1.5e-11  Score=105.18  Aligned_cols=75  Identities=13%  Similarity=0.166  Sum_probs=69.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      ..+|++.+...+....|..+|..||+++|+||.|+|+.+    +|++|||+.||||..+|+++++||+++||+.+...+
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=99.26  E-value=6.7e-12  Score=106.66  Aligned_cols=71  Identities=55%  Similarity=0.826  Sum_probs=64.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      ..|..+|+.||++||+||.++|+++|+..+|++|||+.||||+++|++++.+|++|||..+....++.|+.
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            45788999999999999999999766666999999999999999999999999999999998888888764

>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=99.24  E-value=3.1e-12  Score=104.95  Aligned_cols=69  Identities=52%  Similarity=0.782  Sum_probs=54.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-hHHhhhhHhhhhc
Q 007404          535 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK-NKKRTKHLMQYAI  603 (605)
Q Consensus       535 L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR-~~l~~~~L~~yl~  603 (605)
                      |..+|+.||++||+||.++|+++|+.++|++|||+.||+|.++|++++.+|+++|| ..+....++.|++
T Consensus         4 l~~~l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~~~~~~~~~~~~   73 (73)
T 1ku3_A            4 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFLE   73 (73)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTC----------
T ss_pred             HHHHHHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHhhHHHHHHhhC
Confidence            45678899999999999999976666699999999999999999999999999999 8888888888863

>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=99.19  E-value=8e-12  Score=101.05  Aligned_cols=66  Identities=44%  Similarity=0.674  Sum_probs=59.9

Q ss_pred             HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       538 aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      +|+.||++|++||.++||++|.+.+|++|||+.||+|.++|++++.+|++|||..+....++.|++
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            367899999999999998755556999999999999999999999999999999999888888864

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=98.98  E-value=1.1e-09  Score=96.03  Aligned_cols=82  Identities=12%  Similarity=0.026  Sum_probs=69.6

Q ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404          356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  435 (605)
Q Consensus       356 L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir  435 (605)
                      +.....++..|++.|+..|.+.|+.+|.++ ++..+++|++||+|+.+|+.+.+|++.  ..|.+|++..++|.+.++++
T Consensus        15 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   91 (112)
T 2o7g_A           15 ALSAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIR   91 (112)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHHHHH
Confidence            334445668999999999999999999999 888899999999999999999999974  36999999999999999998


Q ss_pred             hcccc
Q 007404          436 DQSRT  440 (605)
Q Consensus       436 ~~sr~  440 (605)
                      ++.+.
T Consensus        92 ~~~~~   96 (112)
T 2o7g_A           92 HVRSR   96 (112)
T ss_dssp             -----
T ss_pred             Hhhcc
Confidence            87653

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=98.98  E-value=8.2e-10  Score=88.58  Aligned_cols=64  Identities=14%  Similarity=0.141  Sum_probs=53.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  598 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  598 (605)
                      ....|..+|+.||++++.||.++|..+    +|++|||+.||+|+.+|+++.++|+++||+.+....+
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            456788899999999999999999877    9999999999999999999999999999998876543

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=98.92  E-value=1.4e-09  Score=91.05  Aligned_cols=77  Identities=13%  Similarity=0.076  Sum_probs=68.4

Q ss_pred             hccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccc
Q 007404          361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  439 (605)
Q Consensus       361 ~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr  439 (605)
                      .++..+++.|+..|.+.++.+|.++.++..+++|++||+|+.+|+.+++|++.  ..|.+|++.+++|.+.++++++.+
T Consensus         8 ~g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~~   84 (87)
T 1h3l_A            8 AERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQR   84 (87)
T ss_dssp             HHHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC----
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhcc
Confidence            35688999999999999999999999999999999999999999999999975  379999999999999999987653

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=98.82  E-value=1.2e-08  Score=91.13  Aligned_cols=69  Identities=17%  Similarity=0.213  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404          526 LIKKFMKEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  598 (605)
Q Consensus       526 l~~~el~~~L~~aL-~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  598 (605)
                      ++..+....+..++ ..||+++|+||.++|..+    +|++|||+.||+|..+|+.+.+||+++||..+...++
T Consensus         9 ~e~~~~~~~l~~~l~~~L~~~~r~vl~l~~~~g----~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   78 (113)
T 1xsv_A            9 LVKTLRMNYLFDFYQSLLTNKQRNYLELFYLED----YSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   78 (113)
T ss_dssp             HHHHHHHHHHHHHHGGGSCHHHHHHHHHHHTSC----CCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhH
Confidence            44455667788999 999999999999999888    9999999999999999999999999999998866443

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=98.71  E-value=3.5e-11  Score=121.29  Aligned_cols=147  Identities=12%  Similarity=0.054  Sum_probs=107.1

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHH----HHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhcc
Q 007404          363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLV----QEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQS  438 (605)
Q Consensus       363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLI----QEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~s  438 (605)
                      |..+++.+...|.++++.+............|+.    ||.++.+|+.+..|++..  .|.+|++..+++.+.++.+...
T Consensus        95 D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~r~~~  172 (258)
T 3clo_A           95 DLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTP--AGNVWLIFCLYSLSADQRPEQG  172 (258)
T ss_dssp             HHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECT--TSCEEEEEEEEEECSCCCCCSS
T ss_pred             HHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHcchhhhhH
Confidence            3678999999999999999888777777788886    999999999999998754  6888877766655544322110


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhCCCCCCCccccccccCCCCCCcccCCCC
Q 007404          439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLSPKAPRSLDQKIGINQNLKPSEVIADPE  518 (605)
Q Consensus       439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~~~~~~SLD~~i~~d~~~~l~d~l~D~~  518 (605)
                                                                                 +...+.....   .+.... .
T Consensus       173 -----------------------------------------------------------~~~~~~~~~~---~~~~~~-~  189 (258)
T 3clo_A          173 -----------------------------------------------------------IYATITQMER---GEVETL-S  189 (258)
T ss_dssp             -----------------------------------------------------------CCCEEEETTT---TEEEEC-C
T ss_pred             -----------------------------------------------------------HHHHHHhhcc---cccccc-h
Confidence                                                                       0000000000   000000 0


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          519 AETAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       519 ~~spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                                     .+..++..||++||+||.|+ ..|    +|++|||+.||+|..||+.+.+||++|||....
T Consensus       190 ---------------~~~~~~~~L~~~erevl~L~-~~G----~s~~EIA~~L~iS~~TVk~~l~ra~~kL~~~~~  245 (258)
T 3clo_A          190 ---------------LSEEHRNILSEREKEILRCI-RKG----LSSKEIAATLYISVNTVNRHRQNILEKLSVGNS  245 (258)
T ss_dssp             ---------------CHHHHTTSSCHHHHHHHHHH-HTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHTTCSSH
T ss_pred             ---------------hhHHHHccCCHHHHHHHHHH-HcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence                           13556789999999999997 455    999999999999999999999999999997543

>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=98.66  E-value=7.8e-08  Score=85.93  Aligned_cols=64  Identities=17%  Similarity=0.227  Sum_probs=57.3

Q ss_pred             HHHHHHHHH-hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhH
Q 007404          531 MKEDLEKVL-DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHL  598 (605)
Q Consensus       531 l~~~L~~aL-~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L  598 (605)
                      ....+..++ ..||+++++||.++|..|    +|++|||+.||+|+.+|+.+.++|+++||+.+...++
T Consensus        11 ~~~~l~~~l~~~L~~~~r~vl~l~y~~g----~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~   75 (113)
T 1s7o_A           11 RMNALFEFYAALLTDKQMNYIELYYADD----YSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   75 (113)
T ss_dssp             HHHHHHHHHGGGSCHHHHHHHHHHHHTC----CCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            345677788 899999999999999888    9999999999999999999999999999998865443

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=98.52  E-value=4.3e-08  Score=83.56  Aligned_cols=61  Identities=16%  Similarity=0.200  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          529 KFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       529 ~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ......+..++..|+++|++||.+ |..+    +|++|||+.||||..+|+.++.++++||+....
T Consensus        17 ~~~~~~l~~~l~~Lt~~e~~vl~l-~~~g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   77 (91)
T 2rnj_A           17 GSHMKKRAELYEMLTEREMEILLL-IAKG----YSNQEIASASHITIKTVKTHVSNILSKLEVQDR   77 (91)
T ss_dssp             --------CTGGGCCSHHHHHHHH-HHTT----CCTTHHHHHHTCCHHHHHHHHHHHHHHTTCCSS
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHH-HHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence            344566888899999999999999 4555    999999999999999999999999999986433

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=98.44  E-value=2.2e-07  Score=76.19  Aligned_cols=57  Identities=25%  Similarity=0.267  Sum_probs=50.7

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          533 EDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       533 ~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ..|..++..||++|++||.+ |..+    +|++|||+.||+|..+|+++..++++||+....
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            45778899999999999999 5555    999999999999999999999999999996443

>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=98.44  E-value=2.6e-07  Score=79.57  Aligned_cols=59  Identities=19%  Similarity=0.240  Sum_probs=44.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      ....|..++..|+++|++||.++ ..+    +|++|||+.||||..||+.++.++++||+....
T Consensus        17 ~~~~l~~~l~~Lt~~e~~vl~l~-~~g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   75 (95)
T 3c57_A           17 RGSHMQDPLSGLTDQERTLLGLL-SEG----LTNKQIADRMFLAEKTVKNYVSRLLAKLGMERR   75 (95)
T ss_dssp             ----------CCCHHHHHHHHHH-HTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCC
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHH-HcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence            34567888999999999999996 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=98.33  E-value=4.2e-07  Score=79.84  Aligned_cols=66  Identities=17%  Similarity=0.211  Sum_probs=55.2

Q ss_pred             HHHHHHHHHHHH-hcCCHHHHHHHHHHHhcCC---CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          528 KKFMKEDLEKVL-DTLNPRERQVVRWRFGLED---GRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       528 ~~el~~~L~~aL-~~L~~rER~VL~LRyGl~d---g~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      .....+.+..++ +.|+++|+.+|.+|||+.+   +.++|+.|||+.+|+|+.+|..+ +|+|++|...+.
T Consensus        21 ~~~~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k   90 (101)
T 1jhg_A           21 NAYQNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELR   90 (101)
T ss_dssp             HHHHTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHH
T ss_pred             hcCCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHH
Confidence            333445567777 5799999999999999863   34599999999999999999999 899999988654

>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=98.32  E-value=3.4e-07  Score=76.72  Aligned_cols=56  Identities=20%  Similarity=0.367  Sum_probs=48.5

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhh
Q 007404          535 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT  595 (605)
Q Consensus       535 L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~  595 (605)
                      +..++..|+++|++||.+ |..+    +|++|||+.||||..+|+.++.++++||+.....
T Consensus        15 ~~~~~~~Lt~~e~~vl~l-~~~g----~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~   70 (82)
T 1je8_A           15 TERDVNQLTPRERDILKL-IAQG----LPNKMIARRLDITESTVKVHVKHMLKKMKLKSRV   70 (82)
T ss_dssp             --CCGGGSCHHHHHHHHH-HTTT----CCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHH
T ss_pred             HHHHHccCCHHHHHHHHH-HHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHH
Confidence            567788999999999999 5555    9999999999999999999999999999875543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=98.16  E-value=1.7e-06  Score=69.79  Aligned_cols=55  Identities=31%  Similarity=0.304  Sum_probs=46.4

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          535 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       535 L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      +...+..|+++|++||.+ |..+    +|.+|||+.||+|..+|+++..++++||+..-.
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            445578899999999999 5555    899999999999999999999999999987543

>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=97.98  E-value=9.8e-06  Score=69.31  Aligned_cols=50  Identities=32%  Similarity=0.303  Sum_probs=43.0

Q ss_pred             HHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          537 KVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       537 ~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .....|+++|++||.+.+ .|    +|.+|||+.||||..||+.+..++++||.-
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            346789999999999977 55    999999999999999999999999999964

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=97.89  E-value=1e-05  Score=62.99  Aligned_cols=45  Identities=29%  Similarity=0.329  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      ++|++||.+ |..|    +|.+|||+.||+|..+|+.+..++++||+..-
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 6666    99999999999999999999999999998643

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=97.80  E-value=2.8e-05  Score=67.70  Aligned_cols=47  Identities=28%  Similarity=0.277  Sum_probs=42.9

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|++||.+.+ .+    +|.+|||+.||||..+|+.+..++++||.-
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            579999999999854 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=0.00025  Score=69.91  Aligned_cols=46  Identities=26%  Similarity=0.392  Sum_probs=42.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++||.+. ..|    +|.+|||++||||..||+.+..++++||.-
T Consensus       175 ~Lt~~e~~vl~~~-~~g----~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (236)
T 2q0o_A          175 MLSPREMLCLVWA-SKG----KTASVTANLTGINARTVQHYLDKARAKLDA  220 (236)
T ss_dssp             SCCHHHHHHHHHH-HTT----CCHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHH-HcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            5999999999995 455    999999999999999999999999999965

>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=69.88  Aligned_cols=46  Identities=28%  Similarity=0.549  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++||.+. ..|    +|.+|||++||||..||+.++.++++||.-
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=97.08  E-value=0.00059  Score=67.59  Aligned_cols=47  Identities=28%  Similarity=0.542  Sum_probs=42.5

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|++||.+. ..|    +|.+|||++||||..||+.++.++++||.-
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            36999999999986 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=0.0008  Score=67.98  Aligned_cols=46  Identities=26%  Similarity=0.416  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++||.+.. .|    +|.+|||++||||..||+.++.++++||.-
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=96.83  E-value=0.0017  Score=47.07  Aligned_cols=40  Identities=25%  Similarity=0.216  Sum_probs=32.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      .|++.++..+...|..+    +|..|||+.||||+.+|+.++.+
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            47888886666666554    89999999999999999977643

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.21  E-value=0.0099  Score=52.03  Aligned_cols=46  Identities=11%  Similarity=0.172  Sum_probs=41.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      .+++.-..|-.++|..|    +|..|||+.||||+.+|.+++.+|...+.
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            68888888999999877    99999999999999999999999888763

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=96.00  E-value=0.014  Score=54.74  Aligned_cols=52  Identities=21%  Similarity=0.323  Sum_probs=44.3

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          535 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       535 L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +...+..|+++|++|+.+. ..+    +|.+|||+.||+|..||+.+..+.++||..
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

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=95.86  E-value=0.0078  Score=45.57  Aligned_cols=38  Identities=21%  Similarity=0.266  Sum_probs=28.9

Q ss_pred             CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          543 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       543 ~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      ++..+.|+.+ |..+    +|..|||+.||||+.||+.++.+|
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    899999999999999999887653

>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=95.60  E-value=0.02  Score=54.14  Aligned_cols=47  Identities=17%  Similarity=0.309  Sum_probs=41.5

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|++|+.+.. .+    +|.+|||+.+++|..||+.+..+.++||.-
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=95.14  E-value=0.027  Score=54.05  Aligned_cols=47  Identities=19%  Similarity=0.204  Sum_probs=41.2

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|+++|++||.+- ..+    +|.+|||+.+++|..||+.+..+.++||.-
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=94.73  E-value=0.025  Score=54.10  Aligned_cols=48  Identities=23%  Similarity=0.369  Sum_probs=41.5

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ...|+++|++||.+. ..+    +|.+|||+.|++|..||+.+..+.++||.-
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    899999999999999999999999998843

>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=94.53  E-value=0.069  Score=44.67  Aligned_cols=43  Identities=16%  Similarity=0.431  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          545 RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       545 rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .++.||.+....+.|...|..|||+.||||+.+|+    +.|.+|.+
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            45667766554444667999999999999999998    66777764

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=94.21  E-value=0.12  Score=49.92  Aligned_cols=56  Identities=21%  Similarity=0.305  Sum_probs=48.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ........+..|+++++.|+.+.. .+    ++.++||..||+|..+|+....++++||.-
T Consensus       188 ~~~~~~~~l~~L~~r~~~i~~~~~-~g----~~~~eia~~l~~s~~tv~~~l~~i~~kl~~  243 (258)
T 3p7n_A          188 RRERAAEMLKTLSPRQLEVTTLVA-SG----LRNKEVAARLGLSEKTVKMHRGLVMEKLNL  243 (258)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHH-TT----CCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhhcCHHHHHHHHHHH-cC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            345667888999999999999865 33    899999999999999999999999999864

>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=94.05  E-value=0.07  Score=44.00  Aligned_cols=44  Identities=16%  Similarity=0.416  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +.++.||.+-.-.+.|.+.|..|||+.||||+.+|+    +.|.+|.+
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~----~~L~~L~~   57 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEIN----RVLYSLAK   57 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            345677766554544566999999999999999998    45666654

>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=94.05  E-value=0.063  Score=50.76  Aligned_cols=50  Identities=14%  Similarity=0.189  Sum_probs=43.5

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG---VSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG---ISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++||.+-. .+-|..+|.+|||+.++   +|..||+.+..+.++||..
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            59999999998643 44567799999999999   9999999999999999963

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=93.55  E-value=0.098  Score=50.35  Aligned_cols=50  Identities=12%  Similarity=0.012  Sum_probs=42.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  591 (605)
                      .|+++|.+||.+.. .+-|..+|.+|||+.+     ++|..||+.+..+.++||..
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 4456779999999999     99999999999999999963

>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=93.43  E-value=0.089  Score=49.98  Aligned_cols=50  Identities=14%  Similarity=0.135  Sum_probs=43.7

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  591 (605)
                      .|+++|.+||.+-. .+.|+.+|.+|||+.+     ++|..||+.+..+.++||..
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

>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=92.97  E-value=0.023  Score=64.08  Aligned_cols=33  Identities=33%  Similarity=0.603  Sum_probs=12.9

Q ss_pred             CCCCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 007404          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDL  322 (605)
Q Consensus       289 ~~~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~  322 (605)
                      ...||++ ||++| |+.||||+++|++|+++|...
T Consensus        93 ~~~dpvrmyl~em-g~~~ll~~~~e~~~ak~ie~g  126 (613)
T 3iyd_F           93 RTTDPVRMYMREM-GTVELLTREGEIDIAKRIEDG  126 (613)
T ss_dssp             ------------C---------CSSSTTTHHHHHH
T ss_pred             CCCCcHHHHHHHh-cccccCCchhHHHHHHHHHHh
Confidence            3589999 99999 999999999999999999873

>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=92.50  E-value=0.13  Score=48.48  Aligned_cols=50  Identities=20%  Similarity=0.302  Sum_probs=43.5

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++||.+-. .+-|..+|.+|||+.++     +|..||+.+..+.++||..
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 44456799999999998     9999999999999999964

>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=92.32  E-value=0.13  Score=37.28  Aligned_cols=37  Identities=16%  Similarity=0.290  Sum_probs=26.5

Q ss_pred             CCHHH-HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          542 LNPRE-RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       542 L~~rE-R~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      |++.+ +.|+.+ +..+    .|..+||+.||||+.||..++.
T Consensus         6 ~~~~~~~~i~~l-~~~g----~s~~~ia~~lgvs~~Tv~r~l~   43 (52)
T 1jko_C            6 INKHEQEQISRL-LEKG----HPRQQLAIIFGIGVSTLYRYFP   43 (52)
T ss_dssp             SCTTHHHHHHHH-HHTT----CCHHHHHHTTSCCHHHHHHHSC
T ss_pred             CCHHHHHHHHHH-HHcC----CCHHHHHHHHCCCHHHHHHHHH
Confidence            34433 345554 4333    8999999999999999997654

>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=0.12  Score=49.00  Aligned_cols=50  Identities=16%  Similarity=0.082  Sum_probs=42.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  591 (605)
                      .|+++|.+||.+-. .+.|..+|.+|||+.++     +|..||+.+..+.++||..
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     9999999999999999974

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=92.10  E-value=0.22  Score=39.70  Aligned_cols=44  Identities=14%  Similarity=0.229  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +++..+.||.+.-  .++.++|..|||+.+|+|+.+|.    +.++.|++
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    66667765

>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=91.38  E-value=0.036  Score=55.41  Aligned_cols=51  Identities=24%  Similarity=0.382  Sum_probs=0.0

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Q 007404          535 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMG--VSRERIRQIESSAFRKLK  590 (605)
Q Consensus       535 L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG--ISrerVRqie~RALkKLR  590 (605)
                      +...+..|++.++. |...|+.+    .|++|||+.||  ||.++|+.++.+|++.|.
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            45556777777777 44556655    89999999999  999999999999988763

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=90.96  E-value=0.089  Score=49.83  Aligned_cols=50  Identities=8%  Similarity=0.076  Sum_probs=43.5

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMG-----VSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LG-----ISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++||.+-. .+.|..+|.+|||+.++     +|..||+.+..+.++||..
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 34456799999999999     9999999999999999974

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=90.90  E-value=0.58  Score=38.94  Aligned_cols=47  Identities=15%  Similarity=0.271  Sum_probs=35.8

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ...|++.+..+|...+..+  .+.|..|||+.+|+|+.+|+    +.+++|.+
T Consensus        16 ~~~l~~~~~~~l~~l~~~~--~~~t~~ela~~l~is~~tv~----~~l~~L~~   62 (109)
T 2d1h_A           16 CYKITDTDVAVLLKMVEIE--KPITSEELADIFKLSKTTVE----NSLKKLIE   62 (109)
T ss_dssp             HHTCCHHHHHHHHHHHHHC--SCEEHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHcC--CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            4578998888876555322  24999999999999999999    55666643

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=90.58  E-value=0.19  Score=49.08  Aligned_cols=50  Identities=22%  Similarity=0.325  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGE-----LMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe-----~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++||.+.. .+.|..+|.+|||+     .++++..||+.+..+.++||..
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     5888999999999999999864

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=90.52  E-value=0.65  Score=41.03  Aligned_cols=49  Identities=10%  Similarity=0.131  Sum_probs=38.7

Q ss_pred             HHHhcCCHHHHHHHHHHHhcCCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          537 KVLDTLNPRERQVVRWRFGLEDGRM-KTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       537 ~aL~~L~~rER~VL~LRyGl~dg~~-~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ...-.|++.+..||..-...  +.+ .|..|||+.+|+|+.||.    |.+++|.+
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            34557999999998765533  345 899999999999999999    66777765

>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=90.51  E-value=0.25  Score=47.18  Aligned_cols=41  Identities=20%  Similarity=0.276  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          541 TLNPRERQVVRWR--FGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       541 ~L~~rER~VL~LR--yGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      .|+++|++||..-  |....|.|.|.+|||+.||+|..+|+.+
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~   44 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLH   44 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHH
Confidence            5899999999775  3334566799999999999999988743

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=90.46  E-value=0.39  Score=46.47  Aligned_cols=50  Identities=20%  Similarity=0.299  Sum_probs=43.7

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  591 (605)
                      .|+++|.+||.+.. .+.|+.+|.+||++.+     +++..+|+.+..+.++||..
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 4457789999999999     78999999999999999964

>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=90.20  E-value=0.36  Score=42.53  Aligned_cols=40  Identities=25%  Similarity=0.216  Sum_probs=32.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      .|++.++..|...+..+    +|..+||+.||+|+.||+.+..+
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            47777777666656444    89999999999999999987754

>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=89.83  E-value=0.53  Score=40.31  Aligned_cols=41  Identities=15%  Similarity=-0.052  Sum_probs=30.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      .+++.++.-+...+..+    +|..+||+.||||+.||+.++.+-
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            45665555444444443    899999999999999999887664

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=88.52  E-value=0.79  Score=41.42  Aligned_cols=45  Identities=24%  Similarity=0.386  Sum_probs=34.0

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|++.++.||.+-..  + ...|+.|||+.+|+|+.+|+    +.+++|.+
T Consensus         5 ~~ld~~d~~il~~L~~--~-~~~s~~ela~~lg~s~~tv~----~~l~~L~~   49 (151)
T 2dbb_A            5 RKLDRVDMQLVKILSE--N-SRLTYRELADILNTTRQRIA----RRIDKLKK   49 (151)
T ss_dssp             -CCCHHHHHHHHHHHH--C-TTCCHHHHHHHTTSCHHHHH----HHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            3588999998876432  2 24899999999999999999    44555554

>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=87.85  E-value=1  Score=40.56  Aligned_cols=44  Identities=14%  Similarity=0.217  Sum_probs=33.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++.++.||.+-...   .+.|+.|||+.+|+|+.+|+    +.+++|.+
T Consensus         2 ~ld~~d~~il~~L~~~---~~~s~~ela~~lg~s~~tv~----~~l~~L~~   45 (144)
T 2cfx_A            2 KLDQIDLNIIEELKKD---SRLSMRELGRKIKLSPPSVT----ERVRQLES   45 (144)
T ss_dssp             CCCHHHHHHHHHHHHC---SCCCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHc---CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            3788888888765322   24899999999999999999    44555543

>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=87.61  E-value=0.86  Score=40.95  Aligned_cols=41  Identities=17%  Similarity=0.006  Sum_probs=30.7

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      .++..+|.-|...+..+    +|..+||+.||||+.||+.++.+-
T Consensus        32 ~~s~e~r~~iv~~~~~G----~s~~~iA~~lgis~~TV~rw~~~~   72 (149)
T 1k78_A           32 PLPDVVRQRIVELAHQG----VRPCDISRQLRVSHGCVSKILGRY   72 (149)
T ss_dssp             CCCHHHHHHHHHHHHTT----CCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45655555444445433    899999999999999999887764

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=87.54  E-value=0.93  Score=41.82  Aligned_cols=36  Identities=17%  Similarity=0.347  Sum_probs=28.3

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQ  580 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRq  580 (605)
                      |++.++.||.+-  ..+ .+.|+.|||+.+|+|+.+|+.
T Consensus         1 lD~~d~~il~~L--~~~-~~~s~~~la~~lg~s~~tv~~   36 (162)
T 3i4p_A            1 MDRLDRKILRIL--QED-STLAVADLAKKVGLSTTPCWR   36 (162)
T ss_dssp             CCHHHHHHHHHH--TTC-SCSCHHHHHHHHTCCHHHHHH
T ss_pred             CCHHHHHHHHHH--HHC-CCCCHHHHHHHHCcCHHHHHH
Confidence            567788888764  223 348999999999999999993

>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=87.43  E-value=0.99  Score=40.07  Aligned_cols=43  Identities=16%  Similarity=0.373  Sum_probs=32.5

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |++.++.||..-. .+  .+.|+.|||+.+|+|+.+|+    +.+++|.+
T Consensus         2 ld~~~~~il~~L~-~~--~~~~~~ela~~lg~s~~tv~----~~l~~L~~   44 (141)
T 1i1g_A            2 IDERDKIILEILE-KD--ARTPFTEIAKKLGISETAVR----KRVKALEE   44 (141)
T ss_dssp             CCSHHHHHHHHHH-HC--TTCCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             CCHHHHHHHHHHH-Hc--CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            6778888887543 22  24899999999999999999    55666654

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=87.39  E-value=0.75  Score=44.52  Aligned_cols=35  Identities=14%  Similarity=0.176  Sum_probs=28.0

Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404          547 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  586 (605)
Q Consensus       547 R~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL  586 (605)
                      ..+..+ |..|    +|..|||+.||||+.+|.+++..|.
T Consensus        15 ~ria~~-y~~g----~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           15 LRLMRM-KNDG----MSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HHHHHH-HHTT----CCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HHHHHH-HHcC----CCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            345555 5554    9999999999999999999887764

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=86.82  E-value=1.3  Score=39.10  Aligned_cols=48  Identities=13%  Similarity=0.157  Sum_probs=34.4

Q ss_pred             hcCCHHHHHHHHHHHhc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGL-EDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl-~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|++.+..+|..-+.+ ..+.+.|..+||+.+|+|+.+|+    +++++|.+
T Consensus         9 ~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~----~~l~~Le~   57 (139)
T 2x4h_A            9 SNLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVF----EEVSHLEE   57 (139)
T ss_dssp             --CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             hhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHH----HHHHHHHH
Confidence            46888888777665432 23345899999999999999999    55566544

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=86.71  E-value=1.3  Score=36.69  Aligned_cols=44  Identities=14%  Similarity=0.233  Sum_probs=33.8

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++.+..||..-...+   +.|..|||+.+|+|+.+|+    +.+++|.+
T Consensus        17 ~l~~~~~~il~~l~~~~---~~s~~ela~~l~is~~tv~----~~l~~L~~   60 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLERG---GMRVSEIARELDLSARFVR----DRLKVLLK   60 (109)
T ss_dssp             CCCHHHHHHHHHHHHHC---CBCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcC---CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            47888888887654322   3999999999999999999    55555544

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=86.69  E-value=0.49  Score=39.79  Aligned_cols=22  Identities=5%  Similarity=0.166  Sum_probs=20.0

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Q 007404          562 KTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       562 ~Tl~EIAe~LGISrerVRqie~  583 (605)
                      .|..|||+.||||+.+|+++++
T Consensus        31 ~sa~eLAk~LgiSk~aVr~~L~   52 (82)
T 1oyi_A           31 ATAAQLTRQLNMEKREVNKALY   52 (82)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            9999999999999999996554

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=86.56  E-value=1.4  Score=36.54  Aligned_cols=24  Identities=13%  Similarity=0.232  Sum_probs=21.4

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          562 KTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       562 ~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      .|+.+||..||||+.+|+++..+.
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            799999999999999999887543

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=86.50  E-value=4  Score=33.86  Aligned_cols=46  Identities=17%  Similarity=0.351  Sum_probs=31.5

Q ss_pred             HHHhcC-CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          537 KVLDTL-NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       537 ~aL~~L-~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..+..| ++....||.+-   ++  ++|..|||+.+|+|+.+|+    +.+++|.+
T Consensus        23 ~~~~~l~~~~r~~Il~~L---~~--~~~~~eLa~~l~is~~tv~----~~L~~L~~   69 (96)
T 1y0u_A           23 RYNYAVTNPVRRKILRML---DK--GRSEEEIMQTLSLSKKQLD----YHLKVLEA   69 (96)
T ss_dssp             HHHHHHSCHHHHHHHHHH---HT--TCCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHH---cC--CCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            344333 45555666654   22  3999999999999999999    45556654

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=86.20  E-value=1.5  Score=39.75  Aligned_cols=44  Identities=23%  Similarity=0.390  Sum_probs=33.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++.++.||.+-..  + ...|+.|||+.+|+|+.+|+    +-+++|.+
T Consensus         5 ~ld~~d~~il~~L~~--~-~~~s~~ela~~lg~s~~tv~----~~l~~L~~   48 (152)
T 2cg4_A            5 LIDNLDRGILEALMG--N-ARTAYAELAKQFGVSPETIH----VRVEKMKQ   48 (152)
T ss_dssp             CCCHHHHHHHHHHHH--C-TTSCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            478888888876432  2 24899999999999999999    44555544

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=85.82  E-value=1.5  Score=36.17  Aligned_cols=50  Identities=10%  Similarity=0.246  Sum_probs=33.6

Q ss_pred             HHHHHhcCC-HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          535 LEKVLDTLN-PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       535 L~~aL~~L~-~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +..++..|. +.+..||.+-  . .+.+.|..|||+.+|+|+.+|+    +.+++|.+
T Consensus        14 ~~~~~~~l~~~~~~~il~~l--~-~~~~~s~~ela~~l~is~~tvs----~~l~~L~~   64 (99)
T 3cuo_A           14 AAALLKAMSHPKRLLILCML--S-GSPGTSAGELTRITGLSASATS----QHLARMRD   64 (99)
T ss_dssp             HHHHHHHHCSHHHHHHHHHH--T-TCCSEEHHHHHHHHCCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHH--H-hCCCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            344444443 5566666543  2 3446999999999999999999    55556643

>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=85.66  E-value=2.5  Score=36.92  Aligned_cols=53  Identities=19%  Similarity=0.249  Sum_probs=38.3

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          533 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       533 ~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..+...+.  .|++.+..|+.+-+..+  .+.|..|||+.+|+|+.+|.    +.+++|.+
T Consensus        13 ~~~~~~~~~~gl~~~~~~il~~L~~~~--~~~t~~ela~~l~~~~stvs----~~l~~L~~   67 (152)
T 1ku9_A           13 ELFSELAKIHGLNKSVGAVYAILYLSD--KPLTISDIMEELKISKGNVS----MSLKKLEE   67 (152)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHCS--SCEEHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHcCCChhHHHHHHHHHHcC--CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            33444443  58999999887765333  35999999999999999999    55555543

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=85.59  E-value=0.79  Score=41.11  Aligned_cols=35  Identities=26%  Similarity=0.230  Sum_probs=26.3

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHH
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQ  580 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRq  580 (605)
                      ..|+.| .+|+.+-. .+    +|+.|||+.+|+|..||..
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    9999999999999999983

>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=85.55  E-value=1.1  Score=38.21  Aligned_cols=46  Identities=20%  Similarity=0.278  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .+.+....||...+-  .|.++|..|||+.+|+|+.+|+    +++++|...
T Consensus        15 ~~~~~~l~Il~~l~~--~g~~~s~~eLa~~lgvs~~tV~----~~L~~L~~~   60 (110)
T 1q1h_A           15 LLGDDVIDVLRILLD--KGTEMTDEEIANQLNIKVNDVR----KKLNLLEEQ   60 (110)
T ss_dssp             TSCSTTHHHHHHHHH--HCSCBCHHHHHHTTTSCHHHHH----HHHHHHHHH
T ss_pred             HcChHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHH----HHHHHHHHC
Confidence            355666677766543  2334899999999999999999    777887763

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=85.30  E-value=1.5  Score=33.53  Aligned_cols=29  Identities=10%  Similarity=0.154  Sum_probs=23.8

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHhHH
Q 007404          564 LQEIGELMGVSRERIRQIESSAFRKLKNKK  593 (605)
Q Consensus       564 l~EIAe~LGISrerVRqie~RALkKLR~~l  593 (605)
                      +.+||..|||++.+|+++... ...++..+
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            999999999999999998754 55666544

>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=85.28  E-value=1.4  Score=39.82  Aligned_cols=44  Identities=30%  Similarity=0.430  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++.++.||.+-.. + | +.|+.|||+.+|+|+.+|+    +-+++|.+
T Consensus         4 ~ld~~~~~iL~~L~~-~-~-~~s~~ela~~lg~s~~tv~----~~l~~L~~   47 (150)
T 2w25_A            4 ALDDIDRILVRELAA-D-G-RATLSELATRAGLSVSAVQ----SRVRRLES   47 (150)
T ss_dssp             CCCHHHHHHHHHHHH-C-T-TCCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH-c-C-CCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            488889888886532 2 2 4999999999999999999    44455543

>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=84.94  E-value=2  Score=37.56  Aligned_cols=52  Identities=17%  Similarity=0.236  Sum_probs=38.6

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcCC-CCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          532 KEDLEKVLDTLNPRERQVVRWRFGLED-GRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       532 ~~~L~~aL~~L~~rER~VL~LRyGl~d-g~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      ...|...+..|++.|+.|..+....-+ -..+|..|||+..|+|..+|-..-+
T Consensus         9 ~~~i~~~~~~ls~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~k   61 (111)
T 2o3f_A            9 LAIIQSMXHXLPPSERKLADYILAHPHXAIESTVNEISALANSSDAAVIRLCX   61 (111)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHhccCCHHHHHHHHHHHHChHHHHhcCHHHHHHHHCCCHHHHHHHHH
Confidence            345777788999999998875442200 0138999999999999999986554

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=84.92  E-value=1.9  Score=39.05  Aligned_cols=44  Identities=25%  Similarity=0.543  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++.++.||.+-..  ++ +.|+.|||+.+|+|+.+|++    -+++|.+
T Consensus         4 ~ld~~~~~il~~L~~--~~-~~s~~ela~~lg~s~~tv~~----~l~~L~~   47 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN--DG-KAPLREISKITGLAESTIHE----RIRKLRE   47 (151)
T ss_dssp             CCCHHHHHHHHHHHH--CT-TCCHHHHHHHHCSCHHHHHH----HHHHHHH
T ss_pred             CcCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHH----HHHHHHH
Confidence            478888888876432  22 49999999999999999994    4455544

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=84.84  E-value=1.9  Score=34.96  Aligned_cols=27  Identities=22%  Similarity=0.183  Sum_probs=23.0

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +.|..|||+.+|+|+.+|+    +.+++|.+
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            4899999999999999999    56666654

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=84.84  E-value=1.4  Score=40.29  Aligned_cols=38  Identities=18%  Similarity=0.172  Sum_probs=30.4

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      .|++.++.||.+-..  ++ +.|+.|||+.+|+|+.+|+.+
T Consensus         7 ~ld~~~~~il~~L~~--~~-~~s~~ela~~lg~s~~tv~~~   44 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE--NG-RLTNVELSERVALSPSPCLRR   44 (162)
T ss_dssp             CCCHHHHHHHHHHHH--CT-TCCHHHHHHHHTSCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHHHH
Confidence            488888888876543  22 389999999999999999944

>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=84.45  E-value=1.7  Score=39.14  Aligned_cols=43  Identities=12%  Similarity=0.266  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |++.++.||.+-  ..+ .+.|+.|||+.+|+|+.+|+    +-+++|.+
T Consensus         1 ld~~~~~il~~L--~~~-~~~~~~ela~~lg~s~~tv~----~~l~~L~~   43 (150)
T 2pn6_A            1 MDEIDLRILKIL--QYN-AKYSLDEIAREIRIPKATLS----YRIKKLEK   43 (150)
T ss_dssp             CCHHHHHHHHHH--TTC-TTSCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             CChHHHHHHHHH--HHc-CCCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            566777787653  222 25999999999999999999    44555544

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=84.24  E-value=2.3  Score=37.32  Aligned_cols=50  Identities=20%  Similarity=0.270  Sum_probs=35.8

Q ss_pred             HHHHHHHHHhc----CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          531 MKEDLEKVLDT----LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       531 l~~~L~~aL~~----L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      +...+...+..    |++.|..||..-+..+   +.|..|||+.+|+++.+|.+++.
T Consensus        20 ~~~~~~~~l~~~~~~lt~~~~~vL~~l~~~~---~~t~~eLa~~l~~~~~tvs~~l~   73 (142)
T 3ech_A           20 VRTRIQSELDCQRLDLTPPDVHVLKLIDEQR---GLNLQDLGRQMCRDKALITRKIR   73 (142)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHHTT---TCCHHHHHHHHC---CHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCCHHHHHHHHHHHhCC---CcCHHHHHHHhCCCHHHHHHHHH
Confidence            44556666664    9999999988776543   49999999999999999994443

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=84.07  E-value=1.6  Score=36.42  Aligned_cols=42  Identities=17%  Similarity=0.224  Sum_probs=28.7

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      .++.++.-+...|..++|  .|+.+||..+|||+.+|+++..+.
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

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=83.91  E-value=1  Score=46.12  Aligned_cols=35  Identities=14%  Similarity=0.284  Sum_probs=27.4

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404          548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  586 (605)
Q Consensus       548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL  586 (605)
                      .|..++|..+    +|.+|||+.||||+.|||..+..+.
T Consensus        12 ~ia~l~~~~~----~~~~ela~~l~vS~~tIrRdL~~l~   46 (315)
T 2w48_A           12 KIAQLYYEQD----MTQAQIARELGIYRTTISRLLKRGR   46 (315)
T ss_dssp             HHHHHHHTSC----CCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4666666544    9999999999999999996655543

>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=83.85  E-value=4.2  Score=34.44  Aligned_cols=50  Identities=10%  Similarity=0.227  Sum_probs=34.2

Q ss_pred             HHHHHHhcCC-HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          534 DLEKVLDTLN-PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       534 ~L~~aL~~L~-~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .+..++..|. +....||.+-.  ++  ++|..|||+.+|+|+.+|+    +.+++|++
T Consensus        15 ~~~~~~~~l~~~~r~~IL~~L~--~~--~~~~~ela~~l~is~stvs----~~L~~L~~   65 (106)
T 1r1u_A           15 RVTEIFKALGDYNRIRIMELLS--VS--EASVGHISHQLNLSQSNVS----HQLKLLKS   65 (106)
T ss_dssp             HHHHHHHHTCSHHHHHHHHHHH--HC--CBCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH--hC--CCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            4555566666 44455666543  22  3899999999999999999    44555553

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=83.10  E-value=3.6  Score=35.82  Aligned_cols=55  Identities=16%  Similarity=0.219  Sum_probs=39.3

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          531 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       531 l~~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +...+...+.  .|++.|..||..-+..+  .+.|..|||+.+|+|+.+|.    +.+++|-+
T Consensus        22 ~~~~~~~~~~~~~l~~~~~~iL~~l~~~~--~~~t~~~la~~l~~s~~~vs----~~l~~L~~   78 (146)
T 2fbh_A           22 WRAELDRRLSHLGLSQARWLVLLHLARHR--DSPTQRELAQSVGVEGPTLA----RLLDGLES   78 (146)
T ss_dssp             HHHHHHHHTGGGCCTTTHHHHHHHHHHCS--SCCBHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHcC--CCCCHHHHHHHhCCChhhHH----HHHHHHHH
Confidence            3344555554  48999988887763333  35999999999999999999    45555543

>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=82.75  E-value=3.7  Score=38.36  Aligned_cols=55  Identities=22%  Similarity=0.306  Sum_probs=40.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      +...+...+..|++.|..||..-+... +.+.|..+||+.+|+++.+|..    .+++|-
T Consensus        28 ~~~~~~~~~~~lt~~q~~vL~~L~~~~-~~~~t~~eLa~~l~is~~tvs~----~l~~Le   82 (189)
T 3nqo_A           28 IQIEGDKYFGILTSRQYMTILSILHLP-EEETTLNNIARKMGTSKQNINR----LVANLE   82 (189)
T ss_dssp             HHHHHHHHHCSSCHHHHHHHHHHHHSC-GGGCCHHHHHHHHTSCHHHHHH----HHHHHH
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHhcc-CCCcCHHHHHHHHCCCHHHHHH----HHHHHH
Confidence            344555666679999999998766421 2349999999999999999994    455554

>3sqn_A Conserved domain protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MGA family; 2.31A {Enterococcus faecalis}

Probab=82.72  E-value=1.5  Score=47.80  Aligned_cols=107  Identities=12%  Similarity=0.143  Sum_probs=57.3

Q ss_pred             CCCCCHHHHHHhcCCCHHHHHHHHhCCCCC----CCccccccccCCCCCCcccCCCCCCCHHHHHHHHHHHHHHHHHHhc
Q 007404          466 GRHPNNEEVAEATGLSMKRLHAVLLSPKAP----RSLDQKIGINQNLKPSEVIADPEAETAEDLLIKKFMKEDLEKVLDT  541 (605)
Q Consensus       466 gr~PT~eEIAe~lgis~e~V~~~l~~~~~~----~SLD~~i~~d~~~~l~d~l~D~~~~spEe~l~~~el~~~L~~aL~~  541 (605)
                      +..-|..+||+.+|+|...|+.-+..-+..    ..+..+   ..+.    .+..+......+          +   ...
T Consensus        30 ~~~it~~eLA~~L~VS~RTIr~dI~~In~~L~~~~~I~~~---~~Gy----~L~~~~~~~~~~----------~---~~~   89 (485)
T 3sqn_A           30 VPQLTAKRLAAQIQTTERTVFSDLQYIRSQLPADWSIETD---SSGI----RLRNQGNAQTNE----------L---WSL   89 (485)
T ss_dssp             CCSCBCGGGHHHHTSCHHHHHHHHHHHHTTCCTTEEEEEE---TTEE----EEEEC---CTHH----------H---HHH
T ss_pred             CCCcCHHHHHHHhCCCHHHHHHHHHHHHHhcccCcEEEEc---CCEE----EEecCcHHHHHH----------H---HHh
Confidence            344789999999999999998776422111    111110   1111    111110000000          1   122


Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      +++.+|....+.+.+.+ ++.|+.++|+.|.||+.||.+-    ++++++.+...+
T Consensus        90 ~~~~eR~~~Il~~LL~~-~~isi~~Lae~l~VS~sTi~~D----Lk~i~~~L~~y~  140 (485)
T 3sqn_A           90 FLPQSISIQLLKELLFT-KELVTTSFLSTSGVSYETLKRH----IKKMNQALRDFH  140 (485)
T ss_dssp             HGGGSHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHH----HHHHHHHHGGGT
T ss_pred             cCHHHHHHHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHHH----HHHHHHHHHHCC
Confidence            34444543333333322 3699999999999999999954    555555554433

>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=82.47  E-value=5.3  Score=36.74  Aligned_cols=49  Identities=24%  Similarity=0.265  Sum_probs=34.3

Q ss_pred             hcCCHHHHHHHHHHHhcC-CC---------CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          540 DTLNPRERQVVRWRFGLE-DG---------RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~-dg---------~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      ...+.++|-.-.+..... .+         -++|.++||..+|+|+++|.    |++++|++.
T Consensus       136 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~iA~~lg~sr~tvs----R~l~~L~~~  194 (210)
T 3ryp_A          136 AFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVG----RILKMLEDQ  194 (210)
T ss_dssp             HHSCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHH----HHHHHHHHT
T ss_pred             hhCCHHHHHHHHHHHHHHhcCcCCCCCceEeccCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence            456777776443332211 11         25899999999999999999    888888863

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=82.24  E-value=4.7  Score=34.78  Aligned_cols=54  Identities=13%  Similarity=0.148  Sum_probs=39.4

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          531 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       531 l~~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +...+...+.  .|++.+..||..-+..   .+.|..|||+.+|+|+.+|.    +.+++|.+
T Consensus        14 ~~~~~~~~~~~~~l~~~~~~iL~~l~~~---~~~~~~ela~~l~~s~~tvs----~~l~~L~~   69 (138)
T 3bpv_A           14 HRVFIGRELGHLNLTDAQVACLLRIHRE---PGIKQDELATFFHVDKGTIA----RTLRRLEE   69 (138)
T ss_dssp             HHHHHHHHSGGGTCCHHHHHHHHHHHHS---TTCBHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHc---CCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            3344555554  5899999988776643   24899999999999999999    45555543

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=82.12  E-value=4.5  Score=35.71  Aligned_cols=51  Identities=16%  Similarity=0.156  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          530 FMKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       530 el~~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      .+...+...+.  .|++.|..||..-+..+  .+.|..|||+.+|+++.+|..++
T Consensus        23 ~~~~~~~~~l~~~glt~~q~~vL~~l~~~~--~~~t~~eLa~~l~i~~~tvs~~l   75 (150)
T 3fm5_A           23 MVLGAVNKALVPTGLRVRSYSVLVLACEQA--EGVNQRGVAATMGLDPSQIVGLV   75 (150)
T ss_dssp             HHHHHHHHHHGGGTCCHHHHHHHHHHHHST--TCCCSHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHhCC--CCcCHHHHHHHHCCCHhHHHHHH
Confidence            34455555554  49999998888655332  34899999999999999999443

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=82.03  E-value=4.7  Score=34.83  Aligned_cols=44  Identities=7%  Similarity=0.092  Sum_probs=35.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++.+..||..-+..+   +.|..|||+.+|+|+.+|.    +.+++|.+
T Consensus        28 ~l~~~~~~iL~~l~~~~---~~~~~ela~~l~is~~~vs----~~l~~L~~   71 (142)
T 3bdd_A           28 GISLTRYSILQTLLKDA---PLHQLALQERLQIDRAAVT----RHLKLLEE   71 (142)
T ss_dssp             SSCHHHHHHHHHHHHHC---SBCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCC---CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            69999998888765433   4999999999999999999    45555544

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=81.88  E-value=1.5  Score=36.55  Aligned_cols=42  Identities=10%  Similarity=0.030  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHHHHHhc-CCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGL-EDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl-~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      .|+.++..||...+.. ++|.+.|..|||+.+|+++.+|.+++
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l   51 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLII   51 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            4788888888766543 33455899999999999999999443

>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=81.80  E-value=5.1  Score=34.60  Aligned_cols=51  Identities=12%  Similarity=0.051  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          530 FMKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       530 el~~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      .+...+...+.  .|++.|..||..-+..+   +.|..+||+.+|+++.+|.+++.
T Consensus        18 ~~~~~~~~~~~~~~lt~~~~~iL~~l~~~~---~~~~~~la~~l~~~~~tvs~~l~   70 (138)
T 1jgs_A           18 KKDRLLNEYLSPLDITAAQFKVLCSIRCAA---CITPVELKKVLSVDLGALTRMLD   70 (138)
T ss_dssp             HHHHHHHHHHTTTTSCHHHHHHHHHHHHHS---SBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHhhhcCCCHHHHHHHHHHHhcC---CCCHHHHHHHHCCChHHHHHHHH
Confidence            34455666664  49999999888766433   38999999999999999995443

>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=81.69  E-value=0.93  Score=41.31  Aligned_cols=40  Identities=18%  Similarity=0.018  Sum_probs=29.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      .++..+|.-|...+-.+    +|..+||+.||||+.||+.++.+
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    89999999999999999988754

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=81.65  E-value=3.5  Score=35.62  Aligned_cols=53  Identities=11%  Similarity=0.147  Sum_probs=38.7

Q ss_pred             HHHHHHHHh-cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          532 KEDLEKVLD-TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       532 ~~~L~~aL~-~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ...+...+. .|++.|..||..-+..+   +.|..|||+.+|+++.+|.    +.+++|-+
T Consensus        25 ~~~~~~~~~~~l~~~~~~iL~~l~~~~---~~t~~ela~~l~~~~~tvs----~~l~~L~~   78 (140)
T 2nnn_A           25 AALFANGIGNGLTPTQWAALVRLGETG---PCPQNQLGRLTAMDAATIK----GVVERLDK   78 (140)
T ss_dssp             HHHHHHHCSSCCCHHHHHHHHHHHHHS---SBCHHHHHHHTTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHcC---CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            334444444 69999998887765433   4999999999999999999    45555543

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=81.63  E-value=3  Score=34.61  Aligned_cols=50  Identities=12%  Similarity=0.148  Sum_probs=33.1

Q ss_pred             HHHHHHhcCCH-HHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          534 DLEKVLDTLNP-RERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       534 ~L~~aL~~L~~-rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .+..++..|.. ....||.+  ..+  .++|..|||+.+|+|+.+|+    +-|++|++
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            34555555554 44445543  222  35999999999999999998    55566654

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=81.60  E-value=5.4  Score=34.53  Aligned_cols=52  Identities=10%  Similarity=0.205  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          530 FMKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       530 el~~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      .+...+...+.  .|++.|..||..-+..+ +.+.|..|||+.+|+++.+|..++
T Consensus        15 ~~~~~~~~~~~~~~lt~~~~~vL~~l~~~~-~~~~t~~ela~~l~~~~~tvs~~l   68 (139)
T 3eco_A           15 EMKQKADQKLEQFDITNEQGHTLGYLYAHQ-QDGLTQNDIAKALQRTGPTVSNLL   68 (139)
T ss_dssp             HHHHHHHHHHGGGTCCHHHHHHHHHHHHST-TTCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHhcC-CCCcCHHHHHHHhCCCcccHHHHH
Confidence            34455555554  49999999988766542 235999999999999999999443

>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=81.58  E-value=6.1  Score=34.16  Aligned_cols=56  Identities=4%  Similarity=0.122  Sum_probs=40.9

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          531 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       531 l~~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +...+...+.  .|++.|..||..-+..+ +.+.|..|||+.+|+++.+|.    +.+++|-+
T Consensus        19 ~~~~~~~~~~~~~lt~~~~~iL~~l~~~~-~~~~~~~ela~~l~~~~~tvs----~~l~~Le~   76 (141)
T 3bro_A           19 MSTRFDIFAKKYDLTGTQMTIIDYLSRNK-NKEVLQRDLESEFSIKSSTAT----VLLQRMEI   76 (141)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHTT-TSCCBHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHCC-CCCcCHHHHHHHHCCCcchHH----HHHHHHHH
Confidence            3444555554  58999999888766543 336999999999999999998    45555544

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=81.56  E-value=5.4  Score=35.32  Aligned_cols=48  Identities=19%  Similarity=0.191  Sum_probs=36.0

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          533 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       533 ~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      ..+...+.  .|++.|..||..-+..+   +.|..|||+.+|+++.+|.+++.
T Consensus        28 ~~~~~~~~~~~lt~~q~~iL~~l~~~~---~~~~~eLa~~l~~~~~~vs~~l~   77 (149)
T 4hbl_A           28 QFYEKKLKQFGITYSQYLVMLTLWEEN---PQTLNSIGRHLDLSSNTLTPMLK   77 (149)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHSS---SEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHCC---CCCHHHHHHHHCCCHHHHHHHHH
Confidence            33444443  59999999888766443   48999999999999999994443

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=81.39  E-value=5.8  Score=35.32  Aligned_cols=50  Identities=10%  Similarity=0.114  Sum_probs=37.3

Q ss_pred             HHHHHHHHH---hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          531 MKEDLEKVL---DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       531 l~~~L~~aL---~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      +...+...+   ..|++.|..||..-+..+   +.|..|||+.+|+++.+|.+++.
T Consensus        33 ~~~~~~~~l~~~~~lt~~~~~iL~~l~~~~---~~t~~ela~~l~is~~tvs~~l~   85 (162)
T 2fa5_A           33 ISGNIAKVYGDRYGMAIPEWRVITILALYP---GSSASEVSDRTAMDKVAVSRAVA   85 (162)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHHHHHST---TCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHhCC---CCCHHHHHHHHCCCHHHHHHHHH
Confidence            334455555   369999999988766432   49999999999999999995443

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=81.37  E-value=2.3  Score=39.66  Aligned_cols=45  Identities=22%  Similarity=0.302  Sum_probs=33.1

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..|++.++.||.+-..  ++ ..|+.|||+.+|+|+.+|+    +-+++|.+
T Consensus        13 ~~ld~~d~~IL~~L~~--~~-~~s~~eLA~~lglS~~tv~----~~l~~L~~   57 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKK--DA-RLTISELSEQLKKPESTIH----FRIKKLQE   57 (171)
T ss_dssp             -CCCHHHHHHHHHHHH--CT-TCCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH--cC-CCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            3578888888876432  22 4899999999999999999    44455543

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=81.31  E-value=3.1  Score=33.51  Aligned_cols=46  Identities=2%  Similarity=0.087  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELM-----GVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~L-----GISrerVRqie~RALkKLR~  591 (605)
                      .++++...||.+-... ++.+.|..||++.+     +||..||+    |.|+.|.+
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            4788887787754322 11469999999999     99999999    66666655

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=81.12  E-value=5.3  Score=35.02  Aligned_cols=48  Identities=15%  Similarity=0.243  Sum_probs=36.5

Q ss_pred             HHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          532 KEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       532 ~~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      ...+...+.  .|++.|..||..-+..+   +.|..|||+.+|+++.+|.+++
T Consensus        28 ~~~~~~~~~~~~l~~~~~~iL~~l~~~~---~~t~~ela~~l~~~~~tvs~~l   77 (150)
T 2rdp_A           28 KQRGREILTNYPITPPQFVALQWLLEEG---DLTVGELSNKMYLACSTTTDLV   77 (150)
T ss_dssp             HHHHHHHHTTSSSCHHHHHHHHHHHHHC---SBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHcC---CCCHHHHHHHHCCCchhHHHHH
Confidence            344555554  58999998887765432   4999999999999999999544

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=80.69  E-value=4.9  Score=34.93  Aligned_cols=63  Identities=16%  Similarity=0.239  Sum_probs=44.0

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhcC-CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHhHHh
Q 007404          532 KEDLEKVLDTLNPRERQVVRWRFGLE-DGRMKTLQEIGELMGVSRERIRQIESS----AFRKLKNKKR  594 (605)
Q Consensus       532 ~~~L~~aL~~L~~rER~VL~LRyGl~-dg~~~Tl~EIAe~LGISrerVRqie~R----ALkKLR~~l~  594 (605)
                      ...|...+..|++.|+.|...-.-.. .-..+|..|||+..|+|..+|-..-++    ...-||..+.
T Consensus         5 ~~~I~~~~~~lt~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~gf~efk~~l~   72 (107)
T 3iwf_A            5 LYKIDNQYPYFTKNEKKIAQFILNYPHKVVNMTSQEIANQLETSSTSIIRLSKKVTPGGFNELKTRLS   72 (107)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHHHCHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHhCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            45677888999999999986543221 013499999999999999999854433    4444554443

>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=80.35  E-value=5.4  Score=34.70  Aligned_cols=51  Identities=22%  Similarity=0.242  Sum_probs=37.6

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          533 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       533 ~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ..+...+.  .|++.|..||..-+  +  .+.|..|||+.+|+|+.+|.    +.+++|.+
T Consensus        24 ~~~~~~~~~~~l~~~~~~iL~~l~--~--~~~~~~ela~~l~~s~~tvs----~~l~~Le~   76 (146)
T 2gxg_A           24 RELNRRLGELNLSYLDFLVLRATS--D--GPKTMAYLANRYFVTQSAIT----ASVDKLEE   76 (146)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHT--T--SCBCHHHHHHHTTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHh--c--CCcCHHHHHHHhCCCchhHH----HHHHHHHH
Confidence            33444453  49999999887765  2  24999999999999999999    45555543

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=80.33  E-value=4.1  Score=35.62  Aligned_cols=49  Identities=16%  Similarity=0.108  Sum_probs=36.8

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          531 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       531 l~~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      +...+...+.  .|++.|..||..-+..+   +.|..|||+.+|+++.+|.+++
T Consensus        22 ~~~~~~~~~~~~~lt~~~~~iL~~l~~~~---~~t~~eLa~~l~~~~~~vs~~l   72 (143)
T 3oop_A           22 MHLFLMRSIASYDVTPEQWSVLEGIEANE---PISQKEIALWTKKDTPTVNRIV   72 (143)
T ss_dssp             HHHHHHHHTTTSSSCHHHHHHHHHHHHHS---SEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhhhCCCCHHHHHHHHHHHHcC---CcCHHHHHHHHCCCHhhHHHHH
Confidence            3344455554  48999999988766443   4899999999999999999443

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=80.28  E-value=5.5  Score=35.17  Aligned_cols=46  Identities=2%  Similarity=-0.010  Sum_probs=35.2

Q ss_pred             HHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          534 DLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       534 ~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      .+...+.  .|++.|..||..-+..+   +.|..|||+.+|+++.+|.+++
T Consensus        29 ~~~~~~~~~~lt~~~~~iL~~l~~~~---~~t~~eLa~~l~~~~~tvs~~l   76 (154)
T 2qww_A           29 YADQNAASLGLTIQQLAMINVIYSTP---GISVADLTKRLIITGSSAAANV   76 (154)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHST---TEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHHHCC---CCCHHHHHHHHCCCHHHHHHHH
Confidence            3444443  59999999988766432   4999999999999999999443

---

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	605
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	7e-28
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	2e-27
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	7e-26
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	1e-20
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	3e-20
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	4e-18
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	9e-12
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	4e-10
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	1e-08
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	3e-07
d1or7a1	68	a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escheri	7e-07
d1yioa1	70	a.4.6.2 (A:131-200) Response regulatory protein St	2e-06
d1a04a1	67	a.4.6.2 (A:150-216) Nitrate/nitrite response regul	1e-04
d1l3la1	65	a.4.6.2 (A:170-234) Quorum-sensing transcription f	4e-04
d1p4wa_	87	a.4.6.2 (A:) Transcriptional regulator RcsB {Erwin	4e-04
d1s7oa_	106	a.4.13.3 (A:) Hypothetical protein SPy1201 {Strept	0.002
d1fsea_	67	a.4.6.2 (A:) Germination protein GerE {Bacillus su	0.003

>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 =  112 bits (280), Expect = 7e-28
 Identities = 37/72 (51%), Positives = 54/72 (75%)

Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
            K +M+ +N+RLVISIAK Y   G+   DL+QEG  GL++  +KF+  +G+KFSTYA WW
Sbjct: 263 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 322

Query: 426 IKQAVRKSLSDQ 437
           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 =  106 bits (266), Expect = 2e-27
 Identities = 55/181 (30%), Positives = 90/181 (49%), Gaps = 32/181 (17%)

Query: 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK------------------LEGLREV 331
           SDP+R YL        LLT  EE+ L+  +++ ++                  +   + +
Sbjct: 1   SDPVRQYLH-EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKIL 59

Query: 332 LSERCGGSPTFAQWAAAAGVDQ------------RELRRRLNYGILCKDKMITSNIRLVI 379
            + R    P   +      V++            +        G   +  +I +N+RLV+
Sbjct: 60  GTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVV 119

Query: 380 SIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 439
           SIAK Y G G++  DL+QEG +GL+R  EKF+  + FKFSTYA WWI+QA+ ++++DQ+R
Sbjct: 120 SIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQAR 179

Query: 440 T 440
           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 = 99.0 bits (247), Expect = 7e-26
 Identities = 40/75 (53%), Positives = 56/75 (74%)

Query: 527 IKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF 586
           ++  M+E+LEKVL TL+PRE  V+R R+GL DG+ KTL+E+G+   V+RERIRQIE  A 
Sbjct: 4   MRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKAL 63

Query: 587 RKLKNKKRTKHLMQY 601
           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 = 83.6 bits (207), Expect = 1e-20
 Identities = 29/64 (45%), Positives = 43/64 (67%)

Query: 538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH 597
           VL  L  RE +V+R RFG++     TL+E+G+   V+RERIRQIE+ A RKL++  R++ 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61

Query: 598 LMQY 601
           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 = 82.4 bits (204), Expect = 3e-20
 Identities = 33/57 (57%), Positives = 41/57 (71%)

Query: 534 DLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           +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 = 77.3 bits (190), Expect = 4e-18
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 367 KDKMITSNIRLVISIAKNYQG---AGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAH 423
           ++++I   + LV +IA N +      ++++DL+  G  GL++  +        +   Y  
Sbjct: 12  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 71

Query: 424 WWIKQAVRKSLSDQS 438
             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 = 58.7 bits (142), Expect = 9e-12
 Identities = 15/70 (21%), Positives = 37/70 (52%), Gaps = 4/70 (5%)

Query: 523 EDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE 582
           E+ +IK+ + E +++ +  L  RE+ V++  F          +E+ +++  S  R+ Q++
Sbjct: 3   EEEVIKRELTEKVKEAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLK 58

Query: 583 SSAFRKLKNK 592
           + 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 = 53.5 bits (129), Expect = 4e-10
 Identities = 25/60 (41%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSM--KRLHAVLLSPKAPRSL 498
           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 = 49.3 bits (118), Expect = 1e-08
 Identities = 11/51 (21%), Positives = 26/51 (50%)

Query: 439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL 489
            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 = 45.9 bits (109), Expect = 3e-07
 Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 8/68 (11%)

Query: 438 SRTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVL--LSPKAP 495
           SR +R      E   R+KE  ++L  + GR P +EEVA+  G+S + L   L  ++    
Sbjct: 2   SRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI 55

Query: 496 RSLDQKIG 503
            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 = 44.7 bits (106), Expect = 7e-07
 Identities = 11/69 (15%), Positives = 29/69 (42%), Gaps = 4/69 (5%)

Query: 524 DLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES 583
           +L++ + +++ + + +++L    R  +  R         + +EI  +M      +R    
Sbjct: 1   NLMLSEELRQIVFRTIESLPEDLRMAITLRELDG----LSYEEIAAIMDCPVGTVRSRIF 56

Query: 584 SAFRKLKNK 592
            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 = 43.5 bits (103), Expect = 2e-06
 Identities = 13/72 (18%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 532 KEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN 591
           ++ LE++  +L  RE+QV++       G     ++I   +G++   ++    +  +KL  
Sbjct: 3   QDQLEQLFSSLTGREQQVLQL---TIRG--LMNKQIAGELGIAEVTVKVHRHNIMQKLNV 57

Query: 592 KKRTKHLMQYAI 603
           +    +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 = 38.6 bits (90), Expect = 1e-04
 Identities = 11/68 (16%), Positives = 27/68 (39%), Gaps = 6/68 (8%)

Query: 536 EKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRT 595
           E+ ++ L PRER +++        +    + I   + ++   ++       +K+K K R 
Sbjct: 1   ERDVNQLTPRERDILKLI-----AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRV 55

Query: 596 KHLMQYAI 603
                +  
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 = 37.1 bits (86), Expect = 4e-04
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 6/63 (9%)

Query: 541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQ 600
            L+P+E   +RW   +  G  KT++EI ++ GV    +R     A ++   + +  HL  
Sbjct: 4   WLDPKEATYLRW---IAVG--KTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKA-HLTA 57

Query: 601 YAI 603
            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 = 37.5 bits (87), Expect = 4e-04
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 6/62 (9%)

Query: 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
           L+P+E +V+R      +G    + EI + +  S + I   + SA  KL        L+ Y
Sbjct: 23  LSPKESEVLRL---FAEG--FLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDI-ALLNY 76

Query: 602 AI 603
             
Sbjct: 77  LS 78

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]} Length = 106

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]

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 13/70 (18%), Positives = 26/70 (37%), Gaps = 4/70 (5%)

Query: 531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK 590
           M    E     L  ++   +   +  +D    +L EI +  GVSR+ +        + L+
Sbjct: 6   MNALFEFYAALLTDKQMNYIELYY-ADD---YSLAEIADEFGVSRQAVYDNIKRTEKILE 61

Query: 591 NKKRTKHLMQ 600
             +   H+  
Sbjct: 62  TYEMKLHMYS 71

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]} 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: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 6/62 (9%)

Query: 542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQY 601
           L  RER+V      L   +    +EI   + +S + +R   S+A +KL  K R+   +  
Sbjct: 5   LTKREREVFEL---LVQDKT--TKEIASELFISEKTVRNHISNAMQKLGVKGRS-QAVVE 58

Query: 602 AI 603
            +
Sbjct: 59  LL 60

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	605
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.98
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.82
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.75
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.61
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.6
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.51
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.38
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.2
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.17
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.1
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.79
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.77
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.77
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.66
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.33
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.14
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	97.87
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.76
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.67
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.29
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	95.41
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	93.69
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	93.53
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	93.04
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	92.6
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	92.02
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	91.73
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.54
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	89.85
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	89.62
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	89.48
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	89.32
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	88.89
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	88.66
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	88.49
d1zyba1	73	Probable transcription regulator BT4300, C-termina	88.27
d1hlva1	66	DNA-binding domain of centromere binding protein B	88.06
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	87.99
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	87.85
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	86.84
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	86.84
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	86.57
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	86.51
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	86.08
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	85.43
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	83.03
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	82.87
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	82.78
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	82.25
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	82.16
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	81.97
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	81.92
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	81.53
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	81.53
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	81.49
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	81.27
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	81.14
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	80.78
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	80.73
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	80.65
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	80.4
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	80.38
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	80.05

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=99.98  E-value=1e-32  Score=263.37  Aligned_cols=149  Identities=37%  Similarity=0.648  Sum_probs=121.9

Q ss_pred             CCHHH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHhHHHHHH------------------hhcCCCCchHHHHHhhcC
Q 007404          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLS------------------ERCGGSPTFAQWAAAAGV  351 (605)
Q Consensus       291 ~d~l~-yL~~i~~~~~lLT~eEE~eL~~~iq~~~~le~~~~~L~------------------~~~G~~pt~~ewA~a~g~  351 (605)
                      +||++ ||++| +++||||++||++|+++|+.++.+.....+..                  ...+..|...+|......
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            48999 99999 99999999999999999998665433222111                  112344444444433221


Q ss_pred             ------------CHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcch
Q 007404          352 ------------DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFS  419 (605)
Q Consensus       352 ------------d~~~L~~~l~~g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFS  419 (605)
                                  ..+.+.+....|..|+++||.+|++||++||++|.+.|.+++||||||+||||+|+++|||++|++|+
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                        23445566778899999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHhhcccc
Q 007404          420 TYAHWWIKQAVRKSLSDQSRT  440 (605)
Q Consensus       420 TYA~~wIRqaI~r~ir~~sr~  440 (605)
                      |||+||||++|.+++++++|+
T Consensus       160 tya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         160 TYATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHHhCCC
Confidence            999999999999999998874

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

Probab=99.82  E-value=7.6e-21  Score=195.56  Aligned_cols=75  Identities=49%  Similarity=0.936  Sum_probs=72.4

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhc
Q 007404          363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ  437 (605)
Q Consensus       363 g~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~  437 (605)
                      ...|+++||+.|+|||++||++|.++|++++||+|+|++|||+|+++|||.+|++|+|||+||||++|.++|+++
T Consensus       260 ~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         260 ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHHHHHHhCC
Confidence            367999999999999999999999999999999999999999999999999999999999999999999999874

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.75  E-value=9.2e-19  Score=148.28  Aligned_cols=76  Identities=21%  Similarity=0.364  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCC---CCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHhhccc
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQGA---GMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR  439 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~~~---g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir~~sr  439 (605)
                      ...+++||..|++||.++|.+|.++   +++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|.+++|+..|
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            4468999999999999999998764   789999999999999999999999999999999999999999999998653

>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=99.61  E-value=1.5e-16  Score=134.45  Aligned_cols=74  Identities=54%  Similarity=0.818  Sum_probs=70.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhcc
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAIT  604 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~~  604 (605)
                      +++.|..+|+.|+++|+.||.+|||++|++|+|+.|||+.||||+++|||++.+|++|||.......|+.|+++
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            45678999999999999999999999999999999999999999999999999999999999988999999874

>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=99.60  E-value=1.2e-16  Score=129.05  Aligned_cols=66  Identities=44%  Similarity=0.674  Sum_probs=63.4

Q ss_pred             HHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhhHhhhhc
Q 007404          538 VLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKHLMQYAI  603 (605)
Q Consensus       538 aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~L~~yl~  603 (605)
                      +|+.|+++|+.||.+|||+++++++|++|||+.||||+++|||++.+|++|||+......|++|++
T Consensus         2 ~L~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr~~~~~~~L~~yl~   67 (68)
T d2p7vb1           2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD   67 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTTC
T ss_pred             hhhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHhc
Confidence            468899999999999999999999999999999999999999999999999999999999999986

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=99.51  E-value=3.1e-15  Score=118.24  Aligned_cols=58  Identities=57%  Similarity=0.826  Sum_probs=54.7

Q ss_pred             HHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          535 LEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       535 L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      |.++|+.|+++|+.||.+|||+++++++|++|||+.||||+++|||++.+|++|||+.
T Consensus         2 l~~~L~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR~~   59 (61)
T d1ku3a_           2 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH   59 (61)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcC
Confidence            3457899999999999999999999999999999999999999999999999999974

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.38  E-value=6.9e-13  Score=106.39  Aligned_cols=70  Identities=23%  Similarity=0.406  Sum_probs=66.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          521 TAEDLLIKKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       521 spEe~l~~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      +|++.+...+....|..+|+.||+++|+||.++|+.+    +|++|||+.||+|.++|+++.+||+++||+.+.
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            3678888899999999999999999999999999988    999999999999999999999999999999875

>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=99.17  E-value=4e-11  Score=95.57  Aligned_cols=63  Identities=16%  Similarity=0.153  Sum_probs=58.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHh
Q 007404          528 KKFMKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKR  594 (605)
Q Consensus       528 ~~el~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~  594 (605)
                      .++....|..+|+.||+++|+||.++|+.+    +|++|||+.||+|.++|+++.+||+++||+.++
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            356678899999999999999999999998    999999999999999999999999999999764

>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=99.10  E-value=6.5e-11  Score=92.75  Aligned_cols=58  Identities=43%  Similarity=0.661  Sum_probs=55.0

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcC--CCHHHHHHHHhCCCCCCCc
Q 007404          441 IRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATG--LSMKRLHAVLLSPKAPRSL  498 (605)
Q Consensus       441 IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lg--is~e~V~~~l~~~~~~~SL  498 (605)
                      ||+|+|+.+.+++++++.++|.+++||+||.+|||+.+|  +++++|++++..++.++||
T Consensus         1 IRlPvH~~e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~~~p~SL   60 (60)
T d1ku2a1           1 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL   60 (60)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGSSSCCCC
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHccCCCCC
Confidence            799999999999999999999999999999999999997  5588999999999999986

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=98.79  E-value=1e-08  Score=88.84  Aligned_cols=53  Identities=15%  Similarity=0.197  Sum_probs=49.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      -||++||.||.|||..|    +|+.|||+.||||+++|+++++||+++||+....-+
T Consensus        18 LLpe~QR~vl~L~~~e~----ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~ye~kL~   70 (106)
T d1xsva_          18 LLTNKQRNYLELFYLED----YSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLE   70 (106)
T ss_dssp             GSCHHHHHHHHHHHTSC----CCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hCCHHHHHHHHHHHHhC----CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence            49999999999999988    999999999999999999999999999999765443

>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=98.77  E-value=1.1e-08  Score=88.63  Aligned_cols=54  Identities=19%  Similarity=0.258  Sum_probs=49.2

Q ss_pred             hcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHhhhh
Q 007404          540 DTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKNKKRTKH  597 (605)
Q Consensus       540 ~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~l~~~~  597 (605)
                      +-||++||.||.|+|+.|    +|++|||+.||||+++|+++++||+++||+...+-+
T Consensus        15 ~lLp~~qR~v~~L~y~~~----ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~e~kL~   68 (106)
T d1s7oa_          15 ALLTDKQMNYIELYYADD----YSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLH   68 (106)
T ss_dssp             GGSCHHHHHHHHHHHHTC----CCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hhCCHHHHHHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence            349999999999999988    999999999999999999999999999998655433

>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=98.77  E-value=4.2e-09  Score=81.37  Aligned_cols=52  Identities=21%  Similarity=0.369  Sum_probs=49.9

Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHh
Q 007404          439 RTIRLPFHMVEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLL  490 (605)
Q Consensus       439 r~IRlP~~~~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~  490 (605)
                      .+||+|.|+.+.++|++++.++|.+++||+||.+|||+.||+++++|..++.
T Consensus         2 g~IrvPr~~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~   53 (57)
T d1l0oc_           2 GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQE   53 (57)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCEeCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4799999999999999999999999999999999999999999999998875

>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=98.66  E-value=1.6e-08  Score=81.34  Aligned_cols=70  Identities=13%  Similarity=0.070  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHhhhccCCcCCCcchhHHHHHHHHHHHHHHh
Q 007404          364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLS  435 (605)
Q Consensus       364 ~~A~e~LI~~nlrLVvsIAkrY~~~g~d~eDLIQEG~IGLirA~ekFDp~kG~rFSTYA~~wIRqaI~r~ir  435 (605)
                      ..+|++++..|.+.++.+|+++.++..+++|++||.++.+|+..++|++.  .+|.+|++..++|.+++++|
T Consensus         6 ~~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   75 (75)
T d1h3la_           6 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYR   75 (75)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHhC
Confidence            56799999999999999999999999999999999999999999999875  46999999999999998764

>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=98.33  E-value=2.2e-08  Score=81.44  Aligned_cols=68  Identities=31%  Similarity=0.319  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHhcCCCHHHHHHHHhC--CCCCCCccccccccCCCCCCcccCC
Q 007404          448 VEATYRVKEARKQLYSENGRHPNNEEVAEATGLSMKRLHAVLLS--PKAPRSLDQKIGINQNLKPSEVIAD  516 (605)
Q Consensus       448 ~~~i~ki~ka~~~L~~elgr~PT~eEIAe~lgis~e~V~~~l~~--~~~~~SLD~~i~~d~~~~l~d~l~D  516 (605)
                      .+.+++++++...|.+++||.||.+|||+.|||++++|.+++..  ...++|||.+++++ +..+.+++++
T Consensus         6 r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~d~-~~~~~e~lps   75 (77)
T d1rp3a1           6 REKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDF-ARDYSELIPS   75 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHTTTGGG
T ss_pred             HHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCccCC-CCchhccCCC
Confidence            46788999999999999999999999999999999999999864  34678999877543 3345566654

>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=98.14  E-value=3e-06  Score=67.41  Aligned_cols=55  Identities=20%  Similarity=0.346  Sum_probs=48.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          531 MKEDLEKVLDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       531 l~~~L~~aL~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      ..+.+...++.|+|+|++|+.+. ..|    +|.+|||+.||||..||+.+..++++||-
T Consensus         2 ~~~~~~~~~~~LT~rE~~vl~~l-~~G----~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   56 (70)
T d1yioa1           2 TQDQLEQLFSSLTGREQQVLQLT-IRG----LMNKQIAGELGIAEVTVKVHRHNIMQKLN   56 (70)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHH-TTT----CCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             cHHHHHHHHccCCHHHHHHHHHH-HcC----CCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            34667888899999999999884 334    99999999999999999999999999985

>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=97.87  E-value=1.2e-05  Score=63.20  Aligned_cols=48  Identities=17%  Similarity=0.315  Sum_probs=42.9

Q ss_pred             HhcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          539 LDTLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       539 L~~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +..|+|+|++|+.+.- .|    +|.+|||+.||||..||+++..++++||.-
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            5689999999998753 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=2.4e-05  Score=60.98  Aligned_cols=46  Identities=28%  Similarity=0.549  Sum_probs=41.3

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++||.+. ..|    +|.+|||+.||+|..||+.+..++++||.-
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 444    999999999999999999999999999853

>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=97.67  E-value=3.8e-05  Score=60.10  Aligned_cols=46  Identities=33%  Similarity=0.349  Sum_probs=41.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|+++|++|+.+. ..|    +|.+|||+.||+|..||+.+..+.++||--
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=97.29  E-value=0.00018  Score=59.06  Aligned_cols=45  Identities=29%  Similarity=0.302  Sum_probs=41.2

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLK  590 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR  590 (605)
                      .|+++|++|+.+.. .|    ++.+|||+.|++|..||+.+..++++||.
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            59999999998854 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=0.0072  Score=47.43  Aligned_cols=42  Identities=21%  Similarity=0.234  Sum_probs=35.6

Q ss_pred             cCCHHHHHHHHH--HHhcCCCCCCCHHHHHHHHCC-CHHHHHHHH
Q 007404          541 TLNPRERQVVRW--RFGLEDGRMKTLQEIGELMGV-SRERIRQIE  582 (605)
Q Consensus       541 ~L~~rER~VL~L--RyGl~dg~~~Tl~EIAe~LGI-SrerVRqie  582 (605)
                      .|+++|++||..  .|....|-|-|++||++.||+ |..+|+.++
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            589999999875  455667888999999999999 899999664

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=93.69  E-value=0.045  Score=39.51  Aligned_cols=37  Identities=11%  Similarity=0.251  Sum_probs=29.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      .|++.+.+-++-.+-.|    .|..+||..||||+.||..+
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            47777777776666544    89999999999999999864

>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=93.53  E-value=0.051  Score=40.57  Aligned_cols=39  Identities=21%  Similarity=0.314  Sum_probs=33.6

Q ss_pred             HHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHHh
Q 007404          323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN  361 (605)
Q Consensus       323 ~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l~  361 (605)
                      .++.+...+|...+|++||..|.|+++|++.+.+...+.
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            456678889999999999999999999999988876654

>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=93.04  E-value=0.095  Score=39.71  Aligned_cols=42  Identities=21%  Similarity=0.462  Sum_probs=31.1

Q ss_pred             CHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          543 NPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       543 ~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +....+||.+-   .++...|.+|+|+.||||+.+|+    +-+++|++
T Consensus         4 ~~~~~~iL~~L---~~~~~~s~~eLa~~l~vS~~ti~----r~i~~L~~   45 (63)
T d1biaa1           4 NTVPLKLIALL---ANGEFHSGEQLGETLGMSRAAIN----KHIQTLRD   45 (63)
T ss_dssp             CHHHHHHHHHH---TTSSCBCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             cHHHHHHHHHH---HHCCcCCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            34555566543   34567999999999999999999    55666765

>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=92.60  E-value=0.085  Score=41.28  Aligned_cols=38  Identities=29%  Similarity=0.414  Sum_probs=33.1

Q ss_pred             HHHHhHHHHHHhhcCCCCchHHHHHhhcCCHHHHHHHH
Q 007404          323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL  360 (605)
Q Consensus       323 ~~le~~~~~L~~~~G~~pt~~ewA~a~g~d~~~L~~~l  360 (605)
                      .++++....|...+|++||..|.|...||+.+.+.+.+
T Consensus        10 ~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l   47 (77)
T d1rp3a1          10 RRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTL   47 (77)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence            45778889999999999999999999999988776654

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=92.02  E-value=0.2  Score=37.71  Aligned_cols=37  Identities=22%  Similarity=0.314  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      |++.+++||..--..   ...|+.|||+.+|+|..+|+.+
T Consensus         3 lD~~D~~IL~~L~~~---~r~s~~eiA~~l~ls~~~v~~R   39 (63)
T d2cg4a1           3 IDNLDRGILEALMGN---ARTAYAELAKQFGVSPETIHVR   39 (63)
T ss_dssp             CCHHHHHHHHHHHHC---TTSCHHHHHHHHTSCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHc---CCCCHHHHHHHHCcCHHHHHHH
Confidence            677888898875432   2489999999999999999944

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=91.73  E-value=0.18  Score=38.08  Aligned_cols=38  Identities=13%  Similarity=0.216  Sum_probs=30.1

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      +|++.++.||..--.  | ...|+.|||+.+|+|+.+|.++
T Consensus         2 klD~~D~~IL~~L~~--n-~r~s~~~iA~~lgis~~tv~~R   39 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK--D-SRLSMRELGRKIKLSPPSVTER   39 (63)
T ss_dssp             CCCHHHHHHHHHHHH--C-SCCCHHHHHHHHTCCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHH
Confidence            477888888876532  2 2489999999999999999943

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.54  E-value=0.2  Score=37.34  Aligned_cols=37  Identities=19%  Similarity=0.381  Sum_probs=29.0

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      |++.++.||.+--.  | ...|+.|||+.+|+|+++|.++
T Consensus         1 lD~~D~kIl~~L~~--n-~r~s~~~lA~~~gls~~~v~~R   37 (60)
T d1i1ga1           1 IDERDKIILEILEK--D-ARTPFTEIAKKLGISETAVRKR   37 (60)
T ss_dssp             CCSHHHHHHHHHHH--C-TTCCHHHHHHHHTSCHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHH
Confidence            46678888886543  2 2389999999999999999943

>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=89.85  E-value=0.14  Score=40.06  Aligned_cols=28  Identities=32%  Similarity=0.460  Sum_probs=25.5

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          561 MKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      |+|.+|||..+|+|+++|.    |+|++|++.
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            6899999999999999999    888888874

>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=89.62  E-value=0.36  Score=36.18  Aligned_cols=39  Identities=26%  Similarity=0.411  Sum_probs=30.7

Q ss_pred             HHHHhHHHHHHhhcCCCCchHHHHHhhc--CCHHHHHHHHh
Q 007404          323 LKLEGLREVLSERCGGSPTFAQWAAAAG--VDQRELRRRLN  361 (605)
Q Consensus       323 ~~le~~~~~L~~~~G~~pt~~ewA~a~g--~d~~~L~~~l~  361 (605)
                      -++.+...+|...+|++||.+|.|++.|  ++.+.+...+.
T Consensus        12 ~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~   52 (60)
T d1ku2a1          12 NKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLK   52 (60)
T ss_dssp             HHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGG
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHH
Confidence            4566788899999999999999999997  45666655543

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=89.48  E-value=0.48  Score=35.04  Aligned_cols=37  Identities=19%  Similarity=0.412  Sum_probs=28.1

Q ss_pred             CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHH
Q 007404          542 LNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQI  581 (605)
Q Consensus       542 L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqi  581 (605)
                      |++-++.||..--.  | ...|+.|||+.+|+|+.+|..+
T Consensus         1 lD~~D~~Il~~L~~--n-~r~s~~eiA~~l~ls~~~v~~R   37 (60)
T d2cyya1           1 LDEIDKKIIKILQN--D-GKAPLREISKITGLAESTIHER   37 (60)
T ss_dssp             CCHHHHHHHHHHHH--C-TTCCHHHHHHHHCSCHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHH
Confidence            45667778776432  2 3489999999999999999943

>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=89.32  E-value=0.15  Score=38.86  Aligned_cols=27  Identities=37%  Similarity=0.599  Sum_probs=24.3

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          561 MKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      ++|.+|||..+|+|+++|.    |.|++|++
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    77788776

>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=88.89  E-value=0.19  Score=39.29  Aligned_cols=29  Identities=24%  Similarity=0.382  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      -++|.+|||..+|+|+++|.    |++++|++.
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            36899999999999999999    888888874

>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=88.66  E-value=0.2  Score=40.48  Aligned_cols=42  Identities=26%  Similarity=0.233  Sum_probs=33.2

Q ss_pred             cCCHHHHHHHHHH--HhcCCCCCCCHHHHHHHHC--CCHHHHHHHH
Q 007404          541 TLNPRERQVVRWR--FGLEDGRMKTLQEIGELMG--VSRERIRQIE  582 (605)
Q Consensus       541 ~L~~rER~VL~LR--yGl~dg~~~Tl~EIAe~LG--ISrerVRqie  582 (605)
                      +|++|+++||..-  +....|.|.+.++|++.+|  +|..|||...
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m   46 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDM   46 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHH
Confidence            4899999998642  3345789999999999966  5899999554

>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=88.49  E-value=0.72  Score=39.27  Aligned_cols=53  Identities=19%  Similarity=0.249  Sum_probs=40.4

Q ss_pred             HHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          533 EDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       533 ~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +.+...+.  .|++-+-.|+.+-+..+  +|+|..|||+.+|+|+.+|.    +++++|-+
T Consensus        13 ~~~~~~~~~~Gl~~~~~~i~~~L~~~~--~plt~~ela~~l~vsk~~vs----~~l~~L~~   67 (151)
T d1ku9a_          13 ELFSELAKIHGLNKSVGAVYAILYLSD--KPLTISDIMEELKISKGNVS----MSLKKLEE   67 (151)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHCS--SCEEHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHhCC--CCcCHHHHHHHhCCCcchHH----HHHHHHHH
Confidence            33444443  48999999998887543  56999999999999999999    55555544

>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=88.27  E-value=0.19  Score=39.02  Aligned_cols=28  Identities=11%  Similarity=0.309  Sum_probs=25.1

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          561 MKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       561 ~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      ++|.+|||..+|+|+++|.    |++++|++.
T Consensus        27 ~lt~~elA~~lg~sr~tvs----r~l~~l~~~   54 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNIS----KTLNELQDN   54 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHH----HHHHHHHHT
T ss_pred             ecCHHHHHHHHCCCHHHHH----HHHHHHHHC
Confidence            4899999999999999999    888888863

>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=88.06  E-value=0.81  Score=34.99  Aligned_cols=44  Identities=14%  Similarity=0.104  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAF  586 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RAL  586 (605)
                      .|+-.|+.=|..+|-  +|+.++..|||..|||+++||+.|+.+-=
T Consensus         7 ~LT~~eK~~ii~~~e--~g~k~sq~eIA~~fGv~~STvs~IlKnK~   50 (66)
T d1hlva1           7 QLTFREKSRIIQEVE--ENPDLRKGEIARRFNIPPSTLSTILKNKR   50 (66)
T ss_dssp             CCCHHHHHHHHHHHH--HCTTSCHHHHHHHHTCCHHHHHHHHHTHH
T ss_pred             cCCHHHHHHHHHHHH--cCCcchHHHHHHHhCCChhHHHHHHHHHH
Confidence            467777665555553  34447899999999999999999987743

>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=87.99  E-value=0.2  Score=39.01  Aligned_cols=29  Identities=7%  Similarity=0.108  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      -++|.+|||..+|+|+++|.    |+|++|++.
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            36899999999999999999    888888873

>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=87.85  E-value=0.47  Score=35.67  Aligned_cols=37  Identities=24%  Similarity=0.150  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          544 PRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       544 ~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      +|...||.+-.-  ...+.|.+|+|+.||||+.||++-+
T Consensus         7 eR~~~Il~~L~~--~~~~vs~~~La~~l~VS~~TI~rdi   43 (65)
T d1j5ya1           7 ERLKSIVRILER--SKEPVSGAQLAEELSVSRQVIVQDI   43 (65)
T ss_dssp             HHHHHHHHHHHH--CSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHH--cCCCCcHHHHHHHHCCCHHHHHHHH
Confidence            345566665432  2345899999999999999999544

>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=86.84  E-value=0.4  Score=39.31  Aligned_cols=45  Identities=16%  Similarity=0.315  Sum_probs=34.9

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .|++.+..||..-+..+  .++|..|||+.+|+++.+|+    +.+++|-+
T Consensus        18 gLs~~~~~iL~~L~~~~--~~~t~~eLa~~~~i~~~tvs----~~l~~L~~   62 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEIE--KPITSEELADIFKLSKTTVE----NSLKKLIE   62 (109)
T ss_dssp             TCCHHHHHHHHHHHHHC--SCEEHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHcC--CCCCHHHHHHHHCccHhHHH----HHHHHHHH
Confidence            59999999987554333  25999999999999999999    44555543

>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=86.84  E-value=0.85  Score=37.39  Aligned_cols=50  Identities=18%  Similarity=0.286  Sum_probs=37.9

Q ss_pred             HHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          535 LEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       535 L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |.+.|.  .|++.|-.|+..-+-.+   +.|..|||+.+|+++.+|.    +++++|.+
T Consensus         9 l~~~L~~lGlt~~e~~v~~~L~~~g---~~t~~eia~~~~i~~~~v~----~~l~~L~~   60 (109)
T d1sfxa_           9 LVKALEKLSFKPSDVRIYSLLLERG---GMRVSEIARELDLSARFVR----DRLKVLLK   60 (109)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHHHHHC---CBCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHhcC---CCCHHHHHHHhCCCcchHH----HHHHHHHh
Confidence            334444  58899988887766544   4999999999999999999    55666544

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=86.57  E-value=1.5  Score=36.67  Aligned_cols=56  Identities=4%  Similarity=0.118  Sum_probs=41.8

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          531 MKEDLEKVLD--TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       531 l~~~L~~aL~--~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      +...+...+.  .|++.|-.||..-+.. +|.+.|..||++.+++++.+|.    +++++|-+
T Consensus        14 ~~~~~~~~l~~~glt~~q~~vL~~l~~~-~~~~it~~ela~~~~~~~~~vs----~~l~~L~~   71 (135)
T d3broa1          14 MSTRFDIFAKKYDLTGTQMTIIDYLSRN-KNKEVLQRDLESEFSIKSSTAT----VLLQRMEI   71 (135)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHT-TTSCCBHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHCcCHhHHH----HHHHHHHH
Confidence            3444555554  4999999998776654 4566999999999999999998    56666643

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=86.51  E-value=0.36  Score=36.03  Aligned_cols=30  Identities=20%  Similarity=0.178  Sum_probs=25.4

Q ss_pred             HHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          551 RWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       551 ~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      .+|--.+    +|.+|+|+.+|||+.+|+++++-
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            3455555    99999999999999999999973

>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=86.08  E-value=0.61  Score=35.22  Aligned_cols=28  Identities=11%  Similarity=0.144  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          560 RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       560 ~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .+-+..+||+.||+|+.+|.    ++++||.+
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    67777765

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=85.43  E-value=0.64  Score=39.46  Aligned_cols=38  Identities=18%  Similarity=0.071  Sum_probs=28.3

Q ss_pred             CCHHHHH-HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          542 LNPRERQ-VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       542 L~~rER~-VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      ||...|+ ||.+ |..+    ++..+||+.||||+.+|..+..+
T Consensus        17 Ls~dlR~rIv~~-~~~G----~s~r~iA~~~~VS~~tV~k~l~r   55 (123)
T d1pdnc_          17 LPNNIRLKIVEM-AADG----IRPCVISRQLRVSHGCVSKILNR   55 (123)
T ss_dssp             CCHHHHHHHHHH-HHTT----CCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH-HHhc----CCHHHHHHHHCcCHHHHHHHHHH
Confidence            5555555 4444 5444    89999999999999999966554

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=83.03  E-value=0.66  Score=35.51  Aligned_cols=31  Identities=19%  Similarity=0.342  Sum_probs=26.4

Q ss_pred             HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          549 VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       549 VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      +-.+|-..+    +|.+|+|+.||||+.+|.+++.
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

>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=82.87  E-value=0.72  Score=36.63  Aligned_cols=34  Identities=18%  Similarity=0.176  Sum_probs=26.9

Q ss_pred             HHHHHHHh-cCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 007404          548 QVVRWRFG-LEDGRMKTLQEIGELMGVSRERIRQIESSA  585 (605)
Q Consensus       548 ~VL~LRyG-l~dg~~~Tl~EIAe~LGISrerVRqie~RA  585 (605)
                      ++|.+..- .|    +|+.+||+.||||..+|+++..+.
T Consensus        13 ~aV~l~~~~~g----~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          13 DAVALYENSDG----ASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHTTGGG----SCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCC----CcHHHHHHHHCCCHHHHHHHHHHH
Confidence            45666532 23    899999999999999999998764

>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=82.78  E-value=0.66  Score=32.58  Aligned_cols=31  Identities=13%  Similarity=0.190  Sum_probs=25.0

Q ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          548 QVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       548 ~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      +|..|+ ..+    +.-.+||+.|||++.+|..++.
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    9999999999999999996654

>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=82.25  E-value=0.52  Score=34.25  Aligned_cols=48  Identities=15%  Similarity=0.250  Sum_probs=38.8

Q ss_pred             cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRK  588 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg-~~~Tl~EIAe~LGISrerVRqie~RALkK  588 (605)
                      .|++.++.||.-.|-.+.. .....++||..+|++...|+.+...-..|
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 22467899999999999999988776554

>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=82.16  E-value=1.1  Score=33.78  Aligned_cols=35  Identities=9%  Similarity=0.003  Sum_probs=27.3

Q ss_pred             HHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 007404          547 RQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESS  584 (605)
Q Consensus       547 R~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~R  584 (605)
                      ..||.+-+-.+   +.|-.|||+.+|+|+.+|+.+..+
T Consensus         9 ~~Il~~l~~~g---~~sr~eLa~~~glS~~Tv~~~l~~   43 (71)
T d1z05a1           9 GRVYKLIDQKG---PISRIDLSKESELAPASITKITRE   43 (71)
T ss_dssp             HHHHHHHHHHC---SBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHH
Confidence            45776665433   499999999999999999966544

>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=81.97  E-value=1.8  Score=31.93  Aligned_cols=51  Identities=18%  Similarity=0.176  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          541 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg-~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      .+++.+..+|.-.|..+.. ......+||..+|||...|+.....-..|.|+
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            3688899999998876532 33678999999999999999999998888775

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=81.92  E-value=1.1  Score=34.26  Aligned_cols=39  Identities=23%  Similarity=0.276  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHhcCC-CHHHHHHHHh
Q 007404          452 YRVKEARKQLYSENGRHPNNEEVAEATGL-SMKRLHAVLL  490 (605)
Q Consensus       452 ~ki~ka~~~L~~elgr~PT~eEIAe~lgi-s~e~V~~~l~  490 (605)
                      .++-.....+..++|..||..|||+.+|+ |...|...+.
T Consensus         8 ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~   47 (71)
T d1jhfa1           8 QEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   47 (71)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHH
Confidence            34555666777889999999999999999 7888887764

>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=81.53  E-value=0.76  Score=35.53  Aligned_cols=29  Identities=31%  Similarity=0.653  Sum_probs=25.1

Q ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          559 GRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       559 g~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |..+ |..|+|+.||||+.+||    +|++.|..
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            3446 89999999999999999    88888865

>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=81.49  E-value=0.9  Score=35.92  Aligned_cols=49  Identities=20%  Similarity=0.273  Sum_probs=38.4

Q ss_pred             HHHHHHHhcCCHHHHHHHHHHHhcCCC---CCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          533 EDLEKVLDTLNPRERQVVRWRFGLEDG---RMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       533 ~~L~~aL~~L~~rER~VL~LRyGl~dg---~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      ..|...+..|++.|+.|..+  .+++.   ..+|.+|||+..|||..+|-..-+
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            56778889999999998854  33321   348999999999999999985544

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=81.27  E-value=1.5  Score=35.40  Aligned_cols=45  Identities=13%  Similarity=0.212  Sum_probs=31.1

Q ss_pred             HHHHHHhcCCHHHHH-HHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHH
Q 007404          534 DLEKVLDTLNPRERQ-VVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIE  582 (605)
Q Consensus       534 ~L~~aL~~L~~rER~-VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie  582 (605)
                      .+.+++..|...-|. ||.+  ..+ | +++..||++.+|+|+.+|++++
T Consensus        12 ~la~~~kaL~~p~Rl~Il~~--L~~-~-~~~v~ela~~l~is~stvS~HL   57 (98)
T d1r1ta_          12 SLAEFFAVLADPNRLRLLSL--LAR-S-ELCVGDLAQAIGVSESAVSHQL   57 (98)
T ss_dssp             HHHHHHHHHCCHHHHHHHHH--HTT-C-CBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHH--HHc-C-CcCHHHHHHHHCcCHHHHHHHH
Confidence            455566666655444 4433  232 2 4999999999999999999664

>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=81.14  E-value=2.6  Score=32.39  Aligned_cols=52  Identities=13%  Similarity=0.240  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHHHHHhcCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          541 TLNPRERQVVRWRFGLEDG--RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg--~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .+++.|..+|...|...+.  .....++||..+|++...|+.+...-..|+|+.
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            5889999999998865332  335789999999999999999999999998875

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.78  E-value=1.2  Score=34.51  Aligned_cols=52  Identities=17%  Similarity=0.147  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          541 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg-~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .+++.|..||.-.|-.+.. ......+||..+|++...|+........++|+.
T Consensus         9 r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~   61 (76)
T d2ecca1           9 RKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHG   61 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhc
Confidence            4688888999988877532 224678999999999999999999999999873

>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=80.73  E-value=0.66  Score=35.26  Aligned_cols=29  Identities=31%  Similarity=0.434  Sum_probs=25.3

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          559 GRMKTLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       559 g~~~Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |..++..++|+.||+|+.+||    +|+++|..
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            445789999999999999999    88888875

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=80.65  E-value=1.6  Score=32.89  Aligned_cols=52  Identities=13%  Similarity=0.183  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Q 007404          541 TLNPRERQVVRWRFGLEDG-RMKTLQEIGELMGVSRERIRQIESSAFRKLKNK  592 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg-~~~Tl~EIAe~LGISrerVRqie~RALkKLR~~  592 (605)
                      .+++.|..+|.-.|-.+.. ......+||..+|+|...|+.+......|.|+.
T Consensus         8 ~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~   60 (65)
T d1fjla_           8 TFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   60 (65)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhc
Confidence            3678899999999987632 225678999999999999999999999998874

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=80.40  E-value=1.2  Score=36.93  Aligned_cols=40  Identities=30%  Similarity=0.224  Sum_probs=31.7

Q ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 007404          541 TLNPRERQVVRWRFGLEDGRMKTLQEIGELMGVSRERIRQIES  583 (605)
Q Consensus       541 ~L~~rER~VL~LRyGl~dg~~~Tl~EIAe~LGISrerVRqie~  583 (605)
                      .|+|-|.-.-.-++... |  +|.++||+.+|+|+.+|++++.
T Consensus        13 ~L~p~e~A~a~~~l~~~-g--~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_          13 ELTPREIADFIGRELAK-G--KKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             CCCHHHHHHHHHHHHHT-T--CCHHHHHHHHTCCHHHHHHHHG
T ss_pred             CCCHHHHHHHHHHHHHh-C--CCHHHHHHHHCCcHHHHHHHHH
Confidence            48888877665555433 2  7999999999999999998765

>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=80.38  E-value=0.67  Score=38.05  Aligned_cols=27  Identities=30%  Similarity=0.427  Sum_probs=23.7

Q ss_pred             CCCHHHHHHHHCCC-HHHHHHHHHHHHHHHHh
Q 007404          561 MKTLQEIGELMGVS-RERIRQIESSAFRKLKN  591 (605)
Q Consensus       561 ~~Tl~EIAe~LGIS-rerVRqie~RALkKLR~  591 (605)
                      ++|.+|||..+|+| +++|.    |.|++|++
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            58999999999996 99998    77777776

>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=80.05  E-value=0.79  Score=35.51  Aligned_cols=29  Identities=21%  Similarity=0.305  Sum_probs=25.2

Q ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Q 007404          559 GRMK-TLQEIGELMGVSRERIRQIESSAFRKLKN  591 (605)
Q Consensus       559 g~~~-Tl~EIAe~LGISrerVRqie~RALkKLR~  591 (605)
                      |..+ |..++|+.||||+.+||    +|++.|..
T Consensus        19 G~~LPse~~La~~~~vSr~tvr----~Al~~L~~   48 (78)
T d3bwga1          19 GDKLPVLETLMAQFEVSKSTIT----KSLELLEQ   48 (78)
T ss_dssp             TCBCCCHHHHHHHTTCCHHHHH----HHHHHHHH
T ss_pred             cCCCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4456 89999999999999999    88888865